a complete bibliography of ieee/acm transactions on …ftp.math.utah.edu/pub/tex/bib/tcbb.pdf ·...

A Complete Bibliography of IEEE/ACM Transactionson Computational Biology and Bioinformatics

Nelson H. F. BeebeUniversity of Utah

Department of Mathematics, 110 LCB155 S 1400 E RM 233

Salt Lake City, UT 84112-0090USA

Tel: +1 801 581 5254FAX: +1 801 581 4148

E-mail: [email protected], [email protected],[email protected] (Internet)

WWW URL: http://www.math.utah.edu/~beebe/

23 February 2021Version 1.76

Title word cross-reference

((1, 2)) [BJ13]. (∗, 2) [KO15]. (1.5 + ε)[CWZL08]. (L, d) [CW11, DBR07, Tan14]. 1[APPG18]. 1.375 [EH06]. 1β1β [LCH19]. 2[BLR15, HZL19, KD15, LBQ+13, SSF18].2+ [LCOMG14]. 3 [ARP+16, BWRF12,CWT+19, CBF+18, GPF+20, GH15, HS15,KL19, KSMT19, LQV+13, LHQ+18,NPK+07, RG16, RWH+10, Str11, SSF18,VMD+08, YLH+15, YCZ+18]. 4[LBQ+13, MCRC17]. 13 [AAG+18]. 2

[LWL+20]. 3 [PM20, YLY+12]. ATP

[BMH+16]. α [MRB12]. β[AAE11, BMH+16, DNS19, YXS16]. `1[CMR19]. `2 [JXN+16]. F 2 [BCS11]. G[LBQ+13]. K

[CZ20, ARZ+14, PFJ+19, AC12, AFJ12,HC14a, IM14, LMZ14, PSC20]. Lp [LLT10].λ [SPA17]. M [ZWZ16]. N[LZGZ14, MRK18, SLL+19, KNTB18].O(m logm) [SSS+15]. O(N2) [BHS+04].O(n lg n) [WLY14]. Ω(n2/ log n) [BE08]. P[VTGC16, UKV18]. q [CZX19]. R[MTNH17, Pol13]. S [SP11].

-Activation [LCH19]. -Approximation[CWZL08, EH06, HZL19]. -ATPase[BCFCC13]. -Barrel [YXS16]. -bounded[KO15]. -Cell [BMH+16]. -Content[RKDR10]. -D [APPG18, NPK+07].-Exemplar [BJ13]. -Gram [CZX19].-grams [LZGZ14]. -Helix [MRB12].-Information [AC12]. -Labels [MRK18].-Linked [SLL+19]. -Matrix-Based

1

2

[ZWZ16]. -means [IM14]. -Median[UKV18]. -mer[HC14a, LMZ14, CZ20, PFJ+19]. -Mers[CMR19]. -motif [Tan14, CW11]. -Omic[Ano12a]. -Peptide [KNTB18].-Quadruplexes [LBQ+13]. -Separated[Pol13]. -Sheet [AAE11, DNS19]. -shortest[ARZ+14]. -time [SSS+15]. -Transform[SP11]. -Values [VTGC16].

/K [BCFCC13].

1 [AFAAW+11, DCM20, HHL+20, LNY05b,MMB+13, RB16, SYKS15, Vis18]. 10th[HBG16]. 11th [HBG17]. 12th[HBG18, ZC14]. 13th [HC15, HBG19]. 14th[BLP18, HBG20]. 15th [WLC18]. 16th[YSC19].

2 [LNY05a, PCY+19, PZS+20]. 2.0[TAL+15]. 2012 [HCQ14, dSK13]. 2013[AS15, LW15, SA15]. 2014[BPW17, Cat17, ZC15]. 2015[Kim18, MJ18, TH18]. 2016 [BLP18]. 2018[YGFC20]. 25th [STHA15]. 29th [ZLZ20].2SNP [BZ08].

3’ [MSH+11]. 3b [LGN+19]. 3gClust[HCN+19]. 3ST [HS08].

4 [CSZ+19].

7th [GJH19].

9 [LFZ+19].

Ab-Initio [HZZY16]. Abduction [BD19].Aberrations [NVSH18, XL16, XLWL15].Ability [TC13]. Absorbing [Gon13].Abstract [HZZY16, WRH+09].Abundance [JZW17, QTZ15]. Acc[MMFD14]. Acc-Motif [MMFD14].Accelerated[CZX19, GDWK+15, MPP+20, MMFD14].

Accelerating[AKLJ17, CWLZ14, GPScF15, HOS+12a,HOS+12b, LSMW11, IM14]. Acceleration[FVLN15]. Accelerator [DSVMM18].Accelerators [NTR16]. Access[Ano13e, CMSE+15, LBL+10]. Account[MSH+11]. accumulation [LCOMG14].Accuracies [AM12, AM15]. Accuracy[BM13, KWL07, LNR+09, MNW+04, TW10,Xu05]. Accurate [CMS12, CH11, CCE19,GGP08, KG20, MTM+15, NSZK15, SSS+11,SHJL10, WS12, WCX07, WCL11, XWC15,DST+15b, SYV14, SLW15]. Accurately[YSGZ20, XG14]. aCGH [ZYW+13]. Acid[HLG10, JDHL20, Kar12a, NLGG12, BDD18].Acids [LYL+17, YH13]. ACM[AS15, Ano12b, Cat17, Gus04b, KS13,SPK19, Tit16]. ACM-BCB [AS15, Cat17].across [EW04, LTwG+11, MMH15]. ACT[LS10]. Activation [LCH19, RKZ16].Active [GPF+20, HHSC13, LMZ+20,NSMH19, NFM+12, OLZ11, WHKK07].Activities [AFAAW+11]. Activity[LGN+19, SYKS15]. Actors [ZZKW18].Actually [RRTB12]. AD [HYR+19].AD-Related [HYR+19]. Adaptation[JSS+18, RHH16]. Adaptive[AKS13, DLM12, LDM18, MJPP20,NTCO07, PSIM17, PAAG07, SY09, SSS13a,SJS19, TC16, XLZ+15, YWK+07, YCY+15,ZCG+18, XXM+16]. adaptively[YlCW+15]. Additional [WMS09].Adhesin [GAR+09]. Adhesin-Like[GAR+09]. Adjacencies[LJZZ13, LLT+19, ZACS09]. Adjacency[QSJ+20]. Adjacent [WM19a, YH13].Adjoint [FKLS07, MGS17]. Admixture[TBRS13]. Advanced[Che13, HEE+18, ZL19]. Advances [HSS18].adverse [XLC+15]. Advising [DK17].Aerial [ZD17]. Affective [HLSR18].Affinity [AM12, EMDH11, WOYL17,ZWSX12, AM15, CWZW15, DKS+15].Affymetrix [LUdSCH10, MSH+11].

3

African [FMA+20]. against [KKC16]. Age[FS13b]. Ageing [FFT16, WDX+15].Ageing-Related [FFT16]. Agents[NSMH19]. aggregate [SLS+14].Aggregation [APPG18, BRF17, GSC17,SMB12, SPMB13, YOKI09]. Aging[TC13, YFCM17, FZM15]. Agnostic[AALD17]. Agreement[BN06, GB10, RBdlVMPG16, SCPS12].Aided [gCLL+10, MVS+13]. Airflow[RSCX18]. Airway [RSCX18]. AkaneRE[SYM+10]. Albumin [RTA+16]. Algebraic[FM13, LW13b, ZXB11]. Algorithm[ALR+13, AALD17, BHS+04, BPV+11,Bi09, BKLS18, BS08, BHP19, CFOS06,CC09, CAW+19, CBF+18, CWZL08, DT11,EH06, FWXZ19, FM12, FMD18, GZFT15,GSC+18, GAGM11, GK08, GPMH16, Gra04,HBM19, HWPE17, HBC+11, HHYH07,HLSR18, HDS+18, HLH11, HvIKS11,KCD+12, KSMT19, LHL+19a, LTaS13,LCLL10, LLHF15, LLH+17, LTL+19,LLZ+20a, LLW10, LWZ12, LJZZ13, LT07,LWS+20, MWL+12, MGXS15, MTSCO10,MPS18, MCD+11, MGC19, MLZ17, MB16,MM17, NTCO07, NP13, NPD+17, ORCJ13,OMWX09, OP11, PAL+12, PLCW17, PK13,PBJ12, RMV12, RSJK13, SDS18, SREK19,SAE+20, SS04, SIM12, SSS20a, SV16, SR10,TZP17, UJ09, UWLH15, UAH16, WLCP11,WKLL12, WWLL16, Wan16, WDH08,WLC11, WMS09, XHQ+18, XWC15,YWK+07, YCYC12, YXYC13, YC08,ZWL+12, ZZZC17, ZZH18a, ZWM+20,ZLJT17, ZW13, AMBK14, CFIS+15,DST+15b, FWY+15, GRDV14, GM14,GAVRRL15]. algorithm[HLW15, ARZ+14, Nye14, PWZW15,PWC+15, RHH16, SHK14, SSKH15, STT+14,SSS+15, XXM+16, YHV+15, ZSY+14].Algorithmic [LQV+13]. Algorithmics[BvBF+11]. Algorithms[AKS13, ASI+11, AAE11, BEW09, BAK06,BBK+07, BG17, BM13, CMR19, CEFBS06,

CW09b, CW11, CW12, Che13, CAN+08,DBR07, GH08b, HK12, HCLS11, HYW08,HKM+18, JRSS18, Jia10, KB19, LNC+05,LCC+11, MO04, Mai09, MSP+19, MVVR19,MVVR20, MWSM12, NS19, NSNA19, PG18,PH10a, POS+18, Pol13, RZMC17, RAA10,SK08, Shi10, SHUP19, SLH+06a, SDB+07,TS18, TRKRC13, WL11, Wan12, WL19,WBE13, WCLY12, XZG+18, YLCC13,YDM+08, ZD12, ZZ18, vIKKS08, vIJJ+20,PSK+16, Tan14, ZHL+14]. Alignable[PS11]. Aligned [LSTW+17]. Aligner[EMK18]. Aligning [WL14, YlCW+15].Alignment[AH11, AKLJ17, AGMP09, BTTR11,BAK06, CWC04, COW20, CGPW06, DBZ12,DK17, DK13, DBN18, ECK16, FGKH11,FMD18, GPMH16, HT09, HGM18, HB11,IGM+07, JZW17, AKD17, KG20, KK08,LNR+09, LPR+08, MWL+12, MGK08,MKH11, MGC19, MGKG17, NP13, NSZK15,PHX+08, Pol11, Pol12, Pol13, RCM+19,RGN+09, SH11b, SLH+06a, SSFW12,TRKRC13, TDK13b, TED+12, TDA+09,TTWR13, VM18, WS08, WLMW+11,WHKK07, WAK13, WB11, WCLY12, Xu05,YLL+06, YH13, ZLLS17, ZGB+12, CV14,FZM15, FSL+15, MG14, PSK+15, SHS15,SCC+15, SPWF14, XXM+16].Alignment-Free [YH13, CV14].Alignments[BDD+10, HVG04, HPL+13, PT09].All-Mapper [CZX19]. Allele[BBSP08, DLM12]. Allowing [AGMP09].almost [WLY14]. along [AGMP09].Alphabet [SJNS19]. Alphabet-Friendly[SJNS19]. Alphabetical [FMD18].alphabets [YHV+15]. Alter [JLW17].Altering [Zha18]. Alternating [HYL+19].Alternations [XLW20]. Alternative[NHTD17]. Alternatively [RLRH18].Always [BBCP07]. Alzheimer[JHZL19, LWT+18, SSK+20, WLA+13].AMAS [TC16]. Ambiguities [ZZS07].

4

Ambiguity [GzS11]. American [FMA+20].Amino [HLG10, JDHL20, Kar12a, LYL+17,NLGG12, YH13]. Amnioserosa [DABV17].among [PZWC20]. Analog [Pre04].Analog-Spectrum [Pre04]. Analyses[ATA+17, KPP19, SSD19, WYY+13].Analysis[ACC+13, AAT20, APKP18, iAOSS16,AKS20, BB11, BRS18, BGS+12, BKLS18,BSLR05, BCFCC13, CP13, CXW+13,CBM+20, Che10, CBK20, CWZ08, CZM+18,CMC+12, Dal16, DSHM08, DADF+10,DKDD10, DSVMM18, DPW12, FZWS17,FM12, FWY19, FVP+20, GPZ20, GGH+13,GCZ18, GF10, Gos11, GPC+20, GM16,HCN+19, Han10, HB05, HYC12, HSTW06,HLDZ17, HLL18b, IL18, IYA12, JDCC12,JL10, JFR+19, JCF13, JZL13, KPK+17,KMSY20, KB20, KNTB18, KSB12, KSK+18,LCTS08, LEAK11, LFK16, LTM+12, LL11,LKY+11, LLX+11, cLWA07, LJL+15,LHG+16, LPH+13, LXG+16, LLH18, LW19b,LTL+07, MWZY17, MO04, MTNH17,Mam05, MPP+20, MT12b, MC07, MSS+13a,MGS17, MWD11, MBF+13, MBB+17, NU06,NA11, NO09, NNM+12b, OG11, PLMV12,PIPC18, Pau18, POS+18, RdMCBC13,RAM17, Roc11, RWH+10, RPBP18,SDA+06, SKS+19, SDCW11, SZL+20].Analysis [SKD+07, TZH07, TRKRC13,TWZW16, UBP+19, UKV18, VMZM17,WZA07, WMWA12, WYHD17, WHXS17,WWL19, WFY+19, WP08, WHKK07,WWC18, XHY+18, YCCY20, YLXJ04,YM20, YLL+06, YB08, ZMST18, ZZ13,ZZN15, ZWZ16, ZZZW19, ZWHC19, ZC11,ZK16, ZZS07, ZWW17, ZYW+13, ZGDH16,ZCWW19, dCAR11, GTDK15, GMCB14,KG15, LHN+14, LYH+16, LLCZ15, LP15,LLH+14, MEOL14, OFC+14, RTWR15,WZ14, WZC+15, YTLL15, YCY+15,ZMP+14, ZWC15]. analytic [BCLC15].Analytical[HLM+13, KBBD+17, LCOMG14].

analytics [GFG16]. Analyze [LBL+10].Analyzer [GPC+20]. Analyzing[ABS15, BHMA06, CHW+18, GHL05,SCSS05, SC11, TV11, WDL+17, PSK+16].Ancestral[ACPR10, GZFT15, LCSW18, MRS09,NLHL17, SLH06b, WKE11, HZZT14].Ancient [LCSW18, SW09]. Angles[FSX19]. Annealing [BA18, TW10].Annotated [KT07]. Annotation[AALD17, CC11, DGV+17, LJK+12, ZXZ20,CM15, DC15, SLW15]. Annotations[AMGC16, ABVD12, CYJ+19, CM16,CPM18, DKDD10, GSK13, HXXJ18, IQA18,LBM+18, LZH18, LLZ+13, MCC16, WB17,YFWZ18, CXS15, YRD+14b]. Annual[Ano04a, Ano05a, Ano06b, Ano08a, Ano09b,Ano10b, Tit13, XTL12a]. Anomalous[DRS12, DR14]. ANOVA [EAS12]. Answer[WYL07]. Ant[LGZ+17, ORCJ13, GRDV14]. ANTENNA[WLCX18]. Anti[MWZY17, NSMH19, PSIM17, RBB+19,WLCX18, BHW+14, WFD15]. Anti-Breast[RBB+19]. Anti-Cancer[NSMH19, PSIM17, WLCX18, BHW+14].Anti-EGFR [MWZY17]. anti-longevity[WFD15]. Antibiotic [MWD11].Antibiotic-Resistant [MWD11].Antibody [ZWL11]. Antibody-Specified[ZWL11]. Antiepileptic [RBB+19].Antifreeze [KNTB18]. Antilope [AKR12].Antimicrobial [FWY19, JKN+12, VKS17].Any [LPH18]. AP [TDZ+19]. Apex[TRKRC13]. Apocrine [SMPS20]. APP[WZC+15]. Applicability[ARS17, HB05, KK12]. Application[ASP20, BRF17, BD19, BSST08, BHP19,CW11, Che12, CLZ+18, Che10, CZJ17,DCM20, ED15, FKLS07, GF10, GBB+11,HSS18, KCD+12, KHO+20, KM20, LFS06,LLZC12, LLW10, NFM+12, PAL+12,PSN+15, RGI13, RB16, Roc11, SdOD+12,STD20, SPMB13, UKV18, VBG+18, WM19a,

5

WFY+19, WLA+13, WWL+17, XPH12,XLZ+15, YLXS17, YGY+19, ZZM17,dCAR11, Mir14, WDX+15, ZMP+14].Applications [Ano08c, BMT17, BPRZ11,CZ12, DLRW18, HMZ17, LHLY11, LSB+11,MPZ08, MPSZ09, MWZ13, MSZ19b,MNPZ10, MHKR12, OMWX09, Pol13,QKO18, QL09, SZZ+19, Sen19, SHJL10,TS18, WNT+17, WLWN17, ZS19, BCLC15,CEG14, GPScF15, SVM14, TDD14, MPZ07].Applied [GRH08, IGM+07, VMZM17].Applying [ADTAQ16, ATA+17, PIPC18].Appreciation [Gus07a, Gus07b, Xu14b].Approach[AAP06, AJD+12, AKS13, AC12, AHT+18,AKR12, ASI+11, BA18, BHHMCL16,BCVS19, BCL13b, CCA12, CSW11, CW09a,CGW+16, CKWY12, CWZ08, CAN+08,CHK17, DBN18, FJJ11, FYZ+19, Gon13,GET13, GDM12, GG11, HZW+17, HM13,HLHAJ20, HVG04, HMK+07, IGA18, ISK18,JMA17, JZW17, KCD+12, KHO+20, KB20,KCP18, KSS15, LQV+13, LRR08, LTM+13,LH10, LFZ+19, LMZL17, LGB15, LHC18,MRB12, MPF12, MKG20, MSJP19, Mam05,MSB19, ME19a, MMB+13, MNND13,MVS+13, MPY18, MGKG17, MGS17,MWLS18, NSC17, NO09, OC13, PB19,PSPM20, PVB+12, PR12, RKDR11, RV06,SP11, SVZ09, SSS+11, SBW15, SKS+19,SLX+18, SH11b, SYKM17, SW09, SLL+19,TWW+20, TZ16, TDZ+19, TBGL10,TBRS11, TTWR13, TC13, VRK12,VMZM17, WYY+13, WLL+09, WSX11,WWL+17, YHZ+19, YLL+06, ZWZ16,ZwGC17, ZWHC19, ZHG20, ZS18, ZAZ11].Approach [ZZH18b, BHW+14, CZWT15,CA14, GZGX14, GJPSV14, KD15, LLCZ15,LZGZ14, MG14, MM14a, MM14b, PSK+15,SDAA+14, SLW15, SEC15, TYL+16].Approaches [Ano05b, BM08, BH06, GM16,HEE+18, AKD17, MCDD12, RZF07, YB08].Approaching [QSJ+20]. Approximate[ACPR10, HC14a, RFB20, ADTAQ16].

Approximated [PPFG20].Approximating [BPV+11].Approximation[BS08, CP13, CC09, CW09b, CHNW20,CWZL08, EH06, FL18, HZL19, HBC+11,Jia10, LJZZ13, Mne09, NPBD16, ZSY+14].Approximations [RBdJ11]. Aptamers[LH20]. Arabidopsis[MCRC17, MVW+13, TRKRC13, WWL19].Arbitrary [BG13, Jia10].Arbitrary-Shaped [BG13]. Architectural[STD20]. Architecture [MSS19a, SYL19,WCXL18, ZZH19, ZZBH20, ZG19].Architectures [KP12]. Areas [TGK13].Argument [Ozy12]. Arithmetic[MHKR12]. Ark [HBC+11]. Array[CW09a, LHS16, PS15]. Arrays[HKS11, LEAK11, MSH+11, SK08].Arrhythmia [ARM+19, ZCWW19]. Art[SW17]. Article [LS10]. Articles[DLT10, HLV+10, HCQ14]. Artificial[LYW20, PLC+20, SSS20a]. ARTMAP[AFAAW+11, XAW07]. ASAPP [STD20].Asia[HC15, STHA15, WLC18, YSC19, ZC14].ASIP [XLZ+15]. Aspects [dNG17].Aspergillus [OMAdG+12]. ASSA[MPSY18]. ASSA-PBN [MPSY18]. assay[GBTL14]. Assembled [LHKL17].Assembler [GK19]. Assemblies [GAJ+18].Assembling [RG16]. Assembly[CLVT+20, CMC+12, FS13b, GRS+13, HG16,LLH+17, LLL+20, PS11, PGF18, RLR20,TGP+15, XSS17, ZFZ+20, ZKP+07, PV16].Assessing [ARK20, PT09, SMSZ17].Assessment [AM12, CLVT+20, DBK18,GAJ+18, JDHL20, KWL07, AIS+16, AM15,MG14, XLC+15]. Assignment [AAG+18,CCA12, CZF+05, LW13a, WL07, ZKP+07].Assignments [MSG18]. Assisted[PCDP18]. Associate [Ano04b, Gus04a,Gus06a, Gus07a, Gus07b, Sag09b, Wil04a].Associated[CLST+13, DZH16, GTTR+17, KSN+12,

6

KCP18, LHHL19, LDL+17, PSIM17, QLZ16,SAE+20, XYYZ20, XW16, ZHZ+20, GJK15].Associating [NAHT+20]. Association[AMGC16, BDD18, CLH+15, FMA+20,KB20, LRR08, LZW20, LLZC12, LNW20,NJMF19, PNP+18, PAAG07, QKO18,RGI13, SZL+20, TGGF10, Tsa12, VTGC16,WYY+13, YL12, ZZCD19, ZS19, LYH+16,NCMCAR15, WSTL+15, XLC+15].Associations [AAF+13, BKKG19, GZC+17,HYR+19, LWL+18, LZHZ17, MWSM12,WLCX18, YWN+19, YDW+20, YAB13,YKWK18, ZS18]. Associative [KNS+05].Assortative [PPZ12]. Assumption[BCVS19, TM11]. Assurance [PvRV+20].ASTRAL [SRM18]. Asymmetric[FPPR11]. Asymptotic [DR16, ZWZ16].Asynchronous [LW13b, ZWL15].Asynchrony [MPQY19]. Atlas [JZL13].ATPase [BCFCC13]. attachment[PWZW15]. Attack [DMJ+18]. Attacks[HYL+20]. Attention [HLSR18]. Attractor[AKMT12, MPQY19]. Attractors[DT11, FMRS18, KH14]. Attribute[ACWW05, ACWW07, HC13]. Attributed[ZLY+13]. Augmented [ZWHC19]. aureus[AKNB07]. Authentication [CZB+16].Autism [SVdSS+18]. Auto[LHH19, CMS12]. Auto-Filling [LHH19].AutoDock [HOS+12a, HOS+12b].Autoencoder [FZM20]. Automata[HBRU13, MHKR12, RA16]. Automated[BM20, DGV+17, GAR+09, GLG10, LFZ+19,RKDR10, STD20, SGP+20, UBP+19].Automatic [CPQ08, DADF+10, MA12,Ozy12, RV06, SYZ+13, SZCX19, SXL+14,YSC13, YB08, ZCR+17, LZGZ14].Automaton [KHP12]. autophagy[MFS+15]. autophagy-related [MFS+15].autoregressive [JHXP15]. Avenue[ABS17]. Average [HYW08]. Aware[UWLH15]. Awareness [ZWL11].

B [WWC18, LLW+11, XHY+18, ZWL11,

ZHL+14]. B-Cell[XHY+18, ZWL11, ZHL+14]. Bacillus[NPBD16, SSDN12]. Backbone[FSX19, HSTW06]. Bacteria[CZJ17, Cza18, MBP+18, MLZ17, MWD11].Bacterial [IGM+07, Kar12b, LZX+19,LHL+19b, NLGG12, NLW+18, SKK14].Bad [Wan16]. Balanced[BGHM09, BM13, YLC20]. Balancing[KZ10]. Bandwidth [ZACS09]. Barcode[WZZ+18]. Barcodes [YLCC13].Barcoding [MRK18]. Barking [LNR+09].Barrel [YXS16]. Basal [SMPS20]. Base[WOYL17, ZKP+07]. Base-Assignment[ZKP+07]. Basecalled [MRK18].Basecalling [cLWA07]. Based[AAF+13, AOSN+18, ALR+13, APRS11,AWW18, Ano12a, AAT20, AM12, BBW18,BM17, BEW09, BDP11, BZ07, BMM06,BD19, BFM13, BAK06, BU17, BEQD19,BCVS19, BGHM09, BM13, BM20, BHP19,CLVT+20, CSZT19, CCA12, CCYW12,CDB+16, CH11, CLW13, CXW+13, CGZ15,CHZ+16, Che16, CZX19, CLS19, CM16,CDKT09, DLT10, Dal16, DBZ12, DZ11,DBTB09, DT11, DPW12, EAS12, EMK18,ED15, FWXZ19, FJJ11, FYZ+19, FL18,FVLN15, FLM+16, FLAM15, FPC20,GLL+18, GRS+13, GXSZ17, GK19,GAGM11, Gos11, GSC17, GZC+17, GM16,HYW+17, HOS+12a, HOS+12b, HHSC13,HWPE17, HLY+16, HG16, HLDZ17,HLZ+17, HLSR18, HLL18b, HC07, IGM+07,IL18, ISK18, JJH12, JGBR15, JvI18, JMA17,JLYZ16, JXN+16, JLH16, JHZL19, KCCC15,KSS15, LWL+18, LTM+13, LR20, LPH18,LTaS13, LYW20, LLX+11, LLC+13, LLHF15,LLX+16, LDM18, LTL+19, LLL+20]. Based[LRM12, LZ18b, LZX+19, LHZ+19, LLZ+13,LXG+16, LZZ+16, LGZ+17, LHQ+18,LLH18, LCGW19, LHH19, LZQ+20,LLZ+20b, LQY+20, LDL+17, LWS+20,MGL+12, MWZY17, MPF12, MGK08,MCD+11, MKH11, MBJ19, MPA15, MLZ17,

7

MGKG17, MDD18, MB16, MM17, NLGG12,NSC17, NP13, NSZK15, NPD+17, NWZ+20,NHTD17, NLW+18, PSS09, PL17, PTH+18,PZH20, PSN+15, QL16, QD12, QLZ16,QTZ15, QWC+16, RGI13, RC11, RAA20,RV13, SP11, SGC07, STD20, SMB12, SN12,SMPS20, SY09, ST05, SNC+16, SIK20,SPW20, SBM15, SYKM17, SCM19, SWX+19,SSFW12, SDTK19, SSF18, TGLP16,TAAP11, TS18, TZ16, TDY+18, TGGF10,TZY11, TBRS13, TTWR13, TW10,VRJ+10, WZA07, WLWP12, WCMZ15,WLG+16, WWLL16, WGX+17, WZZ+18,WCQ+19, WXS+19, WYL07, WMS09,WDS+12, WZ13a, WGK16, WWC18,WW19, XLW20, XWC15, XZG+18, YSC13,YWN+19, YDW+20, YM11, YXYC13,YM20, YLL+06, YLY+12, YP13, YH13].Based [YSW+17, YG19, YRL+20, YZG+17,ZDL+19, ZWSX12, ZDL12, ZWZ16,ZwGC17, ZD17, ZXLZ18a, ZXLZ18b,ZCG+18, ZLXL19, ZZF+19, ZKW19, ZG19,ZZN+11a, ZZN+11b, ZS18, ZWY+10, dDD18,AMBK14, AAG+18, BM14, CWLZ14, DS14,DPL+14, DWZ+15, DKS+15, FHRG14,GZGX14, GRDV14, GJPSV14, GH15,GAVRRL15, HVD18, HRHP16, HPH+15,HLW15, Jam15, KCZ+15, KH14, KFHK14,LHN+14, LLW+15, LZGZ14, LLZ+20a,LXZ+15, MSS19a, MBS15, MCH+15, MG14,MM14b, PWC+15, RHK14, SQZA14,SDAA+14, SSKH15, STT+14, TWZP14,TAL+15, VPB15, WLL+20, XG14, YTLL15,YCY+14, YLH+15, ZZ15, ZWM+20,ZWL+14b, ZZ14, LFF18].Based-Approach [MPF12]. Bases[PCGS05]. basic [BF14]. Basis [DM09].Batch [SPA17]. Bayes[KB20, SSP+17, WDS+12]. Bayesian[AV17, AAE11, BDBH15, BEQD19,CSK+11, CMMZ20, CGPW06, Dal16, ED14,GZC+17, IBN19, KM20, LCZN16, cLWA07,LW13a, PAL+12, PWT10, RTWR15,SGK12, TIA+11, TTWR13, XZY+14,

ZPW+19, ZKL18, pD20]. BCB[AS15, Cat17, KS13]. Be [AHT+18, Wil11].Bead [CSZT19]. Bead-Chain [CSZT19].Bee [SSS20a, GRDV14]. Behavior[BMH+16, Cza18, DABV17, FL18, QD12,WBP+12]. Belarus [SKS+19]. belief[GBLZ14]. Benchmark [LN17].Benchmarks [MWZ+20]. Benign[ZLXL19]. Best [GSX+18]. Beta[CPQ08, DGRC15]. Beta-Binders [CPQ08].beta-structural [DGRC15]. Better[iAOSS16, BCVS19, CHNW20, NZR11].Between [BKKG19, CLH+15, SMPS20,SYZ+13, AAF+13, ABVD12, CCCY20,DM09, DBK18, HXXJ18, HM15, IQA18,KNS+05, LTM+13, LKLB14, MZS+16,PH10b, SSP+05, Tah18, Wil12].Between-Class [SYZ+13]. Betweenness[BLS12]. Beyond [CV14]. Bi [BA18,LLBL20, UKV18, YDW+20, YFWZ18].Bi-convex [WB17]. Bi-Level[LLBL20, UKV18]. Bi-Objective[BA18, UKV18]. Bi-Random[YDW+20, YFWZ18]. Bias[RKDR10, RKDR11]. Biased[MSS13b, CWZW15]. BIBM[LW15, TH18, YS17]. Bicliques[LLW10, MMB+13, LLL16a]. BiClusO[KHO+20]. bicluster [GM14]. Biclustering[CWZ08, HM15, KHO+20, MO04,MTSCO10, MSB19, MMB+13, MB16,TBKH05, AMBK14]. biclusterings[HC14b]. Biclusters [HTLL12, YNBM05].Bidirectional [CC07, TR07]. Bifurcating[CBM+20]. Big[WYWX16, JZCZ15, LHS16, WLC+15].Bijective [GE18]. Bilinear [HLM+13].Billera [WYH17]. Binarization[HMW+12]. Binary[BG12, CCCY20, HYW+17, KB17, KB19,PK13, WLA+13, YNBM05, YOKI09].Binders [CPQ08]. Binding[AM12, CHZ+16, EMDH11, GLW12,HZTP12, HLZ+17, IDD13, LSTW+17,

8

LPH18, LFF18, MGL+12, MGXS15,MWZY17, PLF12, PIPC18, RTA+16,SDH20a, SDH20b, SLRQ19, WP08, WLL13,WPL15, WLPW16, WZ13a, ZCG+18, ZZH19,ZZBH20, ZLX+20, ZZDY13, AM15, DKS+15,LHWL15, PSK+15, STT+14, WSTL+15].Bindings [HBRU13]. Binning[LHKL17, LZGZ14]. Binomial [PNP+18].Bio [GBTL14, HLLO19, SLX+18, TS17].Bio-Curation [HLLO19]. Bio-driven[GBTL14]. Bio-Images [SLX+18].Bio-Inspired [TS17]. Biochemical[AV17, HM13, QV17, SH11a, SMSZ17,UWLH15, VSR+06]. biochips [AIS+16].bioconductor [VPB15]. BioCreative[Ano09c, gCLL+10, CLM10, LS10, LMK+10,RSK+10]. BioExtract [LBL+10].Biogeography [GGJ+06]. Bioimage[LZQ+20, NBGL19]. Bioimage-Based[LZQ+20]. Bioinformatic [HVD18].Bioinformatical [AHT+18].Bioinformatics[Ano09c, BPRZ11, BBH12, Cas06, Cas07,Che12, CN12, CZ12, Che13, CLR10, FJJ18,GH08b, GJH19, HKK07, HMZ17, HC15,IYA12, KPP19, Kim18, LNY05b, LNY05a,LC10, MPZ07, MPZ08, MPSZ09, MWZ13,MSZ19b, MNPZ10, MJ18, OMWX09, SA15,SPK19, SJNS19, TS18, WYWX16, WDL+17,WLC18, WH11, YSC19, ZC14, ZL19,CEG14, GPScF15, MNA14, TDD14, Ano05b,Ano12b, Gus04b, RZF07, Tit16]. BIOKDD[LC10, YGFC20]. BIOKDD2013 [PR14].BioLMiner [CLM10]. Biologic [CL15].Biological [AAF+13, ASP20, ATA+17,ACCT20, AFJ12, AFAAW+11, ABVD12,BDS12, BvBF+11, BMZM15, BWRF12,CMR19, CMS12, CNM11, DFTC12, DBN18,ED15, FPPR11, GLS+16, GPMH16, GLG10,GHL05, GM16, HB05, HYZ16, JRN+18,KL11c, Kuk13, LBM+18, LLH+07, LN13,LWZ12, LLZ+20b, LNW20, MO04, MJPP20,MBGP12, MNND13, MSS+19b, MVS+13,MB16, NAHT+20, NNM+12a, NNM+12b,

PFJ+19, Pau18, PR18, PLCW17, PZWC20,PCK19, PPZ12, RYK+19, RA16, SFB+08,SdOD+12, SDN+11, SJZ19, SZL+20, TV11,TDK13a, TDK13b, VBB18, WLWN17,WDL+17, Wig15, ZWZS16, ZKW19,ZGZ+20, ZSC+10, ED14, GTDK15, Gu16,HM15, HPH+15, HKLN14, Jam15, MZL15,WZC+15, ZSY+14]. Biologically[BB11, KP12, SMK+12, TNQ08]. Biology[ALWG18, Ano05b, Ano09c, Ano12b, BLP18,BU17, Cas06, Cas07, CSW11, CN12, FS12,FS13a, FJJ18, GCZ18, GTTR+17, GJH19,Gus04b, HKK07, HSS18, Jam13, JFN11,MVVR19, MVVR20, Maz12, MCD+11,RZF07, SPK19, SYL19, SGH12, TS18, Tit16,TC13, WYWX16, WH11, WCXL18, Zha16,ZS19, KG15, TWZ+14]. Biomarker[ALQ17, CBM+20, KGF+14, LLT10,MSB19, MLZ18, PSIM17, PS19, TP18,WDS+12, pD20, OFC+14]. Biomarkers[DHCW18, SQZA14]. Biomechanical[JGBR15]. Biomedical [BMHS13,HLL+18a, HW07, HDS+18, JLH16, LHLY11,LLQ+16, LLQ20, LJ20, LTwG+11, LNC+05,LQY+20, MCC16, NAHT+20, OLZ11,Ozy12, QKO18, WCMZ15, WB17, WGX+17,XLL+18, XLL19, YRL+20, ADTAQ16,GFG16, JZCZ15, MKARB16, Vog15].biomedicine [YN14]. Biomolecular[Bi09, Gon13, GBB+11, HW07, LBL+10,RMV12, RJNN18, YB08, YCY+13].Biomolecule [SMB12]. Biopathways[PAL+12]. Biophysical [MVS+13, SCM19].Biopolymer [SLH+06a]. Bioreductive[KHP12]. Biosequences [SK12]. Bipartite[KPK+17, PCK19, ZS18]. Birth [FMA+20].Bistability [AKS20]. bistable [WLY15].BitMapper2 [CZX19]. Blanket [RC11].bLARS [SV16]. BLAST [CWC04, CW07].BLASTP [LSMW11]. Blebs [GBTW16].Block [HZL19, KPK+17, LNW20, TGLP16].Block-Interchanges [HZL19]. Blocking[Bon07]. Blood [GSC17]. BLOSUM[SCC+15]. BLSTM [LJ20]. BLSTM-CRF

9

[LJ20]. BM [XZY+14]. BM-SNP[XZY+14]. BMExpert [WCMZ15].Boltzmann [TAI+19]. Bone[PLMV12, LLRZ15]. Boolean[AKMT12, AKS20, BHS+04, BD19,CMQ+16, DT11, HAH13, HMW+12, KH14,LT17, LLL16b, MSP+19, MPP+20,MPSY18, MPQY19, MDM13, PSPM20,PH10b, SRLR14, TLSA18, VRK12, ZWL14a,ZWL15, ZZM17, ZK16, Zou13]. Boosted[YMW+12]. Boosting [CMSE+15, HLZ+17,LZX20, WYY+13, YL12]. Bootstrap[CBZ18]. Both [HC13, NSAH19].Botulinum [MWLS18]. Bound[BFK17, MKS+17]. Boundaries [SCM19].Boundary [Gon13]. Bounded[YCCY20, KO15]. Boundedness [HC19].Bounding [NSNA19]. Bounds[BB04, HSlSM11, Lab06]. Bovine[ZWDR20]. Bowel [WCMB19].BowMapCL [NTR16]. Bowtie [FVLN15].BpMatch [FM12]. Brain[DGY05, JZL13, JHZL19, KM20, MBB+17,NPK+07, YCZ+18, ZHG20]. Brain-Wide[ZHG20]. Branch [CBM+20, KMSY20].BRANE [PCDP18]. Brazilian [SA15].break [PS15, SSML15]. break-induced[SSML15]. break-points [PS15].Breakpoint[CC09, FM11, Gru11, JZSZ12, ZW13].Breakpoint-Like [FM11]. Breast[BHMA06, FZM20, Mah10, PvRV+20,PZH20, RBB+19, SMRP15, SMPS20,SDTK19, SWL19, YLCC13, YCCM12,YGY+19]. brief [KSM14]. Brownian[Dem12, KL11c]. Browsing [GTTR+17].Bruijn [AP07, PNA20, PGF18].BRWMDA [YDW+20]. BSB [dSK13].Bubbles [ZL15]. Budding [CAW+19].Budgeted [MPKvH09]. Builder [VSR+06].Building [CKWY12, MEOL14,NCMCAR15, NLHL17, VBG+18]. Bulk[XSS17]. Burial [LHWL15]. Burrows[KK19, KVX12, LHS16, NTR16, TED+12].

Burrows-Wheeler [KVX12]. Byte[KKI20]. Byte-Pair [KKI20].

C [AAG+18, CSZ+19, HEE+18, LHKL17,MP19, SKD+07]. C-detected [AAG+18].C-Means [LHKL17, SKD+07]. Ca[LCOMG14]. Cache [CLR10].Cache-Oblivious [CLR10]. Calcium[JLW17, PTM+19, ZHG20]. Calculating[MKKS20, Vis18, WM19b, SYV14].Calculation [GDM18]. Call[Ano05b, Ano08c, Ano09c, Ano12a, Ano13d,Ano13b, Ano13c]. Calling[BBSP08, LKW+19, XZY+14]. CAMIL[RLR20]. CAMS [SHK14]. Can[AHT+18, Wil11]. Canceller [AKS13].Cancer [BRS18, BHMA06, BD19, CD08,DSZ+06, DZH16, DG19, FYZ+19, FZM20,GXSZ17, GMSD11, GBJ08, GBB+11,Han10, HGC+20, KCP19, KDS+20, KSN+12,KCP18, KKK19, LDM18, LHC18, MWZY17,Mah10, MPF12, MSB19, MSS+13a, MBP+19,NSMH19, OG11, PSS09, PSIM17, PvRV+20,PI09, PB19, PS19, PM20, PZH20, RBB+19,RHAK13, RYK+19, SSS+11, SAE+20,SMRP15, SSV+19, SMPS20, SJS19, ST05,SPW20, SZLL11, SDTK19, SWL19, UBP+19,UKV18, VDS+20, WCX07, WLCX18,WQY18, WLHY19, WDS+12, WGK16,WW19, XHQ+18, XLL+20, XAW07, XPH20,YLCC13, YCCY20, YLY+12, YCCM12,YGY+19, YOKI09, ZHSS07, ZLH+17, ZZ18,ZLXL19, ZW19, ZY20, ZS19, BHW+14, JR14,KPB14, LLCZ15, LWM14, MFS+15, Mir14,SRLR14, TWZ+14, XLWL15, YCY+15].Cancer-Associated [KCP18].Cancer-Related [PZH20, RYK+19].Cancers [LGW20, LWL+20, ZMP+14].Candidate [HYR+19, ZZRPZ19].Capabilities [BLP+12, MM14a]. Capsid[XSS17]. Capsule [PZH20, SDH20a].Capture [LW18]. Capturing [DI15].Carbon [RBdJ11, MZS+16]. Carcinoma[AAT20, CSSS16, DCHW17, YSW+17].

10

Cardiac [LKY+11, MBF+13].Cardiomyocytes [WBP+12]. Cards[PCGS05]. Cargo [WCLY20]. Carlo[ADTAQ16, AKV16, Bi09, GJY+14]. CAS[CYJ+19]. Cascade [HGC+20]. Cascaded[CC07]. Case [CSSS16, GSC17, IYA12,OMAdG+12, SCCDK09, ZWW17, ZMT14].cases [KO15]. Categories [RV13, Tah18].Categorization [BMHS13, LS10].Caterpillar [DR16, Ros13].Caterpillar-Like [DR16, Ros13].caudatum [iAOSS16]. Causal[BD19, JBgLS19, LHL+19a, LLL15, LHC18,YM20, YNN+18]. Causality[ARK20, HLL18b]. Caused [ZLL+20].Cavbase [KFHK14]. CAVER [PSK+16].CaverDock [FVP+20]. Cavities [SCM19].CCA [GLW12]. CCH [LL19]. cDNA[BDP11, BZ10, GK08, HC16, NU06,RGCB05, RV06, SBW15, SYZ+13, TZY11].CDS [SSS13a]. CEDER [WS12]. Cell[BMH+16, BRF17, BU17, BM20, BCFCC13,CSSS16, CLZ+18, CAW+19, CBM+20,DCHW17, DABV17, FKLS07, GGH+13,GBTW16, HCA+10, HGC+20, JGBR15,KBND19, LHQ+18, NFM+12, PN17, SYL19,SCM19, TRKRC13, WCLY20, WWC18,XHY+18, YOGY11, YBGB10, ZZM17, ZZ20,ZWL11, ZWW17, GBTL14, MFS+15, WZ14,ZHL+14]. Cell-Based [SCM19].Cell-Centered [SYL19]. Cell-Cycle[BRF17]. Cell-Free [CLZ+18].Cell-Penetrating [WCLY20]. Cells[DADF+10, Gou06, HKT+18, PPFG20,SDA+06, TAI+19, BLR15, LCOMG14].CellTracker [HKT+18]. Cellular[AVD+12, GPC+20, HBRU13, HLLO19,KHP12, LZL+19]. Censored [CKWY12].Census [DSZ+06]. Center [BO12, ZLXL19].Centered [SYL19]. Centers [RKZ16].Centrality [LLNW17, YM20, TWZP14].Cervical [DZH16, PM20]. CFS [HLSR18].CGH [CW09a, PS15]. CGIDLA [XYYZ20].Chain [AKS20, CSZT19, GJY+14, KCZ+15,

LTaS13, LBL12b, MPY18, SMB12, Vis18,WZ13b, YXS16, GBLZ14, LTaS13].Chain-RNA [LTaS13]. Chain-Shaped[AKS20]. Challenge[gCLL+10, CLM10, LS10]. Change[CW09a, LHWL15, SKK14]. Changes[ATA+17, KKI20, RB16]. Channel[BMH+16, BMT17, GBS11, JLW17,WBP+12]. Channels [KL11c]. Chaos[CYTY13, MEOL14]. Characteristic[WLG+16, WLA+13]. Characteristics[KSN+12, WWL19, ZLS+19].Characterization[BM12, DRS12, HEF17, LSB+11, RSP08].Characterize [NHH+17]. Characterizing[TDK13a, LKLB14]. Characters [BFK17].checker [EES14]. Checking[BBK+12, BCFCC13, RdMCBC13].Chemical[AFMS19, HLM+13, KY19, LR20, MS11,NSNA19, SCCDK09, YSC13, ZYN+19].Chemical-Chemical [KY19].Chemical-Disease [ZYN+19].Cheminformatic [RBdlVMPG16].Cheminformatics [SHJL10]. Chemotaxis[iAOSS16]. Chief [Ano08c, Ano12b, Xu13,Xu14a, Xu15, Zha17]. Child [CRV09, FS18].China [FJJ18, GJH19, ZLXL19]. Chip[LHH13, LHH13, ZGDH16]. ChIP-Chip[LHH13]. ChIP-Seq [ZGDH16]. chirality[MZS+16]. Chordal [GG11]. Chou[NLGG12]. Chromatin[CSZT19, CSZ+19, KSMT19, LW18, MP19].Chromosomal [KSMT19]. Chromosome[LW18]. Chromosome-Wide [LW18].Chromosomes [BWS05, FM13].ChromStruct [CSZ+19]. Chronic[HEE+18, OW20]. Circuit[JZS+18, Kar12b, ZLL+20, CL14]. Circuits[BBN18, CL15, ZLH12]. Circular[BRF17, CZJ17, GBD17, HCMB18,MPKvH09, PB12b]. cis[AJYT+15, GGZZ14, YMT+14].cis-regulatory [GGZZ14]. cis-trans

11

[YMT+14]. CISA [WL07]. Citation[KAHK+10]. Class [DPS+13, HYW+17,LXG+16, Mat07, MCHT17, PI09, SYZ+13,SYKM17, SSF18, YLC20, YLY+12, ZOZ10].Class-Imbalance [SYKM17].Class-Information-Based [LXG+16].ClassAMP [JKN+12]. Classes[BWC17, DKS+15]. Classical [VMZM17].Classification[AV12, ACWW05, ACWW07, BWC17,BLP+12, BWS05, BEQD19, BHHMCL16,Bon07, CLZ+18, CDKT09, CSS11, Dal16,DZA+06, DPA+17, ED15, FMA+20, FLJS20,FWA10, GMSD11, GAR+09, HF12, ISK18,JKN+12, KBNHD18, KBND19, KAHK+10,KK12, Kuk13, LYK07, LH10, LN13,LLL+20, LHZ+19, LZX20, LWT+18,MNR09, NBGL19, OLZ11, OG11, Ozy12,PTH+18, dSRCT+11, SSS+11, SSV+19,ST05, SHJL10, SGP+20, SSF18, WCX07,WZJH12, WDS+12, WLA+13, WW19,XHQ+18, XZC07, XAW07, XPH20, YLXJ04,YRD+13, ZLZ06, ZHSS07, ZwGC17,ZYW17, ZZN+11a, ZCWW19, ZBFK10,wTCAK+20, ED14, GRDV14, LXZ+15,MBS15, RHK14, YRD+14a]. Classifier[AV17, BDP11, GZR+18, HBH12, HC16,IYA12, PI09, SSP+17, SBM15, WGX+17].Classifiers [DPS+13, FFT16, LW13a,NLGG12, QBPEL12, WB17, YOKI09].Classify [ZHG20]. Classifying[AC12, CSSS16, CR14, FZM20, LRM08,SLX+18, YN14]. Clearance [SZCX19].Cleavage [HHL+20]. Climbing [RV06].Clinical[BKP+19, BDP11, CKWY12, HXXJ18,HYC12, LHH19, LTRW19, MLZ18, MBP+19,MCHT17, PvRV+20, RTPM+19, ZY20].cliques [ZZ15]. Clock [BZ07, CL15]. Clone[Kur13]. Closed [PPM+13, PLC+20].Closed-Loop [PPM+13, PLC+20]. Closely[MYCW12]. Closest [CMR19, CW11].Cloud [LFF18, VPB15, WLC+15]. Clouds[FGKH11, Qiu14]. Clust [PCDP18].

Cluster [HCN+19, LFK16, LCLL10,LHY+11, MA12, NPD+17, PCDP18,SKD+07, YCY+13, WZC+15].Cluster-Assisted [PCDP18]. Clustering[ASP20, ACWW05, ACWW07, BBH12,CMS12, CHWY19, CLS19, DGH+06,DWSB11, GLW12, GLG10, HC18, JCF13,JMA17, KNS+05, KK12, KZ10, LHTT11,LSTW+17, LBL12a, LLHF15, LHCL20,LCW+18, LWG+18, LNW20, LT07, MSQ18,MHHJ20, MP13, MW20, MA12, NSZK15,NPD+17, OMWX09, RLR20, RWH+10,SVZ09, SY09, SKD+07, SMK+12, SGK12,TK05, UKV18, VKM07, VF09, WNT+17,WZA07, WLCP11, WLWP12, WLZ+19,WFY+19, WOYL17, XHQ+18, YLY+12,YP13, YCY+13, ZHJ17, ZYW17, CFIS+15,FN14, IM14, LLC+15, LAI+14, MG14,Mir14, RB14, SHK14, SDAA+14, WL14,YCY+14, YCY+15, YLY+12].Clustering-Based[CLS19, YLY+12, MG14, SDAA+14].Clusterings [Mah10]. Clusters[BG13, DSCM20, GDM18, KSvI12, LW18,RdlCGW09, RYK+19, SW09, ZACS09,HKLN14, WDX+15]. ClusterViz[WZC+15]. CMSB [BLP18]. CMStalker[LMPT15]. CNNs [HGC+20]. Co[CHWY19, DZH16, GZFT15, GDM18,MB20, MWLS18, TM11, WOYL17, XLL+20,XZG+18, ZWDR20]. Co-Clustering[CHWY19]. Co-Complex [WOYL17].Co-evolution [TM11]. Co-Evolutionary[GZFT15, XZG+18]. Co-Expression[DZH16, GDM18, MB20, MWLS18, XLL+20].Co-Methylation [MB20]. Co-Occurrence[ZWDR20]. Coalescence[GPE17, TR13, Zha11, GE14, GE15].Coalescent [DR16, Ros13, TBRS13, Wu10].Coalescent-Based [TBRS13]. Coarse[CGLF12, LQV+13, MDPR18, WLYZ+09].Coarse-Grain [LQV+13]. Coarse-Grained[CGLF12]. Coclustering[CD08, JZL13, PR12]. Code

12

[BvdGK+11, CSZ+19, Tho16, UJ09]. Codes[HXXJ18, TSM14]. Coding[LFZ+19, LHHL19, MK16, MCCZC08,dSRCT+11, ZWXL20]. Codon[HEK18, MNR09, SGC07]. Coefficient[WLWP12, WDL+17]. Coevolutionary[HC17, NLW+18]. Coevolving [HHL+20].Coexpressed [PWT10, TZY11, KSM14].Coexpression [BB11, BLR08, RB16, YC08,ZZN15, WDX+15]. CoGI [XZG15].Cognitive [ZYW17, ZWS+18]. Coherent[YNBM05]. cohesive [ZMC+14]. coli[iAOSS16, RBdJ11]. Collaborated[PCY+19, PZS+20]. Collaboration[ANR11, JJH12]. Collaborative[WXWL20, ZLH+20]. Collected [ZYF+18].Collections [SIK20, Mat15]. Collective[Cza18, LDL+17]. CollHaps [TBGL10].Collisions [MBJ19]. Colon[RHAK13, RHK14]. Colony[LGZ+17, ORCJ13, SSS20a]. Color [TZY11].Colorectal [AAT20, KKK19, PB19].Colored [AP07, RSJK13, WLY15].Combat [ZD17]. Combination[AV17, BRS18, DPS+13, VDS+20].Combinational [CL15]. combinations[DWZ+15]. Combinatorial[BM08, HS08, JL10, LRR08, LMPT15,LHZ+19, PAAG07, VGBK19, YHY13].Combinatorics [HCMB18]. Combined[AHT+18, LSY+20, MGXS15, PNP+18,SZLL11, WL07, WWLL16]. Combining[ARP+16, CWZ08, DCHW17, GKPS11,HLZ+17, KS18, KMG+05, LWT+18, LL19,SFMS18, TOYHZ19, VF09, VTGC16, WS12,WYHZ20, YSGZ20, ZLZ+19, ZYN+19,ZLX+20, BDBH15]. Comembership[HRdR09]. Comment [FLW12]. Common[BVD+07, DST07, KL19, LJZZ13, MIC+07,PS11, ST19, Wan12, NYOL15].Communication [GBS11].communications [PV16].communications-inspired [PV16].Communities [PCK19]. Community

[GLL+18, LZ18b]. Comorbidity[HZW+17, JBgLS19]. Compact [SGR+17].Compaction [PNA20]. Compactly[DM09]. Companion [Ano12a].Comparative [AM12, BCVS19, DS19,JCF13, KAP+12, LTaS13, LW18, LNC+05,NNM+12b, ZZS07, AM15, BMM14, BF14].Compared [FMRS18]. Comparing[BCF+07, CW07, QV17, SS06a, VASG10,HC14b]. Comparison[AS05, BM12, CRV09, CLRV11, CCYW12,DZA+06, DPW12, FFT16, FPPR11,GRS+13, HEE+18, HYZ16, LKW+19,LPH+13, MKH11, Roc11, SMPS20,SMK+12, WLPW16, YH13, ZZ20, CV14].Comparisons [BAK06, LFF18].Compatibility [BLS12, SS06b].Compatible [BN06]. Competence[NPBD16, SSDN12]. complement [TSM14].Complementarity[ADPH11, ADPH13, DM09, PBhL+11].Complementary [TNQ08]. Completion[BKKG19, LHCL20]. Complex [BWRF12,DMJ+18, GLS+16, GBB+11, HK20, HC18,HC19, HC13, HRdR09, LLNW17, MTNH17,MVS+13, PG06, SVdSS+18, SJZ19,TGD+16, TP18, WLHY19, WOYL17,WW19, XL16, ZLY+13, DWZ+15, TYL+16].Complexes [FJJ11, HK20, HZL+20,HYL+19, KSK+18, LLH+07, LMZ+20,OYDZ15, YSGZ20, YB08, ZDL12, CWZW15,PWZW15, XG14, ZZ15, ZWL+14b].Complexity [BN06, BCF+07, BS10b,BLS12, CEFBS06, HKM+18, KB17, LLW10,PH10b, Pol12, RZMC17, TZP17].Complicated [HWPE17]. Component[BKLS18, BSLR05, CXW+13, DSHM08,Gos11, GPC+20, Han10, JDCC12, LXG+16,SDCW11, dCAR11, LLH+14].Component-Based [Gos11]. Components[Wan16]. Composite [LMPT15, MSS19a].Composition [CCYW12, KAL+17,LLTC19, NLGG12, RST10]. Compositions[KNTB18]. Compound [CZW+18].

13

Compound-Protein [CZW+18].Comprehensible [FWA10].Comprehensive [GSK13, JDHL20, SGH12,WWBZ19, YZG+19, YOGY11]. Compress[GDM12]. Compressed[CW07, GRS+13, MDM13]. Compressing[XZG15]. Compression[CGLF12, CWLS15, CLS19, How13, KT07,KBSCZ12, LN17, WL13a, WHWP12, Mat15].Computation [CHNW20, KK19, SSK+20,TWG+12, Wu10, GFG16]. Computational[AJD+12, ANR11, ATA+17, ALWG18,Ano05b, Ano09c, Ano12b, BLP18, BBSP08,BRZ+17, BCF+07, BMZM15, Cas06, Cas07,CN12, DBN18, FS12, FS13a, GCZ18,GLL+18, Gus04b, HKK07, HSS18, Jam13,JJH12, KZW+18, LHH13, LHL+19b,LHY+11, LWL+19, MTNH17, MVVR19,MVVR20, MBP+18, Maz12, NSAH19,PLMV12, PM20, PH10b, RZF07, RG16,RCBB19, SK08, SBW15, SPK19, SYL19,SWX+19, TS18, Tit16, WYWX16,WWT+20, YB08, ZDL+19, ZZ20, MM14a].Computations[ZXB11, ZSC+10, MKARB16]. Computer[MVS+13]. Computer-Aided [MVS+13].Computerized [XPH20]. Computers[TIA+11]. Computing[APPG18, BGS+12, BS07, BS09, BWRF12,BBH12, DB14, GLS+16, GDWK+15,GSB+13, GJS11, HZR+19, HM13, HBG16,HBG17, HBG18, HBG19, HBG20, ME19a,MKS+17, MDH11, OP11, PK13, RP13,SNM08, TLSA18, TS17, UAH16, WS08,WYWX16, WL19, CFIS+15, GPScF15].Concentrations [MKKS20]. Concept[TWZW16]. Concepts [BMT17].Concerning [BvdGK+11]. Concise [Son06].Concurrent [MTM+15]. Concussion[WNT+17]. Condition[Gon13, MSQ18, RB16, Son06].Condition-Specific [MSQ18]. Conditional[BLR08, LDM18, WWL+17, GGZZ14,LWG+14]. Conditioning [DBTB09].

Conditioning-Based [DBTB09].Conference [BLP18, FJJ18, GJH19,HBG16, HBG17, HBG18, HBG19, HBG20,Kim18, MJ18, SPK19, STHA15, ZLZ20,ESW14, HC15, WLC18, YSC19, ZC14].Conferences [Kim18]. Confidence [MC07].Configurations [SLH06b]. Conflict [BB04].Confocal [MCRC17, BLR15].Conformation [LW18, YDM+08].Conformational[HZZY16, LSB+11, RJNN18, ZZY+17].Conformations [LHTT11, LBL12b].Confounding [RKDR10]. Conjugation[HS08]. Connected [BvBF+11, HKLN14].Connections [NRV09]. Connectivity[BMK11, MB20, MBB+17, PBV+20, WL07,ZSD08, YLH+15]. Conquer[OC13, SR10, KD15]. Consensus[ASI+11, CLC+17, JSA08, JRSS18, KWL07,Mah10, PAS+11, SPMB13, TBRS11,WSX11, WHS04, WCL11, WWC18,YLY+12, ZWSX12, YMT+14, YCY+15].Conservation [DST07, MGL+12].Conserved[BMM06, CDKT09, CAN+08, HK12].Considerations [WAG19]. Consistency[BGHM09, SR06]. Consistent[MMH15, MR10, PG06, STB+20].Consolidation [DLM12]. Constant[TZP17]. Constant-Time [TZP17].Constitutive [SDA+06]. Constrained[FHH+11, GHL05, NWW19, QD12,TWG+12, ARZ+14]. Constraint[LCW+18, Pol12, SHUP19, TAAP11].Constraint-Based [TAAP11]. Constraints[ACP10, HYW08, TRBK09, YHCS19,ZmCXS17, vBdRD+11, TSM14]. Construct[SHUP19, WP08]. Constructed [Wil11].Constructing [BEQD19, BWRF12, DH04,GHL05, LZL+19, NWZ+20, SNM12, VRK12,WL11, WLY14, WZZ+18, vIKK+09, Nye14].Construction [AAH+18, KBSCZ12,LCEMO18, LNC+19, MPA15, OC13,WCL11, ZPW+19, ED14, LHS16, MW16].

14

Constructive [CH11, LH20]. Contact[CGPW06, DFM+11, Gra04, VMD+08,KD15]. Contact-Map [Gra04]. Contacts[KL19, KSMT19]. Contagion [FSD+11].containing [FSL+15]. Content[CAN+08, DBK18, GTTR+17, RKDR10,SLS+14, TSM14]. contents [WLL+20].Context [FLW12, NAHT+20, SLRQ19,ZZCY10, ZWL11, ZYN+19, FZM15].Context-Awareness [ZWL11].Contextual [DBTB09]. Contig[LTL+19, MS10]. Contigs[LHKL17, LCSW18, WLL+20]. Contiguous[ZWZS16]. Continuous [ALQ17, CHW+18,CWZ08, JLH16, JFN11, RPBP18, SH11a].Continuous-State [CHW+18].Continuous-Time [SH11a]. Contour[LK11]. Contrast [FYZ+19].Contrast-Enhanced [FYZ+19].Contrastive [JRN+18]. Contributors[PKRD12]. Control [BD19, FKB19,GCB+18, HZL+20, IBN19, JZS+18, LT17,LJ20, LLL16b, PPM+13, PLC+20, PSPM20,QD12, SJS19, ZMST18, ZZM17].Controllability [CWG+18, TGD+16,WWL19, ZMST18, LP15, SRLR14].Controlled [BMHS13, AKS13]. Controller[iAOSS16]. Controllers [iAOSS16].Controlling[ANR11, SPA17, TWG+12, TGK13, Zha18].Controls [HYL+20]. Conventional[AM12, AM15]. convergence [GJY+14].Converter [YWW+18]. Convex[BFK17, HZZY16, JDCC12, WCQ+19,ZGDH16, WB17]. Convex-Relaxed[ZGDH16]. Convolutional [LLQ20,SDH20b, WYHZ20, ZZH19, ZZBH20].Cooperative [GZFT15, XZG+18, ZLJT17].Cooperativity [JBP08]. Coordinate[WWLL16]. Coordinates [FSB+11].Cophenetic [ME19b]. Cophylogenetic[WHBM15]. Cophylogeny [USMS19].Coprocessor [MPA15]. Copula [HLL18b].Copula-Based [HLL18b]. Copy

[BHMA06, CW09a, NVSH18, SDCW11,TWW+20, WHXS17, XL16, XLW20,YCCM12, ZANN20, ZmCXS17, ZRK19,dNG17, LWM14, MMSH14, SB16].Copy-Number [YCCM12, SB16]. Core[DADF+10, LHL+19a, YFCM17, PWZW15].core-attachment [PWZW15]. Coreceptor[LSMF08]. Cores [LSTW+17, WSTL+15].Corner [SSD+16]. Coronary [FLJS20].Coronavirus [XHY+18]. Correct [JZW17].Correcting [ZKP+07]. Correction[ACWW07, BDD18, LCEMO18, LTL+19,LLBL20, SLGK17, WLL+20, ZXLZ18a].Correlated[BVN+11, DFM+11, HKT+18, JM12].Correlation [BHP19, IQA18, LLC+13,MGL+12, NU06, SSP+05, SLX+18,TGGF10, WZJH12, ZCR+17, AMBK14].Correlation-Guided [SLX+18].Correlations[DMJ+18, GLW12, TWZW16].Correspondence [YHYY12]. Cortical[TWG+12, ZWS+18]. COSPEDTree[BM15]. Cost [KBBD+17, TR13, WCC+18,WZ13a, ZwGC17, GE14]. Cost-Based[ZwGC17]. Cost-Sensitive[WCC+18, WZ13a]. Costs[GE18, dSMDB17]. Cotemporal [JFN11].Count [PNP+18]. Counting[BO12, SREK19, SLH06b]. Coupled[HPL+13]. couplet [BM15]. Coupling[SZCX19, TRBK08, ZHL+14]. Course[EAS12, IVA11, OMAdG+12, CZWT15].Courses [SCSS05]. Covariance [Smi09].Covarion [AR09]. Cover[DNS19, HMK+07]. Coverage[AOSN+18, GGP08, ZANN20, HKLN14].Coverage-Based [AOSN+18]. Covering[BNV+13, HYY11, RCM+19]. Cox [RKZ16].CpG [SKD+07, XYYZ20]. CPU[PCY+19, ZWcF17]. Creating [VSR+06].Credibility [MG19]. Credible [JWZ+20].CRF [LJ20]. Criteria[LLC+13, WWC18, ZSD08]. Criterion

15

[CLVT+20, GZG17]. Critical [MMH15].Cross [AMGC16, HKS11, LPH+13,PBhL+11, SLRQ19, WGK16, PS15].Cross-Context [SLRQ19]. Cross-Entropy[PBhL+11, PS15]. Cross-Hybridization[HKS11]. Cross-Laboratory [LPH+13].Cross-Ontology [AMGC16].Cross-Sectional [WGK16]. Crossing[Gra04]. cruzi [GAR+09]. Cryo[BRZ+17, LDS+07, ARZ+14, ZCR+17].Cryo-EM[BRZ+17, LDS+07, ARZ+14, ZCR+17].CryoEM [ALR+13]. Cryptographic[JHW+19]. Cryptographically [BKLS18].Crystal [DDS+17]. Crystallization[STB+20]. Crystallography [Str11]. CSD[Wil12]. CSS [AKS13]. cuBLASTP[ZWcF17]. Cuckoo [AKS13]. CUDA[BBH12, CNM11, LSMW11, ZLS+15].CUDA-BLASTP [LSMW11].CUDA-Enabled [LSMW11, ZLS+15].cumulative [TYA15]. Curatable [HK15].Curated [GTTR+17]. CURatio [KMSY20].Curation [HLLO19]. Current[MSS+13a, SW17]. Curvature [MBF+13].Curves [IGA18, KGK14]. Cut[BFM13, NSNA19, SR06]. Cutting[NSZK15]. cyber [KSA16]. cyberphysical[AIS+16]. Cycle [BRF17, CAW+19, SSS20a,ZZM17, ZWW17, WZ14]. Cycles [Gru11].Cytogenetic [LYK07]. Cytometry[PN17, Qiu14]. cytoscape[NCMCAR15, WZC+15]. cytosolic[LCOMG14].

D [ABS17, APPG18, ARP+16, BLR15,BWRF12, CWT+19, CBF+18, GPF+20,GH15, HS15, KL19, KSMT19, KD15,LQV+13, LHQ+18, LBQ+13, MCRC17,NPK+07, RG16, RWH+10, Str11, SSF18,VMD+08, YLH+15, YCZ+18]. D-Map[ABS17]. D-pattern [KD15]. DAG[BM15, TGP+15]. DALI [WAK13]. DALIX[WAK13]. Damage [ZLL+20]. DAPD

[GJK15]. Data[AGAS18, AAH+18, AFAAW+11, ABVD12,ASI+11, ACWW05, ACWW07, BKP+19,BDD18, BMK11, BTTR11, BDP11, BZ10,BHMA06, BLP+12, BMHS13, BKLS18,BHHMCL16, Bon07, BMZM15, BLR08,CMR19, CCCY20, CMS12, CSSS16,CSZ+19, CKM+17, CW09a, CHL+12,CHWY19, CMMZ20, CBM+20, Che10,CKWY12, CCE19, CWZ08, CZM+18,DNR15, DCHW17, DHCW18, DG19,DMJ+18, DWSB11, EAS12, EAS13,FHH+11, FJJ11, GZG17, GKPS11, GXSZ17,GMSD11, GZR+18, GJZH17, GBJ08,GLG10, GM16, HYW+17, HBH12, HYY11,HZW+17, HYL+20, HYC12, HAH13,HMW+12, How13, HLY+16, HC16, HW07,HLL18b, HDS+18, HHCY20, HTLL12,IGA18, IMA13, JCF13, JXN+16, JHX17,JFN11, KCD+12, KBND19, KHO+20, KB20,KNS+05, KMG+05, KBSCZ12, KZ10,LTM+13, LHH13, LBM+18, LH10, LLW+11,LN13, LLHF15, LW18, LKW+19, LJL+15,LLZ+20a, LXG+16, LZHZ17, LW19b,LYY+19, LLZ+20b, LNW20, LLL15]. Data[LC10, LLA19, LTRW19, LBL+10, MSZ19a,MHHJ20, MO04, MTSCO10, MP13, MP19,MJPP20, MWZ+20, ML18, MPM11,NJMF19, NNSZ07, NSAH19, NNM+12b,OLZ11, OMWX09, OLS+13, OC13, PLC+20,PSS09, PIPC18, PAS+11, PI09, PR18, PL17,PZH20, PH10b, PNP+18, PAAG07, PN17,QV17, QKO18, QBPEL12, RLR20, RCP+18,RTPM+19, RKZ16, RM18, RBdlVMPG16,RGCB05, RWH+10, SSD19, SDN+11, Sen19,SBW15, SC11, SY09, SIM12, ST05, SDCW11,STB+20, SMK+12, SK12, SWX+19, SGK12,SWL19, TWW+20, TZH07, TZ16, TGGF10,TDZ+19, TZY11, TBRS13, TTWR13, TK05,TC13, TWZW16, TOYHZ19, TBKH05,UC10, UKV18, VBG+18, WZA07, WGP11,WYWX16, WLWN17, WFY+19, WHF+20,WP08, WAG19, Wil09, WMS09, WDS+12,WGK16, XHQ+18, XLL+20, XSS17, XZC07,

16

XAW07, XOYHZ18, YSC13, YM11,YWW20, YLXJ04, YC08, YNWC07,YNBM05, YLL+06, YHB12, YP13, YCY+13,YWW+18]. Data [YGY+19, YNN+18,ZZKW18, ZANN20, ZLW+11, ZWSX12,ZDL12, ZXLZ18a, ZXLZ18b, ZZZW19,ZWHC19, ZZ20, ZXZ20, ZC11, Zha16,ZKL18, ZY20, ZHG20, ZWD+17, ZYW+13,ZYF+18, ZGDH16, ZGB+12, dCAR11,BMM14, CWZW15, CZWT15, FN14,GFG16, GMCB14, IM14, JZCZ15, JR14,KSM14, KGF+14, LLCZ15, LXZ+15, LHS16,MM14b, OFC+14, PS15, Qiu14, SHK14,Vog15, WLC+15, XZY+14, YN14, YCY+15].Data-Dependent [XZC07]. Data-Driven[CCE19, HLY+16, PLC+20, ZHG20].Data-Fusion [KZ10]. Database[ANR11, GKPS11, LYK07, SDN+11,WNT+17, WQL+16, XPH12, dAc17].Databases [Ano13b, Ano13c, HW07, Jam17,LTwG+11, ZSC+10, Ano13d, XHS15].Dataset [LN17]. Datasets [CKM+17,FFT16, MB16, WDL+17, ZZH18a, BCLC15].Day [MSH+11]. Day-to-Day [MSH+11].DB [WQL+16]. DDE [ZSY+14].De-Noising [YFCM17]. Decision[Smi09, TNQ08, YNBM05]. declarative[LV14]. Decoding [PV16, UJ09].Decomposition [FWXZ19, LLQ+16,RGCB05, SK19, XL16, XLW20, YWK+07,ZZN+11b, ZGDH16, LYH+16, SB16].decompositions [GMCB14]. Decoupling[LLL16b]. Decoy [MSS13b]. Decoys[LBL12a]. Decrease [TC13]. Deep[CZ20, CGW+16, DSCM20, FSX19,FYZ+19, FZM20, FMA+20, FPC20, GPE17,JHZL19, LFZ+19, LHCL20, LZQ+20,MWZ+20, NLXS19, OLS+13, RFFB+20,SSV+19, SGP+20, SWL19, TR13, UBP+19,WCC+18, WYHZ20, WWL+17, WCXL18,ZLH+20, Zha11, ZG19, wTCAK+20, GE14,GE15, LLCZ15, SEC15]. Deep-Learning[FPC20]. deepSOM [SYKM17]. Defects[LUdSCH10]. defines [LHWL15]. Defining

[WS08]. Definitions [NRV09].Deformation [ASJ+07]. degenerate[CFIS+15]. Degradation [WMWA12].Degree [GF10, SS06a, TWZP14]. Delay[EAS13, JSS+18]. Delayed[JZS+18, KCCC15, LCZN16, LLL15].Delays[AGAS18, FZWS17, ZWZ16, ZWC15].Deletions [QLLX10, HZZT14]. Delivery[MWD11]. Dementia [ZWS+18].Dempster [RGI13]. Dempster-Schafer[RGI13]. Dendrogram [NSZK15].Denoising [NNM+12b, GH15]. Dense[DADF+10, Wil09, YNWC07]. Dense-Core[DADF+10]. Density[GLG10, MRB12, QL16, SKD+07, XYYZ20].Dependence [LGN+19]. Dependences[YP13]. Dependencies [KNS+05, SZL+20].Dependency [CL08]. Dependent[AKV16, KKK19, KSB12, XZC07, MZS+16,WDX+15]. Depends [LCH19]. Depth[GAGM11, IMA13, KBBD+17]. Derivative[NVSH18, XSS17]. Derivative-Free[XSS17]. Derivatives [NSMH19, KPB14].Derived [HYR+19, JS12, WQL+16].Descent [NGY+16]. Description[FS18, GAGM11]. Descriptor[ADPH11, YCZ+18]. Descriptors[ARP+16, HZTP12, WB11, YZG+19].Design [AKS13, Che16, GJZH17, mHB13,IL18, IYA12, JSS+18, JZS+18, LHDS18,MDD18, MM17, OMAdG+12, SK08, SB12,TRBK09, VDS+20, WLC11, YCYC12,DYD15, HPH+15, KH14, MG14, MM14a].Designer [BPP+13]. Designing[GBB+11, Jam13, MDM13, NTCO07, SB09,SBY12, THH+19]. Designs [GK08].desired [HPH+15]. Detect[HK12, YLC20, YWW20, YBGB10, ZYF+18,LLL16a, SSML15]. detected [AAG+18].Detecting[ALQ17, ABVD12, AALD17, HLHAJ20,HYL+19, JLYZ16, KSM14, LZ18b, NVSH18,OYDZ15, RH05, TWG+12, TBRS11, UJ09,

17

YSGZ20, ZXLZ18a, ZXLZ18b, ZRK19,ZWL+14b, SSS+15, ZZ15]. Detection[ARM+19, AGGM11, AAT20, BBN18,CW09a, CWL12, DADF+10, FYZ+19,FMD18, GLL+18, GDWK+15, GPC+20,HLL+18a, HGC+20, HTLL12, IGM+07,LGW20, LL19, LCGW19, LYY+19, LGB15,LCB17, MYCW12, MB20, MPQY19, NSC17,PCK19, RHAK13, RB14, Shi10, SIK20,SCM19, TWW+20, TP18, WS12, Wer06,WOYL17, XGWW19, YC08, ZANN20,ZLW+11, ZmCXS17, dNG17, CBN15,DGRC15, GBTL14, HWK14, LWM14,MMFD14, PS15, SB16, SXL+14, Vog15].Determination[BRZ+17, BKR11, WL07, DST+15b].Determining [AAF+13, Tah14].Developing [SWX+19, XYYZ20].Development[Che12, HSS18, MMH15, TZH07]. Devices[GTTR+17, MKARB16]. DFseq [YWW20].DFT [NSMH19]. diabetes [GJK15].Diagnosing [HC16, WW19]. Diagnosis[BBN18, JHZL19, OW20, PTH+18, YOKI09,ZHSS07, GJY+14]. Diagnostics[Ano12a, BDP11]. Diagonal [YHCS19].Diagrams [YNBM05]. Diameter[HZR+19, HSlSM11, GE15]. Diameters[GPE17, GE18]. Diazoxide [WLCX18].dibenzopyrrole [KPB14]. DICLENS[MA12]. Dictionary [KBSCZ12].Difference[JRSS18, ME19a, ME19c, WL19, DWZ+15].Differences [vBdRD+11]. Different[DPS+13, ZWL14a]. Differential[CHW+18, CBK20, CZM+18, LEAK11,LL11, LW19a, LYY+19, MSS19a, NI07,RCP+18, SdOD+12, YWW20, ZZY+17,dJP08, ABS17, BMM14, HLW15, ZSY+14].Differentially[AAP06, EAS12, HHSC13, LXG+16,LWG+18, PS19, SDTK19, WS12, KSM14].Differentiating [ZLXL19]. Differentiation[CBM+20, ZRK19]. Difficult [BBCP07].

Diffused [WWC18]. Diffusion[FZWS17, SHJL10]. Digest[BBK+07, JR14]. digital [AIS+16].Dimension [ST05, YTLL15]. Dimensional[Che10, CHC+05, DZA+06, HDS+18,LHL+19a, LTaS13, LN13, NPBD16, PL17,SWL19, WWLL16, WRH+09, WWL+17,ZMT13, ZD17, ZZZW19, ZKL18, BF14,Qiu14, YN14, ZMC+14]. Dimensionality[LRM08, YLC20]. DipC [WCLY20].Diploid [KWL07]. Direct [SZL+20].Directed [ARS17, PPZ12, Zha18].Direction [HYL+19]. Directional [ZS19].Dirichlet [CGZ15, PRZ+14, RdlCGW09].Disagreement [MW20]. Disambiguation[HVD18, HWK14]. DiscMLA [ZZH18a].Discordance [PT09]. Discover [MSZ19a].Discovering [AOSN+18, ACP10, BHS+04,KN05, LSTW+17, LLH+07, LNC+05,MPF12, RB16, RM18, RA16, WHWP12,WSTL+15, XL16, YNBM05]. Discovery[ANR11, ABS17, Bi09, BD19, BVN+11,CLST+13, CHK17, GXSZ17, GCB+18,Han10, JL10, KL19, KC11, KZ10, LDS+07,LHL+19a, LMPT15, LCLL10, LCW+18,LT07, MLZ18, PWT10, PZH20, RLV04,SKDA19, SS04, SGP+20, TP18, UBP+19,WLCP11, YAB13, YLY+12, YNN+18,ZDL12, ZZ18, ZZN+11b, ZMC+14, ZAZ11,pD20, CWDS15, CA14, FWY+15, JZCZ15,KGF+14, OFC+14]. Discrete[CWZ08, ED15, GPZ20, HGM18, LCW+18,PTM+19, SH11a, WZ13b]. Discrete-State[SH11a]. Discriminant[FWY19, NO09, OG11, WYHD17, YLXJ04].Discriminate [THH+19]. discriminating[SQZA14]. discrimination [DI15].Discriminative [KC11, hLMBJ11, ZZH18a].Disease [BKKG19, DHCW18, GSC17,HZW+17, JBgLS19, JZZQ19, JHZL19,LWL+18, LRR08, LZHZ17, LWT+18,LDL+17, LTRW19, MS17, MSB19, NWZ+20,OW20, PBV+20, QLZ16, QBPEL12,SSK+20, VBG+18, WLCX18, WCMB19,

18

WLA+13, XPH12, XW16, YDW+20, YG19,ZLLZ17, ZLH+20, ZWS+18, ZZCD19,ZZRPZ19, ZYN+19, YWN+19].Disease-Associated [LDL+17].Disease-Related [JZZQ19]. Diseases[GZC+17, HC16, TP18, YWN+19, DWZ+15,LLRZ15, TYL+16]. Disequilibrium[LLC+13]. Disjoint [DNS19]. Disorders[GSC17, SVdSS+18]. Disparate [QKO18].Disrupt [GED+17]. Disruption [HK20].Dissect [WLHY19]. Dissecting [KDS+20].Dissimilarity [FB19]. Distance[AKNB07, AS05, BFK17, BG12, BS10b,BHP19, BODD20, BJ13, CHNW20,CWZL08, DS14, FM11, GRS+13, Lab06,LTM+13, Pol12, RFB20, SGC07, SWH+12,WM19b, WZ13b, ZZY+17, ZWM+20,ZSC+10, ZW13, dSMDB17, DNR15, TSM14].Distance-based [DS14]. Distances[BPV+11, JZSZ12, OP11, WL19]. Distant[VSKJ11]. Distinguishing [AD12].Distorted [Mos07]. Distributed[BHP19, GZR+18, LBL+10, PFJ+19,PNA20, PSN+15, RTPM+19, SSD19,WWC18, GFG16]. Distribution[ASI+11, BS09, DADF+10, Gru11, LLH+17,MT12a, WLL+20, YWW20, DWZ+15].Distribution-Free [YWW20].Distributions [APPG18, LTM+13,PPFG20, SZZ+19, SHUP19, WM19a].Disturbance [LL11, LLL16b, YM20].Disulfide [YLH+15]. Disunited [SSS20b].Diurnal [KM20, WGP11]. Divergence[EW04, ZZS18]. Diverse [LSB+11].Diversity [FWY19, MPKvH09, SNM08].Divide [KD15, OC13, SR10]. Divisive[MA12]. DLBCL [WWC18]. DMBIH[YGFC20]. DNA [ASJ+07, BTYC13,CFOS06, CLST+13, CW09a, CH11, CLZ+18,CWLS15, CLS19, CL08, CAN+08, DCHW17,DSVMM18, DPW12, FPC20, GZGX14,GKPS11, HEK18, HHSC13, HG16, HLZ+17,HLH11, KCD+12, KC11, KBSCZ12,LSTW+17, LPH18, LLW+11, LZL+20,

cLWA07, MGL+12, MRK18, MMSH14,NVSH18, PKRD12, PG12, PGF18, RLV04,RG16, SSS20b, SLRQ19, SIK20, TDA+09,TSM14, UJ09, WZZ+18, WP08, WSTL+15,WLPW16, WW19, ZZH19, ZLL+20,ZZBH20, ZLX+20, ZZDY13, ZL15].DNA-Binding[MGL+12, ZLX+20, ZZDY13].DNA-Protein [WP08, ZZH19]. DNAzyme[EES14]. Dnmt3a [LGN+19]. DNRLMF[YWN+19]. Do [RRTB12]. Dock[ADPH13, BCS11]. Docking[ADPH11, ADPH13, BCS11, GED+17,LSB+11, PSN+15, SZ11]. Documents[AC12, KAHK+10]. Does [BCVS19].Domain[CYJ+19, KCP19, LB19, LNW20, WWT+20].Domains [HMK+07, LDS+07, QLZ16,WCMZ15, ZHZ+20, DC15, PWC+15].Dominating [ZWW17]. donovani[SSP+17]. Dose [SWX+19]. Double[SZCX19, YCY+14]. Downhill [SS04]. DP1[IDD13]. DPNuc [CGZ15]. Drawing[Hus09, SNM12]. Drawings [VASG10].drift [SPWF14]. Driven[CSW11, CCE19, FMA+20, HLY+16,PLC+20, YCCM12, ZHG20, GBTL14, KG15].Driver [LGW20, SPW20, ZZ18, ZW19,LP15, LWM14]. Drosophila[GGH+13, LK11, LJK+12, MBJ19].DrPOCS [WCQ+19]. Drug[BD19, CCCY20, DCM20, EZW+17, HLN20,JQH+20, KCP19, KHP12, KS18, LC19,LWL+19, MWZY17, PSIM17, RV13, SZ11,SYKS15, SSP+17, SWX+19, UBP+19,UKV18, WLCX18, WCQ+19, WXWL20,XYZ19, BHW+14, FHRG14, KPB14,LYH+16, XLC+15]. Drug-Gene-Disease[WLCX18]. Drug-Induced [SWX+19].drug-pathway [LYH+16]. Drug-Response[CCCY20, UKV18]. Drug-Target[EZW+17, FHRG14]. DrugBank [RV13].Drugs [PG12, YSW+17]. Dual[LLQ+16, RBB+19, WXWL20]. Dual-Layer

19

[WXWL20]. Duchenne [BCL+13a]. Ductal[CSSS16]. Duplication[BE08, BEW09, BS11, BG05, HZR+19,HCMB18, KB17, KB19, LCWZ13, LCC+11,PG18, ZZS18, vIJJ+20, ZZ14].Duplication-Transfer-Loss [KB17, KB19].Duplications[BCF+07, CDW12, SS06a, THL11]. during[HK12, KCZ+15, TC13]. Dynamic[BBK+07, CHZ+16, CLR10, GCL+18, HL16,HHYH07, HT09, LCZN16, NSZK15,PAL+12, PZS+20, RBdJ11, SMSZ17, TP18,WLL+09, WMWA12, WWLL16, XZG+18,ZLH12, ZD17, WZ14]. Dynamic-Pattern[WMWA12]. Dynamical [CBM+20, KKC16,LLH+07, MDD18, SCM19, ZZKW18].Dynamics [AVD+12, APKP18, CGLF12,Dem12, GBJ08, KL11c, LLES18, LW13b,PB12a, PTM+19, Pau18, RTA+16, RSCX18,SH11a, ZLL+20, MFS+15, PSK+16].Dysfunction [FLJS20]. Dystrophy[BCL+13a].

Early [BCL+13a, JHZL19, TP18]. East[XHY+18]. Ebola [MBP+18]. EBWS[KPP19]. ECD [YKW17]. ECG [ZCWW19].Edge [GPC+20, WLWP12, HKLN14]. Edit[RFB20]. Edition [MVVR19, MVVR20].Editor [Ano10c, BLP18, HMZ17, Ano04b,Ano08c, Ano12b, Cas06, Cas07, Cat17,Gus07a, Gus07b, LNY05a, Xu13, Xu14a,Xu15, Zha17]. Editor-in [Xu13].Editor-in-Chief[Ano08c, Xu14a, Xu15, Zha17]. Editorial[Che12, CN12, Che13, FJJ18, FK19, GJH19,Gus05, Gus08, Gus09a, Gus09b, GM16,HC15, HBG16, HBG17, HBG18, HBG19,HBG20, KS13, KJ04, KJ05, Kim18, MJ18,Mur18, Sag09a, Sag09b, Sag09c, Sag10,Sag11a, Sag11b, Sag12, SPK19, TS17, TH18,WYWX16, WLWN17, WLC18, WH11, Xu13,Xu14a, Xu15, YSC19, YGFC20, YS17, ZC15,Zha17, ZLZ20, ZCM19, dSK13, ESW14,LW15, MNA14, MKARB16, PR14, STHA15,

Xu14b, ZC14]. Editorial-State [Gus05].editors[CEG14, XHS15, AS15, BPW17, BPRZ11,CZ12, FS12, FS13a, GH08b, Gus04a, Gus06a,LNY05b, MPZ07, MPZ08, MPSZ09, MWZ13,MSZ19b, MNPZ10, RZF07, Sag09b, Wil04a].EEG [AKS13, HLSR18]. EEG-Based[HLSR18]. EEG/ERP [AKS13]. Effect[AD12, BMH+16, GSC+18, GSC17,GPC+20, JQH+20, MRS09, RKDR10,SZCX19, WHXS17, ZZ14, WFD15].Effective [AAP06, BRZ+17, CMSE+15,CZJ17, HC07, SSS20a, WOYL17].Effectively [CZW+18]. Effectiveness[ARK20, Jam15]. Effects[ALQ17, BCFCC13, MWLS18, SSK+20].Efficacy [LRM08, QL09, CWDS15].Efficiency [KBBD+17, LHY+11, RKDR10,RKDR11, ZLLS17]. Efficient [BPV+11,BHHMCL16, CMR19, CZ20, CFOS06,CCE19, DLRW18, DBZ12, DLM12, DHC12,FM12, GPMH16, GSK13, HLV+10, HT09,JZW17, KVX12, LR20, LYH+16, LJL+15,LLZ+20a, LZX20, LHG+16, MWL+12,ME19c, MS11, MCDD12, NSZK15, PG18,PSPM20, PH10a, PCK19, PBJ12, POS+18,SP11, SAE+20, SK08, SN12, SLH+06a,SDB+07, SK12, SDTK19, TZP17, VTGC16,WBP+12, WKLL12, Wan16, WBE13, Wer06,WCLY12, YDM+08, YHZ+19, ZZH18a,ZGZ+20, GM14, LMZ14, LHS16, SDAA+14,SSKH15, SYV14, YHV+15, ZHL+14].Efficiently[HYL+19, TK05, ZLZ+19, NYOL15]. EGA[Sen19]. EGFR [MWZY17]. EHR[ZDL+19]. EHR-Based [ZDL+19]. EHRs[MZSL19]. EIC[Gus08, Gus09b, Sag09a, Sag09b, Sag09c,Sag10, Sag11a, Sag11b, Sag12]. Eigen[MWZY17, WMWA12]. Eigen-Binding[MWZY17]. Eigen-Genomic [WMWA12].Eigenmap [ZYW17]. EKF [ZWL+12].EL LSTM [ZLX+20]. Elastic[WMK16, ZLH+17]. Electrical [BMH+16].

20

Electron [MRB12]. Electronic [SGR+17].Electrostatic [BTYC13]. Electrostatics[Gon13]. Element [WQL+16]. Elementary[UAH16, DB14]. Elements[AOSN+18, AD12, GGZZ14]. ELF [FW20].Elimination [CZJ17, DLM12, LZX20,LHY+11, PGHT12, STT+14]. ellipse[SXL+14]. Ellipsoid [XAW07]. ELLPACK[BBH12]. ELLPACK-R [BBH12]. ELM[SSS+11, WYHZ20]. Elucidating [LW19a].Elucidation [LZW20]. Elusiveness[KSvI12]. EMatch [LDS+07]. Embedded[BHHMCL16, CYTY13, JS12]. Embedding[LC19, YSGZ20, ZDYH17]. Embeddings[HLL+18a, LLQ+16]. Embryonic[GBTW16, GBTL14]. Embryos [LK11].EmDL [XYZ19]. Emerging[KSA16, GPScF15, MKARB16]. Empirical[FFT16, JQH+20, KB20, KK12, LS10,MSB19]. Emulation [ACCT20]. Enabled[LSMW11, ZLS+15]. Enables [LR20].Enabling [LLZ+20b, LBL+10, RTPM+19].Encoding[CBES11, HYW+17, JDHL20, KKI20,OM07, PR18, RH05, SSS+11, WYHZ20].Encouraging [ANR11]. Encryption[RCP+18]. End [Gus09a, KY19, LLH+17,Sen19, WLL+20, YRL+20]. End-to-End[KY19, Sen19, YRL+20]. Endogenous[AD12]. Endoplasmic [LLES18]. Energetic[ZXB11, LHWL15]. Energy [ASJ+07,ACC+13, BCFCC13, mHB13, MSS13b,NA11, NSAH19, RJNN18, SDS18, DWZ+15].Engineer [ACCT20]. Engineered[MBP+18]. Engineering [BGS+12, INT11,LLA19, RPB+13, SdOD+12, TS17].Enhance [SR06]. Enhanced[CPM18, FYZ+19, WBE13, ZZZC17,ZZDY13, KFHK14]. Enhancement[DNS19]. enhancers [CV14, LKLB14].Enhancing [ANR11, SIK20, YXS16,ZZY+17, ZGDH16, FSL+15]. ENISI[MCH+15]. Enough [MZSL19, SRM18].Enriched [MSS+19b]. Enrichment

[FLAM15, PSN+15, YM20]. Ensemble[CHZ+16, DPS+13, GMSD11, LYL+17,LZQ+20, MKG20, MA12, MSKC19, OLZ11,TDZ+19, YHZ+19, YCY+13, YRD+13,ZYW17, ZCG+18, ZLX+20, RHK14,STT+14, YCY+14, YRD+14a, YN14].ensemble-based [STT+14]. Ensembles[ALWG18, LSB+11, RSP08, Val11].Ensembling [DSCM20]. Entities[PZWC20]. Entity [AV17, LJ20, HK15].Entropic [POS+18, CA14]. Entropy[CCYW12, GMP08, PBhL+11, SPW20,ZWY+10, PS15, RB14]. Entropy-Based[SPW20]. Enumerating [NSNA19].Enumeration [SS06b, SN12]. Enumerative[BBK+07, Tan14]. Envelope [XHY+18].Environment [SAM+19, XZG+18, ZD17,LHN+14, LLH+14]. Environmental [ZS18].Environments [BWRF12, PNA20].enzymes [SFH+14]. epi [WHF+20].Epidemics [ZYF+18]. Epigenetic[MSZ19a]. Epileptic [ZHG20]. Epistasis[APKP18, GDWK+15, HLHAJ20, LZW20].Epistatic [FMA+20]. Epistatic-Driven[FMA+20]. Epithelial [AVD+12, SDA+06].Epitope [ZWL11, ZHL+14]. Epitopes[AGGM11, XHY+18, YBGB10]. eQTL[YZG+17]. Equation [LL11, dJP08].Equations[HLM+13, SdOD+12, SCCDK09].Equilibrium [BBW18]. equivalence[BM15]. Eradicate [Vis18]. ERDS[TWW+20]. ERDS-Exome [TWW+20].Erosion [BBH+18]. ERP [AKS13].Erratum [HOS+12a, YRD+14a].Erroneous [PVB+12]. Error [BvdGK+11,GGP08, HZL+20, LTL+19, LLBL20,MDD18, SLGK17, WLL+20, FSL+15].error-containing [FSL+15]. Errors[ZKP+07]. Escherichia [iAOSS16, RBdJ11].ESDA [WMWA12]. ESLTAGs [RAA10].Essential [KPP19, LYW20, LLNW17,LNC+19, LZX+19, Mam05, QL16, WLWP12,XGWW19, ZXLZ18a, ZXLZ18b, ZXZ20,

21

DI15, LLW+15, PWC+15, TWZP14].Establish [PS19]. Estimate [CSZ+19].Estimates [JZW17]. Estimating[GKPS11, NGY+16, NSAH19, SS04,SWH+12, TIA+11]. Estimation [ASI+11,BBW18, CSZT19, CAW+19, GAGM11,JRN+18, LWZ12, MNND13, MR10, SRM18,SNC+16, SGH12, TGGF10, WLMW+11,WWLL16, YWK+07, YAB13, ZWL+12,Gu16, GJY+14, HLW15, TDD14, ZSY+14].Estrogenic [NSMH19]. ETD [YKW17].ETD/ECD [YKW17]. Euclidean [ME19c].Eukaryotic [SSS13a, SSS20b, TR07].Evaluate [LGX10]. Evaluating[WLYZ+09]. Evaluation[BKLS18, CAN+08, DM09, MSJP19,OMAdG+12, YLCC13, KPB14]. Event[BM20, CBM+20, HLL+18a, JRN+18,LLQ+16, PTM+19, SYM+10, YRL+20,MZSL19]. Event-Level [MZSL19]. Events[BB04, LLQ20, MG19, NAHT+20, TBRS13,Zha11]. Evidence [KK12, RLRH18, WZ14].Evolution[AGMP09, BJ10, BPJ12, BGHM09, BM13,BSST08, CM13, DST07, GBS11, HK12,HB11, LW19a, LB19, NI07, SRLR14,ZZY+17, ZACS09, HLW15, TM11, ZSY+14].Evolutionary[CS15, GZFT15, GSC+18, GK08, HC18,HHYH07, HTLL12, HLW15, HRdR09,KCD+12, KTLM15, LCWZ13, LSY+20,LT07, MG19, NLGG12, SDS18, TWG+12,TBRS11, WDH08, WLC11, XZG+18,YWK+07, YHZ+19, ZZS18, DPL+14, Mat15].Evolved [AD12, HF07, LSMF08]. EvoMD[WLC11]. Exact [CW11, CHNW20,CMQ+16, GRS+13, HBM19, KB19, MS11,RW07, TED+12, Wu10, ZS19, ZW13,ABH+14, Tan14, YHV+15]. Examining[GAJ+18]. Example [DSZ+06, OLZ11].Examples [CZW+18, KK08]. Excisions[SS06a]. Excitation [MBF+13]. Exclusive[SPW20]. Exemplar[BVD+07, BJ13, QSJ+20, ZW13].

exhaustive [Qiu14]. Existence [Son06].Exocytosis [SDA+06]. Exome[TWW+20, TWW+20]. Exons[SSS20b, WS12]. Expanded [mHB13].Expanding [PBV+20]. Expansion[NSC17, XLL19, ZZKW18]. Expectation[MB16]. Expected [Pol11, Vis18].Experiences [MCHT17]. Experimental[AHT+18, GK08, MDD18, NSAH19,VDS+20, DYD15]. Experiments[BDS12, BSST08, IVA11, IYA12, MGS17,MDM13, NFM+12, OMAdG+12, SVZ09,SC11, THH+19]. expert [GRDV14].Experts [WCMZ15]. Explained [AHT+18].Explaining [TGP+15]. Explicit [ZMT13].Exploiting [ASP20, AL12, CHL+12,HXXJ18, KDS+20, NSNN12]. Exploration[LTwG+11, RTPM+19, WRH+09].Explorations [mHB13]. Exploratory[BLR08, Mah10, ZWHC19]. Explore[BKKG19, YDM+08]. Exploring[BSST08, CLC+17, CRK+19, DHC12,GTTR+17, JBP08, KNS+05, SLGK17,TYL+16, USMS19, VRJ+10]. Exponential[WFY+19]. Exponential-Family[WFY+19]. Expressed [AAP06, EAS12,LXG+16, LWG+18, PS19, SDTK19, WS12].Expression[ACWW05, ACWW07, BGS+12, BDP11,BHMA06, BLP+12, Bon07, CCCY20,CHWY19, CMMZ20, CBK20, CWZ08,DZH16, DCHW17, DWSB11, GZG17,GMSD11, GZR+18, GDM18, GJZH17,GBJ08, HBH12, HHYH07, HMW+12, HC16,HTLL12, JCF13, KBND19, KG12, KCCC15,KCP18, KKK19, KK12, KMG+05, LEAK11,LTM+12, LTM+13, LBM+18, LRM08,LJK+12, LLHF15, LW19b, LYY+19, LLL15,LLA19, MTSCO10, MSH+11, MSS19a,MB20, MWZ+20, MWLS18, NPK+07, PI09,PAAG07, RdlCGW09, RWH+10, RMS15,SCSS05, SSP+05, SIM12, SDCW11,SKD+07, SGK12, TZH07, TK05, TWZW16,TOYHZ19, UC10, UKV18, WZA07,

22

WLL+09, WRH+09, WP08, XHQ+18,XLL+20, XAW07, XOYHZ18, YWW20,YLXJ04, YNBM05, YLY+12, YP13,YCCM12, YOKI09, ZZKW18, ZMT13,ZHSS07, ZWSX12, ZXLZ18a, ZXLZ18b,ZXZ20, ZWY+10, dCAR11, vBdRD+11,BMM14, FN14, JR14, KSM14, LXZ+15,PJN+14, RHK14, YCY+14]. Expressions[ARM+19, BRF17, SSK+20, WCX07,WLHY19]. Expressivity [FMRS18].Extend [CLH+15]. Extended[KFHK14, dSRCT+11, WLL+09].Extended-Sequence [dSRCT+11].Extending [ATA+17, ARS17, FM13].Extensible [ACP10]. Extension[LLH+17, LTL+19, STB+19]. Extensions[GG11]. Extensive [FFT16, MG14].Extract [FW20, DPL+14]. Extracted[ASP20, AD12, MSJP19]. Extracting[AMGC16, GBJ08, HC17, LLQ+16, LLQ20,NZR11, NAHT+20, RSG18, SYM+10,XYZ19]. Extraction[BLR15, CBZ18, DLT10, DPS+13, DPA+17,GBTW16, HLV+10, HVD18, LK11, MCC16,SYM+10, XTL12c, YSC13, YRL+20,ZLY+12, ZYN+19, TAL+15]. Extreme[LSY+20, ZHSS07].

Facilitate [GJZH17]. Factor [CRP12,LPH18, PIPC18, WPL15, ZS18, LLRZ15].Factored [ASP20, PAL+12]. Factorization[EZW+17, JHX17, JZZQ19, LW17, LWG+18,LWL+20, MHHJ20, RM18, WLG+16,WHF+20, YHCS19, YWF+20, ZWXL20].Factors [BPP+13]. FAD [YZG+19]. False[ANR11, GCB+18, HZTP12, SS04, YAB13,CWDS15]. Families[DR16, Ros13, TRBK08, WWL19]. Family[CSS11, GzS11, HZL+20, RGI13, WFY+19].Family-Based [RGI13]. Family-Wise[HZL+20]. Fast[ADPH11, BCS11, BM12, BBH12, CBFB12,CW11, CA14, DBR07, DWSB11, FVP+20,FSB+11, GZG17, GK19, GAGM11,

LHL+19a, MW16, OG11, OP11, PNA20,PVB+12, RMV12, RSJK13, Shi10, SBY12,TGLP16, WYY+13, WLCP11, WL19,WXS+19, XWC15, YXYC13, ZCG+18,ZS19, ZL15, dAc17, GJY+14, ZLLS17].Fast-Adaptive [ZCG+18]. Fast-Known[SBY12]. Faster [BAK06, CW07, CHNW20,HC16, SN12, SB09]. FastEtch [GK19].FASTQ [How13, GDM12]. FastR[ZHEB05]. Fault [BBN18]. FC [YWW+18].FEAST [HB11]. Feature[AWW18, AMHH16, AAT20, BM17, BHP19,CZ20, DPS+13, DPA+17, GZG17, GCB+18,HZZY16, HLL+18a, HBC+11, HDS+18,KCD+12, LTM+12, LHLY11, LSY+20,LJL+15, LLZ+20a, LZX+19, LZX20,LPH+13, LHH19, MCHT17, NO09, PGHT12,PBhL+11, SLX+18, SIM12, SDH20a,SGP+20, SZLL11, TZ16, TRKRC13,WZA07, WYHZ20, WCLY20, WXS+19,YSC13, YM11, YZG+19, YXS16, YH13,ZWSX12, ZLPW16, ZwGC17, ZZZW19,ZWM+20, ZWY+10, ZCWW19, BCLC15,GMCB14, HRHP16, LZGZ14, WFD15].Feature-based [ZWM+20].Feature-Integrated [LZX+19]. Featured[CLW13]. Features[AD12, BYZ+18, BS10a, CHW+18, FLW12,FW20, HC17, HLZ+17, KTLM15,KAHK+10, LLX+16, LHZ+19, LZQ+20,NBGL19, QWC+16, VF09, WB11, ZZCY10,ZKW19, ZZDY13, DPL+14, GJPSV14].Federated [SAM+19]. Feedback [BSV10].Feedbacks [LCH19]. Few[TGP+15, WCX07]. FHAST [FVLN15].fibers [SXL+14]. Fibrosis [HEE+18]. Field[WWL+17]. Fields[ZHE19, DGRC15, GGZZ14]. Fifth[MVVR20]. Filaments [CMC+12, BLR15].Files [GDM12]. Filling[JZSZ12, LJZZ13, LHH19, LWS+20, ST19].Filter[FLAM15, HKT+18, JSS+18, LTM+12,LH10, LHQ+18, MNND13, HPH+15].

23

Filtering [KAP+12, MJPP20, SP11,WLL+09, ZLH+20, pD20, HPH+15, SB16].Filters[BHHMCL16, SBY12, WZJH12, XLZ+15].Filtration [KNR05, TC16, LMZ14]. Final[Gus09a]. Finder [CXS15]. Finding[AAP06, AKMT12, BvBF+11, BLS12,CMR19, DT11, GAVRRL15, HLH11,HKM+18, IVA11, KVX12, hLMBJ11,LHL+19b, MIC+07, NYOL15, PG06, PRU11,RHH16, RSJK13, VSKJ11, WL11, Wan12,WCMZ15, ZSC+10, SSKH15]. Findings[WWC18]. Fine [DSHM08, ZWcF17].Fine-Grained [ZWcF17]. Fine-Scale[DSHM08]. Fingerprint [KKI20].Fingerprinting [LZ18a, dAc17]. Finite[FZWS17, EES14]. Finite-Time [FZWS17].Fireworks [ZZZC17, ZLJT17]. First[Tho16]. Fish [LYW20]. Fitting[FKLS07, SHUP19, TSMMG+13, SXL+14].Five [Gus09a]. Five-Year [Gus09a]. Fixed[BS11, BS07, GB10, PK13, ABH+14, CV14].Fixed-Parameter [BS07, GB10].fixed-resolution [CV14]. flagellin[MZS+16]. Flat [ZBFK10, BLR15].Flavivirus [RAA20]. Flex [FMD18].Flexible[ARP+16, BWC17, FSB+11, FMD18,JGBR15, JZZQ19, LSB+11, MTNH17,OLS+13, PFJ+19, Shi10, YDM+08, HM15].Flip [CEFBS06]. Flow [FJJ11, MT12b,MT12a, PN17, RZMT15, SK19, YXYC13,ZMT13, ZMST18, ZWL+12, Qiu14, ZMT14].Flower [AKS20]. Flower-Shaped [AKS20].Fluctuations [JLW17]. Flux[MGS17, UAH16, YWK+07, DB14]. Fluxes[vBdRD+11]. FM [CMSE+15]. FM-Index[CMSE+15]. fmpRPMF [LZ18a]. fMRI[RKZ16]. FNphasing [YXYC13]. Focal[SSD+16]. Focus [WH11]. FocusALL[SSD+16]. Focusing[BTYC13, SW17, JR14]. Fold[LCGW19, Xu05, DPL+14]. Folding[JBP08, LZZ+16, KGK14, SHS15]. Foraging

[NLW+18]. Force [DZ11, LLA19]. Forest[CSK+11, ISK18, MGXS15, ZLZ+19,YLH+15]. Forests [Mos07, PGHT12]. Form[LHH19, MS10]. Formal [TWZW16, KG15].Formalism [FM13, VBG+18]. Format[BBH12, PR18, YWW+18]. formation[BM15]. Forming [AAG+18]. Formula[CP13]. Formulas [ZGC+05]. Formulation[CLH13, MKS+17]. Formulations [MS11].Foulds [CLRV09a, CBFB12]. Fourier[ZLLS17, BCS11, Mat09, MEOL14]. FPGA[CWLZ14, FVLN15, GDWK+15, HG16,MPP+20, PGF18]. FPGA-Based[FVLN15, CWLZ14]. FPGAs [AKLJ17].Fractal [BMH+16, HLDZ17, YTLL15].Fragment [MW20, ZGC+05].Fragmentation [CLZ+18]. Fragments[JL10]. Frame [RLRH18]. Framework[ANR11, BHHMCL16, BSLR05, CMS12,gCLL+10, CBZ18, CHC+05, DHC12, ED15,GLL+18, GLG10, HXXJ18, HYZ16, KP12,LHLY11, LW17, LB19, LCSW18, MSZ19a,MTNH17, PCY+19, PZS+20, QL09,RFFB+20, RCBB19, SC11, TMLI19,WHXS17, XLW20, YLY+12, YCY+13,YRL+20, ZD12, ZW19, ZK16, ZFZ+20,ZLJT17, BDBH15, DC15, Gu16, KD16,LAI+14, VPB15, WLC+15, YCY+15].Frechet [WZ13b]. Free[ALR+13, CLZ+18, HF12, NA11, XSS17,YWW20, YH13, CV14, RTWR15].Frequencies [GKPS11, DI15]. Frequency[CZ20, JRSS18, LCGW19, CL14, MEOL14].Frequent [MB16, SKDA19]. Frequented[CRK+19]. FRESCO [WL13a]. Friendly[SJNS19]. Frog [HDS+18]. Frontier[PAL+12]. Fronts [RM13]. Fuel [TAI+19].Full [DLT10, HLV+10, IGA18, KAHK+10,LS10, ZOZ10]. Full-Text[DLT10, HLV+10, KAHK+10, LS10]. Fully[GZS12]. Function[BS10a, CC11, FB19, FWA10, mHB13,JLwC11, JM12, KAL+17, KG12, LBM+18,LLZ+13, LHDS18, RFFB+20, SZCX19,

24

Val11, WYHD17, YRD+13, YFWZ16,YWF+20, ZD12, TYA15, WHZ14, XG14,YRD+14a, YRD+14b, YRD+15].Functional[CNM11, CHL+12, CM16, DSZ+06, GLW12,GPC+20, JLYZ16, Kar12a, KNS+05, KL11a,KK12, LFK16, LLH+07, LHHL19, MS17,MFS+15, MFF+18, MBB+17, SKDA19,Tah18, WMK16, WLCP11, WWL19,WLHY19, WWBZ19, YNN+18, ZD12,ZZN15, ZS19, DC15, JC15, LLL16a].functionality [WL14]. Functionally[MP13, PB19, SFH+14]. Functions[AM12, DM09, MSKC19, MPM11, PLCW17,RMV12, Tah18, WP08, YSGZ20, ZZF+19,AM15]. Fusarium [KZW+18]. Fusing[NLGG12]. Fusion[CMMZ20, JXN+16, KZ10, LLZ+20a,QWC+16, WWT+20, YM11, ZHJ17]. Fuzzy[AGAS18, AFAAW+11, BMZM15, JXN+16,LHKL17, MP13, NPD+17, NNM+12a,PKM06, SY09, SKD+07, SBM15, TNQ08,YCCY20, YCY+13, GRDV14, HC14a,YCY+15]. Fuzzy-Adaptive-Subspace-Iteration-Based[SY09].

G [LBQ+13, WCLY20]. G-DipC [WCLY20].GA [MWSM12]. Gabor [MCCZC08].Gabor-Wavelet [MCCZC08]. Gain [AC12].Galled [CLRV11, Son06]. Galled-Tree[Son06]. Game [LQV+13, MEOL14].Game-Theory [LQV+13]. GaMRed[MJPP20]. GaMRed-Adaptive [MJPP20].Gap [LNR+09, LWS+20]. Gapped[CWC04, CZ20, WS08]. GapReduce[LWS+20]. Gaps [COW20, GGP08, ST19].Gastric [MBP+19]. Gate [Kar12b, LJ20].Gated [SDH20b]. Gating [JLW17, Qiu14].Gaussian [BEQD19, KDS+20, NFM+12,YBGB10, ZC11]. GBM [PL17].GBM-Related [PL17]. GC[RKDR10, TSM14, WLL+20]. GC-content[TSM14]. GC-contents [WLL+20]. GECC

[RHK14]. gEFM [UAH16]. Gelsius[AAF+13]. Gender [YCZ+18]. Gene[AJD+12, ASP20, AMGC16, AKNB07,ARK20, AOSN+18, ADR18, AWW18,AKV16, AMHH16, ABS17, ACWW05,ACWW07, APPG18, BGHC20, BM17, BE08,BEW09, BS11, BGS+12, BDP11, BHMA06,BCL+13a, BA18, Bon07, BLR08, CCCY20,CDB+16, CDW12, CHWY19, CMMZ20,Che10, CM16, CPM18, CWZ08, DLT10,DGH+06, DRS12, DZH16, DCHW17,DKDD10, DHC12, DBK18, DSCM20, EAS13,ED15, FWXZ19, FKB19, FLAM15, GZG17,GMSD11, GDM18, GE15, GE18, GSC17,GHL05, HL16, HYW+17, HBH12, HXXJ18,HHYH07, HMW+12, HWK14, HLY+16,HC16, HC07, HF12, HTLL12, INT11,IGM+07, IQA18, IBN19, IL18, JCF13,JZS+18, KBNHD18, KBND19, KSN+12,KN05, KP12, KG12, KCCC15, KCP18,KKK19, KB17, KB19, KK12, LCEMO18,LEAK11, LTM+12, LTM+13, LBM+18,LRM08, LH10, LJK+12, LLHF15, LCZN16,LW17, LDM18, LB19, LZH18, LJL+14].Gene [LNC+05, LHDS18, LW19b, LYY+19,LLL15, LLA19, LLT+19, LHY+11, LCC+11,LTRW19, MNR09, MTSCO10, MSS19a,MSJP19, MB20, MPP+20, MT11, MWZ+20,MZL15, MPM11, MDD18, MBF+11, MSG18,MG19, NRV09, NPK+07, NI07, NSNN12,PGHT12, PI09, PBV+20, PCDP18, PG06,PAAG07, PKM06, PKA20, QD12, RM13,RC11, RdlCGW09, RMV12, RRTB12,RWH+10, RMS15, SSS+11, SSK+20,SCSS05, SMRP15, SSP+05, STO06, SIM12,SDCW11, SV16, STB+19, SPA17, SKD+07,SW09, SGK12, TIA+11, TAAP11, TZH07,TGGF10, THL11, TK05, TWZW16,TOYHZ19, UC10, UKV18, Val11, VRK12,VRJ+10, VF09, WZA07, WLL+09, WL11,WKLL12, WLG+16, WLCX18, WWL19,WLHY19, WRH+09, WP08, WWC18,XHQ+18, XAW07, XOYHZ18, YLC20,YWW20, YLXJ04, YNBM05, YHB12,

25

YLY+12, YWF+20, YCCM12, YGY+19,YNN+18, YOKI09, ZZKW18, ZLZ06,ZHSS07, Zha11, ZWSX12, ZZN15, ZLH+17].Gene [ZXLZ18a, ZXLZ18b, ZZS18,ZWHC19, ZXZ20, ZACS09, ZWY+10,dCAR11, vBdRD+11, BM14, CZWT15,CM15, DYD15, DR14, FN14, HZZT14, JR14,JC15, LXZ+15, LLH+14, MM14a, MM14b,PJN+14, RHK14, RHH16, WLY14,WDX+15, XLC+15, YCY+14, ZZ14].Gene-Duplication [BE08, BEW09, BS11].gene-environment [LLH+14].Gene-Expression [CCCY20, UKV18].Gene-Gene [ASP20]. Gene-Module[MB20]. Gene-Species [MSG18].Gene-Team [WKLL12]. Gene-to-Class[HYW+17]. Gene-to-Gene[GHL05, LNC+05]. Gene/Protein [ED15].Genecast [GTTR+17]. GeneChip[MSH+11]. GeneChips [LUdSCH10].GeneNetFinder2 [HL16]. GeneOnEarth[TSMMG+13]. General[SC11, WKLL12, Wan12, YP13].generalizable [TAL+15]. Generalizations[CLRV09a]. Generalized[AAT20, BBN19, BSLR05, HHSC13, JMA17,ZACS09, ZAZ11, FN14]. Generate[YLCC13]. Generated [ZZS18].Generating [PCGS05]. Generation[BBN18, FS13b, KCD+12, AKD17, LHLY11,PNP+18, PSC20, WPL15, YSC13,YWW+18, CWLZ14, KD16]. Generative[ZDL12, ZZDW13]. Generator [HLG10].Generators [ZWZS16]. Generic [BVN+11].Genes [AAF+13, AAP06, BGHC20, BRF17,CZF+05, CHN+18, DZH16, DG19, EAS12,EFLA08, FFT16, HAH13, JZZQ19, KCP18,KM20, LFK16, LTM+13, LLX+11, LGW20,LZX+19, LXG+16, LWG+18, MP13, MS17,MMH15, PS19, PWT10, PL17, PZH20,RYK+19, SSS+11, SBW15, SRM18, SPW20,SDTK19, TZY11, WS12, WCX07, WGP11,XPH12, ZLLZ17, ZLH+20, ZOZ10, CBN15,DI15, KSM14, KKC+14, LWM14, MFS+15,

SKK14, Tah14, WFD15]. GENESHIFT[LTM+13]. Genetic [AGAS18, BMK11,BvdGK+11, CSW11, CL15, CAN+08,DSHM08, FZWS17, GPZ20, GZFT15,Gos11, GJZH17, HYR+19, HCLS11, JSA08,JSS+18, JZS+18, KSMT19, KB20, KN05,LL11, LLZC12, LWZ12, MTNH17, MIC+07,MDH11, MWSM12, MVW+13, NJMF19,OMAdG+12, PB12a, PI09, RKDR11, Sen19,Tho16, TSMMG+13, TED+12, TBRS13,VMZM17, VKS17, VBG+18, WFY+19,WAG19, WCL11, XWF07, YCYC12,YLCC13, YAB13, ZLH12, ZWZ16, ZSD08,dJP08, ADTAQ16, CL14, HRHP16, PV16,RHH16, TYL+16, WLY15, ZWC15].Genetics [SLH06b]. Genome[AP07, AJM18, ANT19, BGS+12, BMM06,CZF+05, CHN+18, DGV+17, DWSB11,FLW12, FM13, FMA+20, FS13b, GZFT15,GSK13, GJZH17, GZC+17, HKS11,HWS+18, HBM19, KMSY20, Kim18, LN17,LW19a, LZW20, MSS+13a, MPA15, NPK+07,PIPC18, PS11, RZMC17, SKS+19, STHA15,SSS13b, TGLP16, TIA+11, TGP+15, Val11,VTGC16, WYY+13, WHZ14, XHY+18,ZZCY10, ZZS18, ZLZ20, ZAZ11, ESW14,LHS16, SVM14, TYL+16, WLC+15].Genome-Guided [FS13b, TGP+15].Genome-Scale[DWSB11, GJZH17, MPA15].Genome-Wide[BGS+12, DGV+17, FLW12, GZC+17,KMSY20, LW19a, LZW20, NPK+07, PIPC18,SKS+19, TIA+11, Val11, VTGC16, WYY+13,ZZCY10, ZAZ11, WHZ14, TYL+16].Genomes[BCF+07, GK19, HCMB18, LHL+19b,MS10, NLHL17, QLLX10, QTZ15, XZG15,YBGB10, ZHEB05, BS15, CA14, RB14].GenomeTools [GSK13]. Genomic[BBH+18, BKP+19, BKLS18, CKM+17,CHL+12, CHW+18, CBZ18, CRK+19,DHCW18, DMJ+18, DBTB09, FM12,FLM+16, GRS+13, HYL+20, HYC12,

26

HCQ14, KPK+17, MWL+12, MCC16,OLS+13, PHX+08, PG18, PWT10, RCP+18,RTPM+19, RH05, SHUP19, WMWA12,ZZZW19, dSMDB17, GMCB14, SSKH15,XLWL15, ZMP+14]. genomic-range[SSKH15]. Genomics [KNS+05, PR18,RCM+19, WHF+20, YNN+18]. GenoPri’16[AJM18]. GenoPri’17 [ANT19]. Genotype[CCE19, DLM12, GMP08, PVB+12,YLCC13, ZPW+19]. Genotype-Phenotype[ZPW+19]. Genotypes [HYL+20].Genotypic [HXXJ18]. Genotyping[Che16, QBPEL12, YCYC12]. GENSIPS[HCQ14]. Geodesic [BPV+11, OP11].geodesics [Nye14]. Geometric[DM09, FSDR16, BCLC15]. Geometrically[KL19]. Geometry [LLES18]. GeRNAMo[MIC+07]. GEVD [TDD14]. Gibbs [AM19].Gibbs/MCMC [AM19]. Gillespie [BU17].Give [BCVS19]. Given [WMS09]. GIW[ESW14, Kim18, STHA15, ZLZ20].GIW/InCoB [Kim18]. GIW/ISCB[STHA15]. GIW/ISCB-Asia [STHA15].GLAlign [MGC19]. GLBIO [MJ18].Gleason [XPH20]. Glioblastoma[CHW+18, ZLPW16]. Global [ARP+16,DBN18, ECK16, FZM15, GPMH16, HSS18,HOS+12a, HOS+12b, HGM18, Tsa12,WQY18, ZKW19, ZYF+18, XXM+16].Globally [ZWZ16]. Globe [TSMMG+13].GLProbs [YlCW+15]. Glucose [RTA+16].Glucose-Binding [RTA+16]. Glutamate[KAL+17]. Glycan[BKR11, SLL+19, DST+15b]. Glycans[KSS15]. Glycogenolysis [PPM+13].Glycolysis [PPM+13]. GMM [ZYW17].GO [CXS15, LBM+18, SSP+05, SLS+14,YKWK18, YFWZ18, ZXZ20]. GP[VBG+18]. GPCR [WWL+17]. GPCRs[CSS11]. GPD [SHJL10]. GPU[BBH12, COW20, CMSE+15, CZX19,GDWK+15, LFF18, LHG+16, NSZK15,SYL19, WWC18, ZWcF17].GPU-Accelerated [CZX19, GDWK+15].

GPU-Based [LFF18, NSZK15].GPU-Oriented [LHG+16]. GPUDePiCt[CFIS+15]. GPUs [TED+12]. Gradient[HOS+12a, HOS+12b, HC07, IGM+07,LZX20]. Gradient-Based[HOS+12a, HOS+12b, HC07, IGM+07].Grain [JLYZ16, LQV+13]. Grained[CGLF12, ZWcF17]. Graining [MDPR18].Gram [CZX19]. grammars [SHS15].Grammatical [RAA10]. grams [LZGZ14].Granger [HLL18b]. Graph[AFJ12, BB04, BRS18, BDP11, BMHS13,BCL13b, CHK17, DBK18, EZW+17,GLW12, Gru11, GG11, HC18, JLH16,KPK+17, LHQ+18, LNW20, MKH11,MSS+19b, NWW19, PNA20, RFB20, Roc11,RSJK13, SHJL10, THH+19, UAH16,VKM07, WLG+16, WFY+19, WHKK07,XWC15, YSGZ20, YM20, YFWZ18,ZWXL20, ZACS09, ZZDY13, DKS+15,JHXP15, KFHK14, ARZ+14, ZWL+14b].graph-based [DKS+15, KFHK14].Graph-Theoretical [BCL13b, CHK17].Graphical [HLDZ17, SMPS20, TRBK08,TRBK09, WQY18]. Graphics[Dem12, LSMW11, CFIS+15, ZLS+15].Graphlets [ARS17]. Graphs [AP07,BSV10, CRK+19, DH04, LFS06, NLHL17,NSNA19, PGF18, SVM14, ZHL+14].GRASP [dDD18]. GRASP-Based[dDD18]. Gray [ALR+13]. Gray-Scale[ALR+13]. Great [MJ18]. Green[BdOS+18]. GRegNetSim [GPZ20]. Grid[LHCL20]. Gridding [RV06, SYZ+13].GRO [AALD17]. GRO-Seq [AALD17].GROMACS [PCY+19]. Group[APRS11, GCB+18, IMA13, LDM18,WHF+20, ZRK19]. Group-Based[APRS11]. Group-Wise [GCB+18].Grouped [LDM18]. Grouping [ACWW05,ACWW07, GSX+18, MP13, TDY+18].Groups [LLW10]. Growing[BdOS+18, HAH13, SCM19]. Growth[DST15a, KHP12, TRKRC13]. GSEH

27

[KCP18]. GSGS [AJD+12]. Guaranteed[HYZ16]. Guarantees [BM13]. Guest[BLP18, BPW17, CEG14, Che12, CN12,Che13, ESW14, FJJ18, GJH19, GM16,HMZ17, HC15, HBG16, HBG17, HBG18,HBG19, HBG20, KS13, KJ04, KJ05, LW15,MNA14, Mur18, PR14, SPK19, STHA15,TH18, WYWX16, WLWN17, WLC18,WH11, XHS15, YSC19, YGFC20, YS17,ZC15, ZLZ20, ZC14, dSK13, MKARB16,AS15, BPRZ11, Cas06, Cas07, Cat17, CZ12,FS12, FS13a, GH08b, LNY05b, LNY05a,MPZ07, MPZ08, MPSZ09, MWZ13,MSZ19b, MNPZ10, RZF07]. Guidance[GSX+18, MSS13b]. Guided[FS13b, HYR+19, MPS18, SLX+18,TGP+15, ZZY+17]. Guidelines [HLY+16].Guiding [HZZY16]. gwAs [SAM+19,BDD18, GDWK+15, MWSM12, ZPW+19].

H1N1 [BPJ12]. H3K4me2 [MMH15].Hadamard [HS08]. Halving [AP07].Hamiltonian [GFS13]. Hamming[TSM14]. Handcrafted[NBGL19, SDN+11]. Handling [BM20].Handover [LHH19]. HapBoost [WYY+13].Haplotype [BH06, FHH+11, GKPS11,ICL11, PBJ12, TGLP16, TBGL10,WYY+13, YXYC13, PRZ+14, PV16].Haplotyping [BBSP08, BVD+10, GGP08,LRR08, SHI06, XWC15, vIKKS08, KO15].Hard [LGZ+17, Roc06]. Hardness[BO12, JNST09, RCM+19, LV14].Hardware [DSVMM18, FVLN15, AKD17,LSMW11, ZLS+15]. Harris [SSD+16]. Hash[ZLY+12, HC14a]. HBase [LLZ+20b]. HCD[SLL+19]. HDS [CMS12]. Head [NPD+17].Health [LKY+11, SPK19, SGR+17].Healthcare [SJZ19, SGR+17, WLWN17].Heart [LKY+11, BCMW15]. Heat [CRP12].Heavy [NVSH18]. Heavy-Tailed[NVSH18]. Hedou12 [JWZ+20]. Helical[ZHZ+20]. Helix [MRB12]. Heme[ZCG+18]. HEMEsPred [ZCG+18].

Hepatitis [HEE+18, LLW+11].Hepatocellular [YSW+17].Hepatotoxicity [SWX+19]. Herbal[SYKS15]. herpesvirus [RB14].Heterocomplexes [CWL12].Heterogeneity[AGMP09, KDS+20, KCP18].Heterogeneous[CKM+17, HHCY20, Jam17, JGBR15,LZHZ17, LWL+19, LBL+10, MHHJ20,Mat15, NTR16, PL17, WLC+15, XLW20,XW16, ZZCD19, ZYF+18, XLWL15].Heterozygosity [CLH13]. HeteSim[ZLLZ17]. HetRCNA [XLW20]. Heuristic[CH11, GGP08, HT09, HLH11, JNST09,PWT10, SK19, TBGL10, TDA+09,YXYC13, dDD18, GM14, IM14]. Heuristics[AOSN+18, BE08, BODD20, HOS+12a,HOS+12b, NI07]. Hexagon [LBL12b]. Hi[CSZ+19, MP19]. Hi-C [CSZ+19, MP19].Hidden [Gou06, cLWA07, LGN+19,PAS+11, YHCS19, SPWF14]. Hierarchical[FFT16, GLG10, Kar12a, Mah10, PJN+14,TNQ08, Val11, WZA07, WLCP11, YP13,ZLW+11, ZBFK10, LLC+15, WFD15]. High[AS05, BGS+12, BWRF12, CNM11, Che10,DPW12, GGP08, HF07, How13, HDS+18,Kur13, LDS+07, LHL+19a, LN13, LCZN16,LW18, LJL+15, LHG+16, MJPP20, Maz12,MC07, MDM13, PZS+20, SYKM17,WYHZ20, YP13, ZZH18a, ZZZW19, ZZH19,ZKL18, dSMDB17, DWZ+15, GCC+14,LHWL15, Qiu14, WLG+14, XZY+14, YN14].High-Dimensional[Che10, HDS+18, LN13, Qiu14, YN14].High-Order [LCZN16, ZZH19, DWZ+15].High-Performance [BGS+12].high-quality [WLG+14]. High-Resolution[DPW12]. High-Scalable [PZS+20].High-Throughput[HF07, How13, Kur13, LW18, LJL+15,MJPP20, MDM13, YP13, ZZH18a, GCC+14].Higher [MGKG17, ZLLS17].Higher-Order [MGKG17]. Highly

28

[CCE19, GMP08, SSS+11, WL13a, HKLN14,SQZA14]. Hilbert [GZG17, LKY+11]. Hill[RV06, KG12]. Hill-Climbing [RV06].Hinge [FMD18, Shi10]. Hippocampal[SSK+20]. Histone [CMMZ20].Histopathological [FZM20]. Histories[DR16, Ros13]. History [BB04, CW09b,LCWZ13, MKS+17, TBRS11]. HIV[AFAAW+11, DCM20, HHL+20, KS18,LSMF08, MMB+13, NTCO07, PRZ+14,RB16, RM18, SYKS15, Vis18]. HIV-1[AFAAW+11, DCM20, HHL+20, RB16,SYKS15, Vis18, LSMF08]. HIV-1-Human[MMB+13]. HLA [IDD13]. HLA-DP1[IDD13]. HMM [SB09]. HMMCAS[CYJ+19]. hMuLab [WGX+17]. Holmes[WYH17]. homeostasis [MFS+15]. Homo[LUdSCH10]. Homogeneous[MT12a, ZMT13, ZMT14]. Homologous[QTZ15]. Homologs [SZZ+19].Homologues [LDS+07]. Homology[Bro05, LL19, LCGW19, LGB15, LCB17,MPM11, Zha07, CWDS15, DGRC15].Homomorphic [RCP+18].Homomorphisms [Wil12]. Honeycomb[LHQ+18]. Horizontal [MSG18]. Hospital[WCC+18]. Host [STD20, USMS19].Host-Pathogen [STD20]. Host-Symbiont[USMS19]. Hot[LZ18b, LZX20, SP11, ZLZ+19]. Hotspots[RYK+19]. Hough [TZY11]. Housekeeping[SBW15]. Hub [DZH16, LZX20]. Human[BMT17, BKKG19, BWS05, CHN+18, CD08,DKDD10, FLW12, GAR+09, GBTW16,HCN+19, HLG10, LZQ+20, LWL+20,MMB+13, RLRH18, RTA+16, Sen19,SKD+07, SWL19, TBRS11, XPH12, YG19,YCZ+18, ZZCY10, Zha18, ZRK19,GJPSV14, GBTL14, LP15, WLG+14].Human-Readable [HLG10]. Hybrid[BU17, BHHMCL16, CNM11, CKWY12,FPC20, GRDV14, JHW+19, KHP12, KN05,LLX+16, PAL+12, SDH20a, TWW+20,WGX+17, YCY+13, YFWZ18, ZWL+12,

SAM+19, BM14, GAVRRL15, SDAA+14,XXM+16]. Hybridization[BS07, CH11, HKS11, LHCL20, LS09, PK13,Pre04, MW16]. Hydrophobic [CDKT09].Hyper [PTH+18]. Hyper/Hypocalcemia[PTH+18]. Hyperflows [AFMS19].Hypergeometric [KPW13]. Hypergraph[LCW+18]. Hypergraphs[RPB+13, RAM17]. Hyperplasia [ZLXL19].Hypocalcemia [PTH+18]. Hypothesis[BZ07].

I/O [HPH+15]. i2b2 [RCP+18]. IAS[YKWK18]. ICD [HXXJ18, LFZ+19].ICD-9 [LFZ+19]. ICGA [SSS+11].ICGA-PSO-ELM [SSS+11]. ICIC[HBG16, HBG20, HBG17, HBG18, HBG19].ID [Jam15]. Identifiability[AR09, APRS11, Wig15]. Identification[ALQ17, AGGM11, BBN19, BGHC20,CWZW15, CFOS06, CYJ+19, CDW12,CMQ+16, DMD13, DABV17, EAS12, FJJ11,GGJ+06, HYY11, HC18, HC19, HZL+20,HHYH07, HC13, JXN+16, JRN+18,KCCC15, KSK+18, LLNW17, LZ18a,LHHL19, LMZ+20, LLT10, LMZL17,MRB12, MTSCO10, MS17, MSB19,MCCZC08, NWW19, Ozy12, PB19, PS19,PM20, PWZW15, RBB+19, RTA+16,RYK+19, SSS20b, SSP+17, SFH+14, SBY12,SLL+19, TGK13, THL11, WGP11,WLWP12, WCMB19, WDS+12, XLWL15,YMW+12, YFCM17, YCZ+18, ZOZ10,ZZDY13, GM14, WLG+14]. Identify[HHSC13, KM20, LYW20, LXG+16, LHC18,MMH15, NHH+17, TWZW16, XLW20,KKC+14, SQZA14]. Identifying[BRS18, CCCY20, CSK+11, CGZ15,CZW+18, DCHW17, DG19, DKS+15,GGZZ14, HYR+19, HXXJ18, IMA13,JWZ+20, KSN+12, LW18, LZL+20, LZX+19,LLTC19, LP15, LWG+18, MSQ18, MM14b,NLGG12, PL17, PN17, QLZ16, RKZ16,SAE+20, SDN+11, SBW15, SPW20,

29

UWLH15, XLL+20, XOYHZ18, YAB13,YNWC07, ZW19, ZZDW13, ZDYH17,BMM14, LLW+15, PWC+15]. Identity[NGY+16]. IEEE[HCQ14, Ano12b, Ano13e, Gus04b, Tit16].IEEE/ACM [Ano12b, Gus04b, Tit16]. IEF[KBBD+17]. IEF-LC [KBBD+17].IEF-LC/MS [KBBD+17]. IFN [ZZ13]. II[CLRV09b, EMDH11, FLW+14, KJ05,Zha11]. II.5 [Ano09c, gCLL+10, CLM10,LS10, LMK+10, RSK+10]. IL- [LCH19].ILP [BCVS19, HWS+18, KH14, WHBM15].ILP-Based [BCVS19]. ILP/SMT [KH14].ILP/SMT-based [KH14]. Image[LYK07, MCD+11, MCRC17, NU06, XZG15,YCZ+18]. Image-Based [MCD+11].Images [ALR+13, BRZ+17, BdOS+18,DDS+17, FZM20, RV06, SYZ+13, SLX+18,SSD+16, SSF18, UBP+19, XPH20, BLR15].Imaging [BMT17, BWRF12, DHCW18,IGA18, WHF+20, ZHG20, TWZ+14].Imbalance [SYKM17]. Imbalanced[BDD18, LYK07, OLZ11, YN14]. Imbedded[ZC11]. IMM [LHQ+18]. Immune [SJS19].Immunoassay [ZWL+12]. Immunological[IGA18]. Impact [KAL+17, LNR+09,SWH+12, WLMW+11, MFS+15].Impairment [ZWS+18]. Implement[Gon13]. Implementation[BKLS18, HG16, LZ18a, CFIS+15, ZLS+15].Implications [QV17]. Importance[FWA10, MMS10]. Improve [Bon07,MFF+18, PSN+15, XLL+18, ZLPW16].Improved [BN06, CWC04, CW09b, Che16,GH08a, GSC+18, HL16, HPL+13, HDS+18,HLH11, ISK18, LWL+18, LZ18b, LJZZ13,LHKL17, Pol13, RAA10, SFMS18, SLL+19,Tan14, TDY+18, WL11, WCLY20, WLG+14,YLCC13, ZCR+17, SB16, YN14, ZWC15].Improvement [TW10]. Improvements[GG11]. Improves [HRdR09, KL11a, DI15].Improving [AV17, ALWG18, CWDS15,CWL12, HYC12, Jam15, JBP08, JXN+16,LLL+20, LWT+18, LWM14, LHY+11,

MG14, Tsa12, VKS17, WSX11, YMW+12,YFCM17, ZWDR20, TYA15]. Imputation[CCE19, PVB+12, WCA+19, YPS11].Imputing [ZZ20]. In-Frame [RLRH18].In-silico [SYKS15]. Inapproximability[BJ13]. Inception [FSX19]. Include[FM13]. Including [WHS04]. InCoB[Kim18]. Incompatible [TM11, Wil09].Incomplete [ED15, KBND19, MR10,PVB+12, SM08, ZAZ11, YRD+14b, ZZ14].Inconsistent [JSA08]. Incorporating[BRZ+17, HLY+16, HHL+20, KB20, WP08,YPS11, ZD12, WLG+14]. Incorporation[ED14, GSC+18]. Increase [TC13].Increment [FWY19]. Indel[dSMDB17, LKW+19]. indels [BS15].Independence [GZG17]. Independent[DSHM08, FLAM15, SREK19, SDCW11,PSK+15]. Index[Ano04a, Ano05a, Ano06b, Ano08a, Ano09b,Ano10b, BG13, CZX19, EMK18, Tit13,Tit16, XTL12a, FN14, CMSE+15].Index-Based [EMK18]. Indexed [dAc17].Indexing [PFJ+19, SVM14]. Indicator[CPM18]. Indices [WLA+13]. Indirect[ASJ+07]. Indispensable [Zha18].Individual [GGP08, HYL+20, MZ17, VF09,XWC15, ZHZ+20, BLR15]. Individuals[BZ08, MYCW12]. Induced[SSDN12, SWX+19, TP18, WQY18,GCC+14, SSML15, WLY15]. inducing[MMSH14]. Inductive [BKKG19].Inequalities [Mat09]. inequality [ZWC15].Infer[CLH+15, QTZ15, SV16, VBB18, ZS18].Inference [ARK20, ADR18, ABS17, BDS12,BGHM09, BH06, CMMZ20, CAN+08,DMJ+18, EAS13, FHH+11, GZFT15,GZC+17, GHL05, HL16, HYL+20, HLY+16,ICL11, LCWZ13, LHHL19, LWZ12,MVW+13, PSS09, PCDP18, PBJ12, QV17,RC11, Rho20, SN12, SLB+08, TMLI19,TBGL10, WKE11, WPL15, Wu11, XWF07,YHY13, YFCM17, YGY+19, ZZKW18,

30

Zha11, ZPW+19, ZZCD19, ZWDR20,ZWD+17, vIJJ+20, DNR15, PRZ+14, ZZ14].Inferential [SVZ09]. Inferring[FWXZ19, FSD+11, KCZ+15, LBM+18,LZHZ17, LLL15, MSG18, NI07, NSNN12,PKRD12, PNP+18, PAAG07, SSS13b, Tah18,TDZ+19, TOYHZ19, WLCX18, WGK16,XW16, ZHZ+20, ZSD08, CZWT15, LAI+14].Infinite [BCVS19, Wu10, ZMT13].Infinite-Dimensional [ZMT13].Inflammasome [LCH19]. Inflammatory[WCMB19]. Influence[FMRS18, RSCX18, TAAP11]. Influential[ATA+17, BTYC13]. Influenza[BPJ12, ZYF+18]. Informatics [Kim18,MZ17, STHA15, ZLZ20, ESW14, SPK19].Information [AC12, AL12, BLR08,CKWY12, CAN+08, DGH+06, DMJ+18,DBK18, DSCM20, FPC20, GKPS11, GBS11,HYW+17, HXXJ18, HC13, HHL+20,HLG10, LLH+17, LDM18, LSY+20,LXG+16, MGL+12, MPA15, NLGG12,PVB+12, RSG18, SMRP15, SWH+12, TZ16,VRK12, WL07, WDL+17, XTL12c, XLL+18,XLL19, YHYY12, YCCY20, YHZ+19, ZM12,ZXLZ18a, ZXLZ18b, ZXZ20, ZSD08,ZGB+12, BDBH15, CA14, GZGX14,HRHP16, MM14a, SLS+14, TAL+15,YLH+15]. Information-Theoretic[GBS11, ZSD08]. Informative[LLC+13, LLZC12, LLRZ15, LLC+15].infrastructures [MKARB16]. Inheritance[HWPE17]. Inhibition [SYKS15].Inhibitors[AFAAW+11, RAA20, SB12, KPB14].Initializing [Mai09]. Initiation [MVW+13].Initio [HZZY16, MSS13b, SEC15]. iNJclust[LAI+14]. Injection [HC07]. Inner[LTM+13]. inorganic [DKS+15]. Insert[LLH+17]. insertion [DI15]. Insertions[QLLX10, HZZT14]. Inspection [MBP+19].Inspired [BB11, GLL+18, LZW20, SSS20a,SMK+12, TNQ08, TS17, ZD17, PV16].Instability [WQY18]. Instance

[EMDH11, LJK+12, RLR20, WHZ14].Instances [Lab06]. Instantaneous[ZYW17]. Instruction [XLZ+15]. Integer[AFMS19, BH06, CLH13, CSSS16, SLB+08,WCL11]. integral [ZWC15]. Integrated[DS19, HXXJ18, Jam13, LB19, LZX+19,LBL+10, MZ17, PB19, SDCW11, TV11,Tsa12, VF09, ZW19, BHW+14, DC15,MZL15, OFC+14, PSK+15]. Integrating[DHCW18, HZW+17, HLL+18a, HLG10,LTM+13, LLQ+16, LJ20, LHL+19b,LQY+20, LTRW19, MHHJ20, MB20, PL17,RM18, RWH+10, SWL19, XOYHZ18,YHZ+19, ZZCD19, ZXZ20, ZY20].Integration [CKWY12, GJZH17, Kar12b,LBM+18, MSJP19, MCC16, STB+20,TWZ+14, WHF+20, WOYL17, YFWZ16,YGY+19, ZZN15, ZWD+17, Jam15].Integrative[GXSZ17, KPK+17, LLCZ15, MSZ19a,UKV18, GMCB14, LYH+16, TYL+16].Integrity [NFM+12]. Intel [MPA15].Intelligence [Ano05b, KP12, RZF07].Intelligent [HHYH07, HBG16, HBG17,HBG18, HBG19, HBG20, YMT+14, SHK14].Intensities [MSH+11]. Intensity[ALR+13, YHYY12]. Intensity-Based[ALR+13]. Intentions [WAG19]. Inter[CWLS15, NAHT+20]. Inter-Sentence[NAHT+20]. Inter-Sequence [CWLS15].Interacting [LYL+17, LLW10, YZG+19].Interaction[AM19, AC12, BM17, BVN+11, BNV+13,CLM10, CLW13, DS19, DSCM20, ECK16,EMK18, EZW+17, FSDR16, FJJ11, HYL+19,JLYZ16, KAHK+10, KY19, LS10, LNC+19,LMZ+20, MSZ19a, MSJP19, MMB+13,Mne09, MDM13, NWW19, OYDZ15, PR12,QL16, QKO18, SBM15, THH+19, Tsa12,WLCP11, WFY+19, XGWW19, YKWK18,ZLY+12, ZDL12, ZLY+13, ZLH+17, ZZZC17,Zha18, ZWXL20, ZG19, ZWW17, ZZDW13,ZGDH16, ZDYH17, FHRG14, HLW15,LLH+14, PJN+14, PWC+15, XG14].

31

Interaction-Related [AC12]. Interactions[ASJ+07, ABVD12, BSV10, BNV+13,CSK+11, CZW+18, GED+17, GBB+11,HLV+10, HC17, HHCY20, HMK+07, JJH12,LW19a, LSY+20, LLZ+13, MB20, Mam05,RSG18, SYM+10, STD20, VBG+18,WYHZ20, XYZ19, YLC20, YSGZ20,YHZ+19, ZZDW13, ZDYH17, BDBH15,CXS15, HM15, JHXP15, MZS+16].Interactive [ALQ17, LTL+07, MBB+17].Interactome [ZWW17, ZWD+17, WZ14].Interactor [DLT10]. Interchanges[HZL19]. Interdependent [WAG19].Interface[CWL12, Jam17, SKDA19, VSR+06, ZG19].Interfaces [LZX20, LHWL15]. Interleukin[AHT+18]. Interleukin-8 [AHT+18].Intermediate [CMC+12, LDS+07, MRB12].Internal [FSB+11]. International[AJM18, ANT19, BLP18, HCQ14, HBG16,HBG17, HBG18, HBG19, HBG20, Kim18,SPK19, STHA15, ZLZ20, ESW14]. Internet[ZYF+18]. Interpolation [HLDZ17].Interpretability [KZ10]. Interpretable[WMK16]. Interrelationships[HSlSM11, Tah18, ZD12]. Interspecies[MPM11]. Interspersed [TDA+09].Interval [HYW08, ZWC15]. Intervals[BMM06, DST07, Wan12]. Intervention[CSW11, NNM+12a, QD12]. Intra[CWLS15]. Intra-Sequence [CWLS15].Intracellular [DADF+10]. Intrastructure[AL12]. Intrinsic [AHT+18, FSDR16].intrinsically [CBN15]. Introducing[CBZ18, Sag09b]. Introduction[Ano04b, BLP18, BPW17, BPRZ11, Cas06,Cas07, Cat17, CZ12, FS12, FS13a, GH08b,Gus04b, Gus04a, Gus06a, HMZ17, LCTS08,LNY05b, LNY05a, MPZ07, MPZ08, MPSZ09,MWZ13, MSZ19b, MNPZ10, MKARB16,RZF07, Wil04a, AS15, CEG14, XHS15].Intron [SSS20b]. Intronless [CHN+18].Invariant [LSY+20]. Invariants [JS12].Invasive [WCMB19]. Inverse [IBN19].

Inversions [dDD18]. Invertibility[ZZM17]. Investigating[BLP+12, BJ10, IQA18, LRM08].Investigations [LS10]. Involving[vIJJ+20, DB14]. Ion[JLW17, KL11c, WM19a]. Ionizing[ZLL+20]. Ionotropic [KAL+17]. Ions[ZGC+05]. IPED2 [HWPE17]. iPFPi[TYA15]. IR [gCLL+10, NSC17]. IR-Aided[gCLL+10]. IR-Based [NSC17].IsAProteinDB [dAc17]. ISB [ZC15].ISB/TBC [ZC15]. ISBRA [BPW17].ISCB-Asia [STHA15]. Ischemic [MFF+18].ISEA [LLH+17]. Island [XYYZ20]. Islands[SHI06, SKD+07, vIKKS08]. Isoforms[RLRH18]. isolated [SXL+14]. Isolating[BTYC13, RKDR11]. Isolation [RKDR10].isomerization [AJYT+15, YMT+14].Isomorphism [BG17]. Isotope[MGS17, ZGC+05]. IsoTree [ZFZ+20].Issue [Ano05b, Ano09c, Ano12a, Ano13b,Ano13c, Cas06, LNY05b, LNY05a, Ano13d].itemsets [ZMC+14]. Iteration[SY09, FWY+15]. iterations [TYA15].Iterative [KBSCZ12, LLH+17, PGHT12,STB+19, LAI+14].

JigCell [VSR+06]. jobs [VPB15]. Join[BFM13]. joining [HS15, LAI+14]. Joint[BWS05, HLN20, JHX17, LYY+19, MHHJ20,SMRP15, SMPS20, WHXS17, WHF+20,ZWL+12, Kim18]. Jointly[BHMA06, LQY+20]. Journal[Gus06b, Gus07c]. Junction [SN12].junctions [LKLB14]. Just [PTH+18].Just-in-Time [PTH+18].

K* [STT+14]. Kalman[MNND13, WLL+09]. KAMI [HLLO19].KATZ [ZZF+19]. KATZLGO [ZZF+19].Kemeny [SPMB13]. Kernel[GLW12, HRdR09, IGM+07, JXN+16, OG11,QL09, SLRQ19, SHJL10, SCPS12, WB11,XZC07, ZLY+12, ZLPW16, ZC11, LLC+15].

32

Kernel-Imbedded [ZC11]. Kernel-Target[IGM+07]. Kernels [BMHS13, IGM+07,Kuk13, WYH17, YRD+15]. Key[DG19, KSK+18, YFCM17]. Kidney[DCHW17, OW20]. Kimura [HS08].Kinetic [BMZM15, WBP+12]. Kinship[DMJ+18]. Kit [OLS+13]. Kmerind[PFJ+19]. KNN [HLSR18]. Know[RRTB12]. Knowledge [ASP20, CSW11,DZ11, ED15, HLY+16, JZCZ15, KDS+20,KB20, Mam05, MCC16, NP13, TAAP11,WBE13, ZYN+19, ED14, MZL15].Knowledge-Based [DZ11, HLY+16, NP13].Knowledge-Driven [CSW11].Knowledge-Enhanced [WBE13].knowledgebase [GJK15]. Known[MYCW12, SBY12]. Kriging [WWLL16].Kriging-Based [WWLL16]. Kronecker[CP13]. KungFQ [GDM12].

L1000 [MWZ+20]. Label[JM12, LJK+12, SLX+18, WMK17, WL13b,WYHD17, ZHE19, RTWR15, WHZ14,YRD+13, WGX+17]. label-free [RTWR15].Labeled [FGKH11, KSM14]. Labeling[BMT17, MGS17, PH10a]. labelled [LV14].Labels [MRK18]. Laboratory [LPH+13].lagged [GM14]. Lagrangian[AKR12, ZWHC19]. Lakes [MJ18].Lamarckian [ORCJ13]. Landmark[FW20, MCRC17]. Landscape [RJNN18].Landscapes [SDS18]. Langevin[SCCDK09]. Language[LJ20, WCMZ15, ZDL+19]. Laplace[WDS+12]. Laplacian[BM12, JHX17, LJL+14, MHHJ20, NO09,WLZ+19, WZ13a, ZYW17, ZWHC19].Lapse [DST15a]. Large[BBH+18, DADF+10, FWXZ19, GKPS11,GSX+18, GLG10, GHL05, HAK+12,JGBR15, JLYZ16, KBSCZ12, LFK16,MKKS20, MPQY19, OMWX09, OC13,PAS+11, PZS+20, PG06, PR12, QBPEL12,SSS20a, TZP17, TBRS13, WDL+17, YB08,

ZLY+13, ZZF+19, ZZH18b, IM14, Mat15,SHK14, YHV+15, WWC18]. Large-Scale[BBH+18, FWXZ19, GHL05, HAK+12,JLYZ16, MKKS20, OC13, PZS+20, TBRS13,ZZF+19, IM14, SHK14]. Larvae [MBJ19].Lasso [GHL05, LDM18, SMPS20, FYSM12].LateBiclustering [GM14]. Latent[GMCB14, JZL13, LLA19, Mam05, RGCB05].Lateral[CDW12, MVW+13, THL11, ZWL+12].Lattice [DCVC11, GZS12, JMA17, TAI+19].Lattices [DABV17]. LAUPs [XYYZ20].law [LWM14]. Laws [HLM+13]. Layer[WXWL20, XW16]. Layered[WLCX18, KKC+14]. Layout [GH08a]. LC[BTTR11, RTWR15, TTWR13]. LC-MS[BTTR11, TTWR13]. LC/MS [KBBD+17].Leaf [wTCAK+20]. Leakage [AGAS18].Leaping [HDS+18]. Learn[KMG+05, WB17]. Learned[MRK18, NBGL19, SPWF14]. Learning[AV12, AM12, BMK11, BLR08, gCLL+10,CHZ+16, Che10, CGW+16, Che16, CZW+18,DK17, DGY05, DZ11, DSCM20, FYZ+19,FMA+20, FPC20, FSMJ05, GAR+09,HYR+19, HHSC13, HEE+18, HLN20,HLSR18, HHCY20, HYZ16, HF12, HTLL12,IBN19, IYA12, JM12, JHZL19, Kar12a,KK08, KSS15, KY19, LJK+12, LCZN16,LYL+17, LFZ+19, LSY+20, LZH18, LNY05b,LNY05a, LHL+19b, LTL+07, LDL+17,Mam05, MWZ+20, MSKC19, MFF+18,NLXS19, NHTD17, NFM+12, OLZ11,PTH+18, PH10b, PAAG07, RLR20, SFMS18,SDN+11, SKS+19, SSV+19, SGP+20,TNQ08, TAAP11, TBRS13, UBP+19, VKS17,WMK17, WL13b, WHXS17, WCC+18,WLHY19, WCA+19, WYHZ20, WWBZ19,WCXL18, XPXY11, XLL+18, XLL19,YXS16, YHZ+19, ZHSS07, ZLPW16, ZZH18a,ZCG+18, ZLXL19, ZG19, ZLX+20, ZL19,wTCAK+20, AJYT+15, AM15, BCLC15,CR14, GJPSV14, GAVRRL15, LLCZ15,SLW15, SEC15, SFH+14, WHZ14, YN14].

33

learning-to-rank [SFH+14]. Least[FYSM12, LN13, WWC18, MBS15].Least-Squares [LN13]. Leishmania[SSP+17]. Length[HYW08, LPH18, RFFB+20, RW07, SSS13a,dDD18, MM14b, SSKH15].Length-Weighted [dDD18]. Lengths[KMSY20, FWY+15]. Less [ZSC+10].Lethality [LWL+20]. Level[AS05, AV12, BU17, HvIKS11, KCP19,LB19, LLBL20, MZSL19, PSC20, WGK16,vIKK+09, LHWL15, UKV18]. Level-[PSC20]. Level-1 [HvIKS11]. Level-2[vIKK+09]. Leveraging [AKLJ17]. LGH[XWC15]. LGT [PSC20]. Liability[QBPEL12]. Libraries [VGBK19, HPH+15].Library [GSK13, PFJ+19, UJ09]. Life[HGC+20, IM14]. Ligand[AM12, CHZ+16, FVP+20, GLW12, HF07,STT+14, WLL13, ZCG+18, AM15].Ligand-Binding [CHZ+16]. Ligand-K*[STT+14]. Ligand-Specific [ZCG+18].light [GCC+14, VPB15]. light-induced[GCC+14]. light-weight [VPB15]. Like[DR16, FM11, GAR+09, HEF17, KG12,NSNA19, Ros13]. Likelihood [ACPR10,LCWZ13, MRS09, Roc06, Wu10, TDD14].Limb [BMT17]. Limits [SLGK17].LincRNAs [BKKG19]. Line [ZWL11].Lineage [MR10, XYYZ20, ZZ14].Lineage-Associated [XYYZ20]. Linear[BEW09, BFK17, CSSS16, CWG+18, FM13,HSS18, JNST09, LCC+11, MTSCO10, NO09,OC13, PRU11, RBdJ11, SHUP19, SLB+08,UC10, WGX+17, WYHD17, Wig15, WCL11,dJP08, BS15, KGK14]. Linear-Time[JNST09, LCC+11]. Linearization [CC09].lines [MFS+15]. Linkage[BKP+19, LLC+13, XWC15, Jam15].Linked [SLL+19, WRH+09]. Lipid[HBRU13]. List [Ano06a, Ano08b, Ano09a,Ano10a, Ano13a, KL11b, RSJK13, IEE05,IEE07, XTL12b, Ano16]. List-Colored[RSJK13]. Literature [AAF+13, CLH+15,

HW07, LHLY11, LNC+05, Ozy12, XYZ19,XTL12c, ADTAQ16, TAL+15].Literature-Based [AAF+13].Literature-Oriented [CLH+15]. Little[RRTB12]. Live [TRKRC13]. Live-Cell[TRKRC13]. Liver [DG19, HEE+18, OG11].LMMO [ZZH18b]. LMMSE [GH15]. LNA[BM12]. LncRNA[ZZCD19, ZZF+19, HHCY20, XLL+20, ZS18].LncRNA-Disease [ZZCD19].lncRNA-Environmental [ZS18]. load[ZYW17]. Local[AH11, ABH+14, AWW18, ARP+16,BEW09, BG05, CBFB12, FL18, HT09, HB11,LZ18b, LHQ+18, MGK08, ME19a, ME19c,MGC19, MB16, NI07, QL16, RYK+19, SS04,Sen19, TDA+09, WCA+19, Wu11, YAB13,ZDYH17, DI15, MG14, PSK+15].Local-Nearest-Neighbors-Based[AWW18]. locality [LJL+14]. Localization[KAL+17, hLMBJ11, MGK08, OM07,QWC+16, SP11, TR07, WMK17, YL12,ZXZ20, ZHE19]. Localized [KNTB18].Location [HYW08, LZQ+20, XPXY11].Loci [MR10, DNR15]. locomotor[GCC+14]. Locus[GZC+17, LLC+13, XWC15]. Log [Roc11].Log-Odds [Roc11]. Logic [BMZM15,CSK+11, JZS+18, CL14, FHRG14]. Logical[GBB+11]. Logics [RdMCBC13]. Logistic[CSK+11, JHW+19, LW19b, LWL+20,LLH+14, MLZ18, PSIM17, ST05]. Long[KL19, LHHL19, LL19, LLBL20, MWL+12,ML18, QD12, TR07, ZWXL20, ZLX+20,CWLZ14]. Long-Range [KL19]. Long-Run[QD12]. Longest[BVD+07, RW07, NYOL15]. longevity[WFD15]. Loop[NLXS19, PPM+13, PLC+20, Str11]. Loops[YDM+08]. Loss[CLH13, HZR+19, HCMB18, HBC+11,KB17, KB19, LHDS18, SSK+20].Loss-of-Function [LHDS18]. Losses[CDW12]. Lossless [KNR05]. Low

34

[CDB+16, GGP08, HCLS11, LC19, LCW+18,NPBD16, WLZ+19, XHQ+18, YZG+17].Low-Rank[CDB+16, WLZ+19, XHQ+18, YZG+17].Low-Resolution [HCLS11]. Lower[BB04, BMT17]. LPGNMF [ZWXL20]. LR[SDTK19]. LSTM [YRL+20].LSTM-Based [YRL+20]. LTRs [AD12].Luminal [JLW17, SMPS20]. Lunar[SSS20a]. Lung[MWZY17, WQY18, YCCY20]. Lungs[SZCX19]. Lymphoma [WWC18].Lymphomas [SKD+07].

Machine[AV12, AM12, gCLL+10, CWT+19, Che10,DZ11, GAR+09, HEE+18, KSS15, LLX+16,LSY+20, LNY05b, LNY05a, LHL+19b,MRK18, MSKC19, MFF+18, RTA+16,SDN+11, SKS+19, SSS20a, SZLL11, VKS17,WWBZ19, WLL13, ZHSS07, ZLXL19, ZL19,AM15, EES14, SLW15]. Machine-Learning[SKS+19]. Machine-Learning-Based[AM12]. Machines [AD12, LLX+11, LLT10,MNR09, WZ13a, XZC07]. Macromolecular[RST10]. Macromolecule [GAGM11].macromolecules [PSK+16]. MAFFT[ZLS+15]. Magnetotactic [MLZ17].Mahalanobis [MT11]. Maintenance[FW20]. Majority [JRSS18, PI09].Mammalian [ZZM17, CV14].Management [CKM+17, LLZ+20b, MZ17].Manhattan [ME19a]. Manifold[FZM20, HF12]. Manipulating [SBRK11].Many [BG13, CCCY20, GGP08, SRM18].Many-to [CCCY20]. Map[BCL13b, CGPW06, Gra04, MTNH17,SSD19, KD15, ABS17]. Map-Reduce[MTNH17, SSD19]. MAPK [KCP19].Mapper [CZX19]. Mapping [DGH+06,DSHM08, MTM+15, NJMF19, NPK+07,NTR16, RZMC17, SDS18, STO06, STB+19,TC16, YLXS17, YZG+17, CWLZ14, Jam15].Maps [ABS17, CBES11, JSA08, LDS+07,

MRB12, VMD+08, WZA07, WCL11, ZZS07,HC14a, SDAA+14]. Margin [ZZH18b].Marginalization [SN12]. Marker[DGH+06]. Markers[HCA+10, SSS13b, WCMB19, MM14b].Markov[BBH12, DGRC15, Gou06, GJY+14, JS12,KCZ+15, KL11c, cLWA07, LGN+19, MG14,MPY18, RH05, RC11, SMB12, SPWF14,TM11, VF09, Vis18, ZHE19].Markov-Blanket-Based [RC11]. Mass[ASI+11, BBN19, BM08, BKR11, DABV17,HYY11, KSS15, LZ18a, OG11, PH10a, SN12,YMW+12, ZGC+05, ZLW+11, ZGB+12,dAc17, CWZW15, DST+15b, KGF+14,SHK14]. Mass-Spring [DABV17]. Massive[LLZ+20b, MTNH17]. Massively[BBH12, Dem12, GLS+16, TIA+11]. Master[BGHC20]. Match [RW07]. Matched[XLL+20, SB16]. Matches[GRS+13, PRU11]. Matching [AFJ12,ADPH11, BBN19, BG12, BM20, CCCY20,DR16, Gra04, LRM12, LHQ+18, MCD+11,Pol13, STB+20, ABH+14, HC14a, ARZ+14].materials [DKS+15]. Mathematical[AVD+12, BvdGK+11, MBKK18, MBF+11,TR13, ZZ13]. Matrices [AH11, CDB+16,JS12, PRU11, Roc11, SCC+15]. Matrix[BKKG19, DFM+11, EZW+17, JLwC11,JHX17, JZZQ19, LW17, LWG+18, LCGW19,LWL+20, MHHJ20, RM18, SJNS19,WLG+16, WHF+20, XLW20, YHCS19,YWF+20, ZWZ16, ZWXL20, ZZN+11b,LYH+16]. Matt [DKCM12]. Max[FJJ11, LLC+13, LCZN16, SR06].Max-Correlation [LLC+13].Max-Flow-Based [FJJ11]. Max-Min[LCZN16]. MaxCut [SR10]. Maximal[GRS+13, KVX12, WDL+17]. Maximally[BNV+13]. Maximization [MB16].Maximize [LJZZ13]. Maximizing[GE14, ZMT14]. Maximum [ACPR10,BN06, BFK17, CCYW12, Csu04, DNS19,GRH08, GM09, GB10, HZR+19, LCWZ13,

35

MRS09, Roc06, SYZ+13, SLB+08, SCPS12,TDD14, CZWT15, HKLN14, SSKH15].Maximum-Parsimony [SLB+08].Maximum-Scoring [Csu04]. MCMC[AM19, MMS10]. MCNF [ZY20]. MDA[YWN+19]. mDixon [BMT17]. Mdm2[ZLL+20]. MDR [SKS+19]. MDTE[WQL+16]. Mean [DZ11, WDS+12]. Means[LHKL17, SKD+07, TMLI19, TED+12,IM14]. Measure[BB11, HBH12, HLL18b, KPW13, LTM+13,MB20, MT11, Pol11, SGC07, SSD+16,SLS+14, SMK+12, ZZF+19, BM14].Measurement [TRKRC13, BCMW15].Measurements [BZ10, SVZ09, ZAZ11].Measures[ASP20, AKNB07, BRS18, JCF13, LWT+18,PKM06, RBdlVMPG16, SVdSS+18, CV14,HC14b, RB14, WSTL+15]. Measuring[HC19, LFK16]. MEC [WLL+20].Mechanical [DABV17, RSCX18].Mechanics [VMZM17]. Mechanism[ASJ+07]. Mechanisms[QV17, ZZ13, KSA16]. Mechanistic[TMLI19]. MedCo [RTPM+19]. Median[BMM08, JSA08, ME19a, ME19b, ME19c,UKV18]. mediated [SSML15]. Medical[BWRF12, IGA18, WNT+17, KSA16].Medicine [Ano12a, SJZ19]. medicines[CZB+16]. MEDLINE [NSC17, WCMZ15].Meets [LBQ+13]. Melanoma[Mah10, RPBP18]. Melting [DPW12, ZL15].Mem [WMK16]. Mem-mEN [WMK16].Membership [SBM15]. Membrane[LLX+16, NFM+12, SSP+17, WMK16].Memetic [CBF+18, GPMH16]. Memory[CMSE+15, DBZ12, LL19, PFJ+19, PNA20,TR07, WCLY12, ZLH12, ZLX+20]. mEN[WMK16]. mer[CZ20, HC14a, LMZ14, PFJ+19]. Merging[LV14, LLL16a]. MeRIP [CZM+18].MeRIP-Seq [CZM+18]. Mers[CMR19, ZGZ+20]. Message [Wil04b].Meta [JFR+19, ZZRPZ19]. Meta-Analysis

[JFR+19]. Meta-Path [ZZRPZ19].Metabolic [DMD13, GJZH17, LFS06,LCTS08, MKKS20, MGS17, QV17, SBRK11,SMK+12, TLSA18, WWLL16, YWK+07,vBdRD+11, SYV14]. Metabolism[ACC+13]. Metabolite [MKKS20].Metabolomics [QV17, YCCY20].Metadata [FLM+16]. Metagenomes[LFK16, SWH+12, WWBZ19].Metagenomic[JMA17, LHKL17, QTZ15, RLR20, LZGZ14].Metaheuristic [BVN+11]. Metaheuristics[SGH12]. Metal [PLF12]. Metal-Binding[PLF12]. Metasample [ZZN+11a].Metasample-Based [ZZN+11a]. MeTDiff[CZM+18]. Method[AAG+18, BG05, BRZ+17, BLR08, BZ08,CCYW12, DZA+06, DBZ12, DWSB11,DHC12, FWY19, FVP+20, GCB+18,GCL+18, GPC+20, HYW+17, HZZY16,HLL+18a, HYL+19, HC07, HGM18, JLH16,KMSY20, KTLM15, LYW20, LZL+19,LLZC12, LZX+19, LHG+16, LWZ12,LXG+16, LZZ+16, LHKL17, LLH18, LGX10,MWZY17, MK16, MBJ19, MKKS20,NGY+16, PM20, PL17, PTH+18, RGI13,RLV04, SH11a, SZ11, SNC+16, SIK20,SPW20, SSFW12, TWG+12, TBRS13,TK05, USMS19, VTGC16, WBP+12,WZJH12, WHWP12, WCA+19, WLZ+19,WCLY20, WGK16, WW19, XLW20,YWW20, YCCY20, YM20, YH13, ZWSX12,ZCR+17, ZY20, ZYF+18, DNR15, DPL+14,GCC+14, GH15, IM14, KKC+14, KH14,LLW+15, LLL16a, LLC+15, PS15, SYV14,YTLL15, YN14, ZSY+14, ZZ15].methodological [BF14]. Methodology[JCF13, KG15]. Methods [ARK20, AV17,ADR18, BLP18, CSK+11, CCE19, DLRW18,DPS+13, DPA+17, FS12, FS13a, FYSM12,JDCC12, JDHL20, KSN+12, LN13, LJL+15,LPH+13, LL19, MBF+11, NLXS19, RG16,Rho20, SMK+12, TV11, TAI+19, WNT+17,WWBZ19, Wil09, Wu11, XLL+18, ZZRPZ19,

36

ZZ20, DS14, SQZA14, SFH+14, WFD15].Methylated [HHSC13]. Methylation[CZM+18, DCHW17, FPC20, LZL+20,MSZ19a, MB20, ML18, SKD+07, WXS+19].Metric [BS09, CLRV09a, CLRV09c,CAN+08, HEF17, HYZ16, LRM12, Nak10].Metrics[CLRV09a, CLRV09b, HSlSM11, Mos07].Metrizations [Rho20]. Metropolized[MMS10]. MF [LWL+20]. MGT [LZL+19].MHC [EMDH11, FLW+14]. MHC-II[EMDH11]. MIC [PCY+19]. Microalgae[BdOS+18]. Microarray[ABVD12, BDP11, BZ10, BLP+12,BHHMCL16, BLR08, CLVT+20, Che10,EAS12, EAS13, EFLA08, FJJ11, GK08,HYW+17, HC16, IVA11, JCF13, KZ10,LTM+12, LTM+13, LH10, LPH+13, LTL+07,MP13, MC07, NU06, PSS09, RGCB05,RV06, SVZ09, SBW15, SC11, SY09, SYZ+13,SIM12, ST05, TZH07, TZ16, TGGF10,TZY11, TC13, TBKH05, WGP11, WCA+19,WLPW16, WDS+12, WWC18, WW19,XZC07, YM11, YC08, YNWC07, YPS11,YHB12, ZLZ06, ZHSS07, ZWHC19, ZC11,BMM14, CZWT15, MM14b].Microarray-Based [CLVT+20].Microarrays [BHP19, CD08, PBhL+11].Microbe [YDW+20]. Microbe-Disease[YDW+20]. Microbial[NS19, TAI+19, WCMB19, JHXP15].Microbiome[JHX17, MHHJ20, ZHJ17, ZWDR20].Microbiota [AAT20]. microfluidic[AIS+16]. Microglia [DPA+17].microhomology [SSML15].microhomology-mediated [SSML15].Micron [RA16]. MicroRNA [GZR+18,LWL+18, LZHZ17, LLL16a, MKG20,RPBP18, SPMB13, WZ13a, YWN+19].microRNA-Binding [WZ13a].MicroRNA-Disease[LWL+18, LZHZ17, YWN+19].MicroRNAs

[PB19, WLG+14, WQL+16, YWN+19].Microscopic [SSD+16]. microscopy[BLR15]. Microvascular [FLJS20]. Middle[XHY+18]. Migration [MLZ17, NGY+16].Military [WNT+17]. MIMOSA [NS19].Min [LLC+13, LCZN16].Min-Redundancy [LLC+13]. MinePhos[XTL12c]. Minimal [BNV+13, SMSZ17].Minimization[BvdGK+11, GMP08, JQH+20].Minimizing [Zha11]. Minimum[BGHC20, BGHM09, BM13, BCL13b,CEFBS06, CC09, CD08, HEF17, MW20,MMS10, SK19, TLSA18, vIKKS08].Minimum-Flip [CEFBS06]. Mining[BNV+13, CLW13, CLC+17, HPL+13,HW07, JR14, JLH16, LLW+11, LHLY11,LNC+05, LWG+14, LC10, MMB+13, MC07,MSS+19b, PZWC20, PR12, RMS15,SKDA19, STO06, TK05, WCMZ15,WLWN17, XTL12c, ZWZS16, ZGZ+20,Zha16, KD15, TAL+15, WSTL+15].Minority [ZLZ+19]. MINT [HRHP16].Minutes [LBL12a]. MiRNA[CLW13, CGW+16, HHCY20, LHC18, PM20,SFMS18, SYKM17, XYZ19]. miRNAs[KTLM15, LDL+17, QLZ16, ZZRPZ19].MiRTDL [CGW+16]. Misassembly[WLL+20]. Mismatch [Che16, YCYC12].Missense [MBP+19]. Missing[WCA+19, YPS11, ZZDW13, KS14].Mitigate [CMSE+15]. Mitigation [FKB19].Mixed [HKM+18, PKRD12, SdOD+12,SLB+08, SDTK19, WLZ+19, ZWZ16].Mixed-Model [SDTK19]. Mixed-Norm[WLZ+19]. Mixes [MMS10]. Mixing[PPZ12]. Mixture[BTTR11, BEQD19, CGZ15, HYY11,KDS+20, LMZL17, WFY+19, PRZ+14].Mixture-Model [KDS+20]. Mixtures[APRS11, GM09, RdlCGW09]. ML [BU17].ML-Space [BU17]. MMBIRFinder[SSML15]. MMSE [SSK+20]. Mobile[GTTR+17]. Modal [APPG18]. Mode

37

[MSS19a, SPA17]. Model[AVD+12, AGGM11, AGMP09, BBK+12,BLP+12, BA18, BEQD19, BCFCC13, CP13,CSZT19, CW09a, CW11, CGZ15, CAW+19,CGLF12, CKWY12, FPC20, GXSZ17,GBS11, Gou06, GJZH17, GBB+11, HZR+19,HYY11, HS08, HCLS11, IL18, JJH12,JGBR15, JZL13, JLYZ16, JLW17, JHW+19,KCZ+15, KDS+20, Kar12b, KHP12, LR20,LLX+11, LJ20, LLZ+20a, LHZ+19, LHQ+18,LYY+19, LCH19, MT12b, MT12a, MBF+11,NA11, NWW19, OW20, PNP+18, RAA10,RC11, RST10, RZMT15, RdMCBC13,RBdJ11, SSD19, SNC+16, SCCDK09,SMSZ17, SWX+19, SDTK19, TRBK09,Tho16, TZY11, VSR+06, WCMZ15, WQY18,WKE11, Wig15, Wu10, WDS+12, WWT+20,YXYC13, YOGY11, ZMT13, ZMST18,ZDL12, ZZS18, ZHZ+20, ZXB11, ZWY+10,ZZDW13, DKS+15, HLW15, JHXP15,LWM14, PRZ+14, RTWR15, WFD15,XZY+14, ZMT14, ZWL+14b].Model-Based [IL18, TZY11, ZWY+10].Modeling [CLST+13, CHL+12, DBTB09,DABV17, FSB+11, GGH+13, Gos11,GBB+11, HW07, JFN11, KAL+17, KG12,LLES18, LLW10, LCB17, MPS18, ML18,MVS+13, MNW+04, NLXS19, PLMV12,PZH20, PPFG20, RCBB19, RdlCGW09,RMS15, SdOD+12, SJZ19, SGR+17, TV11,TMLI19, WLL+09, WGP11, WMWA12,WBP+12, WXWL20, WLPW16, WWL+17,WCXL18, ZZ13, BF14, DI15, KPB14, KD16,MCH+15, ARZ+14, PJN+14, YMT+14].modelled [YLH+15, ZSY+14]. Modelling[AKV16, AFMS19, BMZM15, FKB19,GPF+20, LGN+19, TAI+19, ZK16]. Models[ATA+17, AR09, APRS11, ALWG18,AAE11, BTTR11, BHMA06, BU17, CNM11,CGPW06, Dal16, EW04, FL18, FWA10,FKLS07, GzS11, GZS12, HS09b, KC11,KL11c, LL11, cLWA07, LW13a, LLA19,MBP+18, MLZ18, MKKS20, NSNN12,PB12a, PG18, Pau18, SFB+08, SZZ+19,

Smi09, SYL19, TIA+11, THH+19, TRBK08,TBKH05, VdTVV19, VSR+06, VF09,VBG+18, WFY+19, XSS17, XWF07,ZWL+12, ZZ18, dJP08, HM15, KFHK14,SPWF14, ZSY+14]. Modes [UAH16, DB14].Modification [BYZ+18, CMMZ20].Modifications [TLSA18]. Modified[BA18, EAS12, MCCZC08, SSD+16,SKD+07, XLL+18, ZLLS17]. Modular[RM18]. Modularity [HK12, WZ14].Modulated [CHW+18]. Modulator[CRP12]. Module[MB20, NWZ+20, ZZN15]. Modules[JLYZ16, KZW+18, KMG+05, LLH+07,LGW20, LHC18, MSQ18, MSZ19a,MTSCO10, PM20, WLCP11, XLL+20,GGZZ14, LLL16a]. Modulyzer [MBB+17].Molecular [AFAAW+11, ADPH11, BZ07,BS10a, CGLF12, CKWY12, CBES11, DM09,FSMJ05, Han10, KPB14, LCW+18, PZS+20,RPB+13, RTA+16, RCBB19, SSV+19,SMPS20, TMLI19, WLC11, WB11, ZGC+05,ZXB11, ZZN+11b]. Molecules [ARP+16].Moment [BBW18, MLZ17].Moment-Based [BBW18]. MongoDB[LQY+20]. Monitoring [PTH+18]. Monte[GJY+14, ADTAQ16, AKV16, Bi09].MOPSO [CZJ17]. Morphogenesis[CHC+05, JGBR15]. Morphology[ZCWW19]. Morphometric [wTCAK+20].Morphometry [JFR+19]. Most [IMA13].Motif [BNV+13, CW11, CL08, DBR07,HLH11, JL10, Kar12a, KL11a, KC11, LFS06,LMPT15, LCLL10, hLMBJ11, LHL+19b,LT07, MIC+07, MM17, RLV04, RSJK13,WLPW16, FWY+15, MMFD14, Tan14,YHV+15, Bi09, CHK17, MMFD14, ZZH18a].Motif-Based [MM17]. Motifs[AFMS19, ACP10, BvBF+11, BVN+11,CFOS06, CSS11, DS19, KL19, LZL+20,PCGS05, RA16, SKDA19, SREK19, SIK20,SSFW12, WHWP12, Wer06, ZZH18b,FWY+15, LWG+14]. Motifs-Based[SSFW12]. Motion [BM20]. Motions

38

[CBES11]. Mouse[JZL13, NPK+07, RLRH18]. Moves[BGHM09, GZS12, HKT+18]. MPGM[KG20]. MPIGeneNet [GDM18]. MR[BMT17]. MrBayes [LHG+16]. MRFy[DGRC15]. MRI [GH15, HYR+19].MRI-Derived [HYR+19]. mRNA[LHC18, PM20, WMWA12, XLL+20, ZK16].MS [BTTR11, KBBD+17, RTWR15,SLL+19, TDZ+19, TTWR13, ZWD+17].MS/MS [SLL+19]. Multi[ASP20, APPG18, BMT17, BA18, BU17,GSC+18, GZC+17, GCL+18, HZW+17,JFR+19, JM12, KPK+17, LHL+19a,LJK+12, LC19, LLQ20, LZL+20, LLZ+20a,LNW20, NHTD17, PL17, PZH20, SLX+18,SDH20b, SWX+19, SWL19, SSF18,TGP+15, WMK16, WMK17, WYHD17,WLCX18, XW16, XZG+18, YRD+13,YSW+17, YGY+19, ZwGC17, ZHJ17,ZWHC19, ZGZ+20, ZY20, ZHE19, CR14,GMCB14, Gu16, HWK14, KKC+14,LLCZ15, RHH16, WHZ14, WGX+17].Multi-Assembly [TGP+15]. Multi-Block[KPK+17]. Multi-Channel [BMT17].Multi-Core [LHL+19a].Multi-Dimensional [PL17, SWL19].Multi-Domain [LNW20]. Multi-Dose[SWX+19]. Multi-Factored [ASP20].Multi-Feature [LLZ+20a].Multi-Functional [WMK16].Multi-Instance [LJK+12, WHZ14].Multi-Label [JM12, LJK+12, SLX+18,WMK17, WYHD17, ZHE19, YRD+13,WHZ14, WGX+17]. Multi-Laplacian[ZWHC19]. Multi-Layer [XW16].Multi-Layered [WLCX18, KKC+14].Multi-Level [BU17]. Multi-Locus[GZC+17]. Multi-Mers [ZGZ+20].Multi-Modal [APPG18]. Multi-Objective[BA18, GSC+18, GCL+18, XZG+18,ZwGC17, RHH16]. Multi-Omics[YGY+19, ZY20, PZH20]. multi-platform[GMCB14, LLCZ15]. Multi-Pooling

[LLQ20]. Multi-Rank [WLCX18].Multi-Scale [HZW+17]. multi-scope[HWK14]. Multi-Site [JFR+19].Multi-Source [YSW+17]. multi-state[Gu16]. Multi-Swarm [NHTD17].multi-task [CR14]. Multi-Thread[LZL+20]. Multi-View[LC19, SSF18, ZHJ17]. Multicategory[ZHSS07]. Multiclass[RM13, SSS+11, XAW07, YOKI09, ZC11].Multicore [GDM18, MTM+15].Multicriterion [YM11].Multidimensional [HCA+10].Multidomain [JJH12, WKE11].Multidrug [NTCO07]. Multiexpressions[Zou13]. Multifaceted [AL12]. Multifactor[YLC20]. Multiforme [CHW+18, ZLPW16].Multifractal [DSVMM18]. Multigenomic[GXSZ17]. Multilabel [WL13b, YRD+14a].Multilabeled [GJS11, HSlSM11].Multilevel [PLMV12]. Multilocations[WL13b]. Multilocus [LLC+13, MWSM12].MultiMAGNA [VM18]. Multimeme[NTCO07]. Multimodal [GCZ18, HS09a,HS09b, HHCY20, LGB15, SWL19, LLCZ15].MultiMotifMaker [LZL+20].Multinomial [LW13a]. Multiobjective[HKK07, LZW20, MPF12, MMB+13, TGK13,TGD+16, GAVRRL15, MM14b, SB12].Multiparameter [SSDN12]. Multipartite[VKM07]. Multiple[AM19, AAH+18, ALWG18, ABS15, BAK06,BRZ+17, BLS12, BHHMCL16, Bro05,CW12, CWLS15, CGPW06, DBZ12, DK17,DG19, DBN18, EMDH11, GZC+17, HL16,HKT+18, HVG04, HS15, HPL+13, HLZ+17,HB11, JLYZ16, JXN+16, KG20, KKC16,LH10, LZHZ17, LWT+18, LCC+11, LW13b,MSQ18, MMH15, MR10, NP13, NTR16,PS11, PZWC20, PT09, PS15, QL09,QWC+16, RLR20, RM18, SHUP19, SIK20,SK12, SSFW12, SPWF14, TDY+18,TDA+09, VM18, WS08, WLMW+11, WB17,WGX+17, WHKK07, WPL15, WLA+13,

39

YHCS19, YLL+06, YFWZ16, ZLPW16,ZZCD19, ZZF+19, ZLLS17, DNR15, MW16,PJN+14, YlCW+15, YRD+15].Multiple-Filter-Multiple-Wrapper[LH10]. Multiple-Filters [BHHMCL16].Multiple-Grain [JLYZ16].Multiple-Sequence [NP13].Multiple-Structure [WS08].Multiple-Swarm [ALWG18].Multiple-Valued [LW13b]. multiplier[CL14]. Multipliers [HYL+19].Multipositional [GLW12]. Multiprotein[HK12]. Multiresolution[CSZT19, HYC12, ZKL18]. Multisample[PR18, SSS13b, ZYW+13]. Multiscale[GGH+13, GCZ18, HMW+12, NNM+12b,SZL+20, SCCDK09, ZLW+11]. Multiseed[KNR05]. Multistage [DLT10]. Multistate[GG11]. Multitask[FB19, LZH18, XPXY11]. Multivariate[KPW13, Kuk13, PPFG20, ZAZ11, CBN15].Muscle [BMT17, SXL+14]. Muscular[BCL+13a]. Mutagenesis [VGBK19].Mutagenic [Che16, YCYC12]. Mutant[HLG10]. Mutants [DSZ+06, GCC+14].Mutated [LGW20, SAE+20, ZZ18, ZW19].Mutation[DSZ+06, KKI20, LHDS18, MYCW12,RYK+19, Tho16, TOYHZ19, WGK16].Mutations [DFM+11, HCMB18, KCZ+15,KKC16, MBP+19, PBJ12]. Mutli [BYZ+18].Mutli-Features [BYZ+18]. Mutual[DGH+06, LDM18, MPA15, SMRP15,SPW20, TZ16, ZGB+12, HRHP16]. My[MZSL19]. myonuclear [SXL+14]. Myosin[ZLS+19].

NAHAL [FMD18]. NAHAL-Flex[FMD18]. Naive[WDS+12, LW13a, SSP+17]. Nakhleh[CLRV09c]. Name [YSC13, HWK14].Named [AV17, LJ20, HK15].named-entity [HK15]. Naming [STB+20].nanotubes [MZS+16]. Nascent [AALD17].

National [FJJ18, GJH19]. Natural[ZDL+19]. Nature [BS08, LZW20].Nature-Inspired [LZW20]. Naturelike[BPP+13]. NcRNA [SBY12, LTaS13]. Near[BMH+16, BEW09, SDB+07, MW16].Near-Linear [BEW09]. Near-Perfect[SDB+07]. Nearest[AC12, AWW18, ZSC+10]. Necessarily[PK13]. Necessary [Son06]. Negative[JZZQ19, LWG+18, LCH19, PNP+18, RM18,TWZW16, WLG+16, XL16, YHCS19,WLG+14]. neighbor [HS15, LAI+14].neighbor-joining [LAI+14].Neighborhood[BS10a, GRH08, LGN+19, MZL15].Neighborhoods [CCLS13, HW13, LBL12b].Neighbors[AC12, AWW18, ZSC+10, LMZ14]. Nested[Wan12]. Nestedness [GF10]. Net[BRS18, CNM11, ZLH+17]. Nets[RPBP18, WMK16]. Network[AKMT12, AKV16, ABS17, BDS12, BMK11,BA18, BSLR05, BNV+13, CXW+13,CMMZ20, CBM+20, CMQ+16, DFTC12,DS19, EMK18, FHRG14, GLL+18,GPMH16, GSC17, GHL05, HAK+12, HS09b,HW07, HGM18, JDCC12, KCP19, KG20,KZW+18, KAHK+10, LCWZ13, LCZN16,LNC+19, LMZ+20, LLES18, LLZ+13,LZHZ17, LLL15, LWL+19, MSZ19a,MMB+13, MGC19, MLZ18, MKKS20,MGKG17, MM17, MWLS18, MVW+13,NNSZ07, PSS09, PL17, PZH20, PCDP18,RC11, RB16, RV13, SQZA14, SVdSS+18,SMPS20, SDH20a, SMSZ17, SWL19,TIA+11, TLSA18, TDZ+19, TMLI19,TDK13b, TP18, TC13, TOYHZ19, VSR+06,VM18, WHWP12, WWL19, WFY+19,WYHZ20, Wer06, WGK16, WW19, XWF07,XW16, XOYHZ18, YXYC13, YFCM17,YG19, YCCM12, YGY+19, ZZKW18,ZDL12, ZZN15, ZWL15, ZHJ17, Zha18,ZXLZ18a, ZXLZ18b, ZPW+19, ZZH19,ZXZ20, ZZBH20, ZK16, ZS18, ZZDW13,

40

ADTAQ16, BDBH15, FZM15, HLW15].network [LP15, MMFD14, MG14, SEC15,TWZ+14, WZC+15, XLC+15, XXM+16].Network-Based [GSC17, PSS09, RV13,SMPS20, WGK16, FHRG14, SQZA14].Network-Lasso-Constrained [GHL05].Network-Regularized [MLZ18].Networking [DG19]. Networks[AVD+12, ARK20, AGAS18, AAH+18,AFJ12, ARS17, AAT20, ABS15, APPG18,AKS20, BBW18, BGHC20, BGS+12, BZ07,BCL+13a, BvBF+11, BD19, BSV10, BJ10,BPJ12, BVN+11, CZ20, CRV09, CLRV09a,CLRV09b, CLRV09c, CDB+16, CC07,CW12, CXW+13, CHW+18, CWG+18,DZH16, DS19, DBN18, DT11, EAS13,ECK16, EMK18, FMRS18, FZWS17,FWXZ19, FSDR16, FSX19, FPPR11,FKB19, FSD+11, GH08a, GPZ20, GDM18,Gos11, GBB+11, HK20, HLM+13, HB05,HC19, HS09a, HF07, HM13, HAH13,HMW+12, HLY+16, HC13, HYL+19,HHCY20, HvIKS11, HDKS04, Hus09, INT11,IBN19, IL18, JvI18, JBgLS19, JLYZ16,JSS+18, JZS+18, JNST09, JFN11, JHZL19,KBNHD18, KN05, KP12, KCCC15, KSB12,KKC16, LFS06, LCTS08, LSMF08, LLH+07,LL11, LCZN16, LT17, LLNW17, LZL+19,LHCL20, LLQ20, LLL16b, LZQ+20, LNW20,LW13b, LTRW19, MSQ18, MSP+19].Networks [MPP+20, MBGP12, MPA15,MDH11, MPSY18, MPQY19, MDD18,MNW+04, MDPR18, Nak10, NRV09,NWZ+20, NI07, NSNN12, OMAdG+12,OYDZ15, OC13, PB12a, PAL+12, PSPM20,Pau18, PLCW17, PZWC20, PH10b, PCK19,PNP+18, PB12b, PPZ12, PR12, PSC20,PKA20, QD12, RST10, RMV12, RRTB12,RMS15, SdOD+12, SREK19, SS06b,SSV+19, SDH20b, SZL+20, SV16, SPA17,SNM12, TIA+11, TAAP11, TWG+12,TGK13, TGD+16, TV11, TGGF10, TZP17,TR07, TDK13a, UWLH15, VRK12, VBB18,WLL+09, WLCP11, WWLL16, WP08,

Wil11, Wil12, XWF07, XGWW19, YDW+20,YKWK18, YFWZ16, ZM12, ZLY+13,ZZN15, ZWZ16, ZZM17, ZZCD19, ZZF+19,ZWHC19, ZSD08, ZWW17, ZWDR20,ZWD+17, ZZDW13, ZDYH17, Zou13, dJP08,vIKK+09, CZWT15, CXS15, DYD15,GTDK15, HKLN14, KH14, KD15, LLW+15,MW16, MM14a, NCMCAR15, PWC+15,RHH16, SRLR14, XG14, ZWL14a, ZWC15].Neural [AAT20, CZ20, CC07, FSX19, HB05,HF07, HLL18b, KN05, LSMF08, LHCL20,LLQ20, RMS15, SSV+19, SWL19, WYHZ20,XLZ+15, XWF07, ZZH19, ZZBH20].Neural-Genetic [KN05]. Neuroimaging[WLA+13, ZKL18]. Neuroinformatics[NPK+07]. Neuron [PTM+19]. Neuronal[TGK13, TGD+16]. Neurotoxin[MWLS18]. Neurotoxin-A [MWLS18].Neutral [BWC17]. NewGOA [YFWZ18].Newton [CAW+19]. Next[BBN18, FS13b, AKD17, PNP+18, WPL15,YWW+18, CWLZ14]. Next-Generation[BBN18, FS13b, PNP+18, YWW+18].Ngram [LCB17]. NGS[LLZ+20a, SSD19, YWW+18, ZmCXS17].NGS-FC [YWW+18]. Nibble [PWZW15].niger [OMAdG+12]. NMF [Mir14].NMFGO [YWF+20]. NMR[AAG+18, CCA12, WL07]. NNI [BEW09].NNI-Based [BEW09]. No [Wan16]. Noah[HBC+11]. Nodal [CLRV09b]. node [ZZ15].Nodes [ABS15, LP15]. Noise[AKS13, FN14, JRN+18, NVSH18, SSDN12,ZZS07, WLY15]. Noise-Induced [SSDN12].Noising [YFCM17]. Noisy[IGA18, KBND19, MDM13]. Non[HSS18, JZZQ19, KB17, KB19, LHHL19,LWG+18, RM18, WLG+16, Wig15,WCMB19, XL16, YHCS19, ZZKW18,ZWXL20, ABH+14, KGK14, MM14b].Non-Binary [KB17, KB19]. Non-Coding[LHHL19, ZWXL20]. non-fixed [ABH+14].Non-Invasive [WCMB19]. Non-Linear[HSS18, Wig15, KGK14]. Non-Negative

41

[JZZQ19, LWG+18, RM18, WLG+16, XL16,YHCS19]. non-redundant [MM14b].Non-Steady [ZZKW18]. Nonbinary[JvI18, LS09]. Noncoding[CAN+08, ZHEB05, SLW15]. Nonconvex[YZG+17]. nonexcitable [LCOMG14].Noniterative [JDCC12]. Nonlinear[AAT20, DZ11, LRM08, LL11, NSNN12,SdOD+12, WLL+09, YPS11]. Nonnegative[Han10, JHX17, LN13, MHHJ20, WHF+20,YWF+20, ZWXL20]. Nonoverlapping[Kur13]. Nonparametric[LTM+13, LHTT11, LGX10, Mir14, TIA+11].Norm [LZH18, WLZ+19]. normal[WDX+15]. Normalization[CLM10, DLT10, LYY+19, SWH+12,VRJ+10, RTWR15]. Normalized[WPL15, YH13]. Normalizing [WYH17].norms [MMSH14]. Note[Ano10c, BS11, GPZ20]. Noun [Ozy12].Novel[AKNB07, AC12, CSW11, Che16, CWZ08,CZM+18, DPA+17, DBN18, DKDD10, DZ11,FVP+20, GPC+20, HZZY16, HZW+17,HLHAJ20, KHO+20, KCP18, KTLM15,LTL+19, LLZC12, LLTC19, LHC18, MRB12,MPF12, MGC19, NPD+17, PSIM17,PSN+15, RBB+19, SP11, SBM15, SYKM17,SSS13b, TNQ08, TDA+09, TK05, WWC18,XLW20, YLXS17, YXYC13, YM20, YC08,YH13, YSW+17, YCZ+18, ZZCD19, ZY20,CL14, GZGX14, KPB14, LLL16a, STT+14].Novelty [CPM18]. Novo [Bi09, SB12,AKR12, DST+15b, HG16, KSS15, ARZ+14,YKW17, ZFZ+20, CLVT+20, LLL+20,GAJ+18, LLH+17, LMZL17, ZWM+20].NovoExD [YKW17]. NP [LGZ+17].NP-Hard [LGZ+17]. NPPC [GMSD11].NR [ISK18]. NS1 [RAA20]. nsSNPs[GED+17]. Nuclear[HCA+10, ISK18, CZB+16]. Nucleosome[CGZ15, CHN+18, GZGX14]. Nucleotide[CW07, CL08, KT07, LLTC19]. null[LWM14]. Number

[BB04, BHMA06, BFK17, BS07, CW09a,DR16, Gru11, MA12, NVSH18, PKRD12,PK13, QSJ+20, SDCW11, TWW+20,WHXS17, XL16, XLW20, YCCM12,ZANN20, ZmCXS17, ZRK19, dNG17, DR14,LWM14, MMSH14, SB16]. Numbers[YH13]. Numerical [FMD18, SCCDK09].NURBS [IGA18].

O [HPH+15]. Objective[BA18, GSC+18, GCL+18, MDD18,XZG+18, ZwGC17, RHH16, UKV18].Objective-Based [MDD18]. Objects[Str11]. Oblivious [CLR10]. Observable[SPA17]. Occurrence [ZWDR20]. odd[EES14]. Odds [Roc11]. ODE [ZSY+14].ODE/DDE [ZSY+14]. Off [PH10b].Oligomeric [SKDA19]. Oligonucleotide[HKS11, LEAK11]. Omic[Ano12a, BCLC15]. Omics[MZ17, YGY+19, ZY20, PZH20]. OMIM[LTRW19]. Oncogenes [PG12, YCCM12].One [MCHT17, QSJ+20]. One-Sided[QSJ+20]. Online [SNC+16]. Onto[WCQ+19]. OntoGene [RSK+10].Ontologies [HXXJ18, LQY+20, MSJP19].Ontology[ASP20, AMGC16, BM17, CM16, CPM18,DKDD10, DBK18, FLM+16, HXXJ18,IQA18, MPM11, PKM06, YWF+20,ZLY+13, ZXLZ18a, ZXLZ18b, BM14, JC15].Ontology-Based [CM16, FLM+16]. Open[Ano13e]. Operation [BFM13, OLS+13].Operational [WLA+13]. Operations[HS09a]. Operators [GSC17]. Operon[CYTY13]. Optimal[AM19, BBN18, BHS+04, BAK06, BFK17,Dal16, DK13, DYD15, DFM+11, HYW08,MCRC17, Mne09, MDD18, SK08, SPMB13,THH+19, WAK13, YOKI09, pD20, ED14].Optimality [ACC+13]. Optimization[AKS13, CAW+19, Che16, CYTY13,DMD13, ED15, GK08, GSX+18, GCL+18,HKK07, HSS18, HOS+12a, HOS+12b,

42

mHB13, HGM18, HRdR09, IGM+07,JDCC12, LYW20, LZH18, MPF12, Mai09,Mat07, MLZ17, NPD+17, NHTD17,NLW+18, ORCJ13, PAAG07, RKDR11,SdOD+12, SDS18, SB12, SIK20, SMSZ17,SB16, VGBK19, WWLL16, WB17, WZZ+18,XSS17, XWF07, XAW07, XZG+18,ZwGC17, ZD17, ZWM+20, ZGB+12,GAVRRL15, Gu16, SPWF14].Optimization-Based [ED15]. Optimized[EFLA08, HDS+18, GH15]. Optimizer[GSX+18]. Optimizing[Bro05, FW20, Jam18, KBBD+17, LMZ14,PB12b, Pol11, TC16]. Optimum [WS08].Option [QBPEL12]. Order[BRF17, KCZ+15, LCZN16, LCGW19,MGKG17, PB12a, Wig15, ZZH19, DWZ+15].Ordered [ZZKW18]. Ordering [BG17].Orderings [SMB12]. Orders[JSA08, HZZT14]. Organelle[ACC+13, SLX+18]. Organisation[MDPR18]. Organisation-Oriented[MDPR18]. organism [WFD15].Organization [ZHZ+20, ZWW17, WZ14].Organized [WZ14]. Organizing [WZA07].Oriented[CLH+15, LHG+16, MCD+11, MDPR18].Origin [BPJ12, RB14]. Ortholog [VKM07].Orthologous [CZF+05, ZZS18].Oscillation [Wig15]. Oscillations[WGP11]. Oscillators [VMZM17].Oscillatory [ZLL+20]. Oshell [LHN+14].Other [AKS13]. OTU [NSZK15].Out-of-Frame [RLRH18]. Outcome[MFF+18]. Outcomes[HYC12, MCHT17, PGHT12]. Outgoing[Gus09b]. Outlier [CWL12, OFC+14].Outline [IGA18]. Output [Wan12].Output-Sensitive [Wan12]. Ovarian[XLL+20]. Over-Approximation [FL18].Over-Sampling [ZLZ+19]. overlap [KD15].Overlapping [LHDS18]. overlaps[SSKH15]. Overproduction [DMD13].Overview [CBK20, LMK+10]. OWL

[LQY+20]. OWL-Based [LQY+20].

P [CXS15, TAL+15]. P-Finder [CXS15].p53 [DSZ+06, ZLL+20]. p53-Mdm2[ZLL+20]. PacBio [LLBL20, LZL+20].Pacific [HC15, WLC18, YSC19, ZC14].PageRank [PWZW15]. Pair[BNV+13, CLM10, KKI20, Tsa12, WZ13b,ZG19, ZGDH16, OFC+14]. Pair-Wise[ZGDH16]. Paired[LLH+17, WLL+20, SKK14]. Paired-End[LLH+17, WLL+20]. Pairing[BWS05, JBP08]. PairProSVM [MGK08].Pairs [BHS+04, ZZS18]. Pairwise[ALQ17, AH11, BAK06, DK13, MGK08,VF09, ZLY+12]. palindromes [RB14].Palytoxin [BCFCC13]. Pan [CRK+19].Pan-Genomic [CRK+19]. Pancreas[PLC+20]. Pancreatic[BMH+16, VDS+20, MFS+15]. Pandemic[BPJ12]. Panmictic [Wu10]. Papers[Ano05b, Ano09c, Ano12a, Ano13d, Ano13b,Ano13c, Cat17, Kim18, LC10, YGFC20,AS15]. ParaCells [SYL19]. Paradigm[SSD19, XG14]. Parallel[BBK+12, BBH12, Dem12, GLS+16,GDM18, KK19, LLQ20, LHS16, MBGP12,MPA15, OMWX09, PFJ+19, PTM+19,PCY+19, PZS+20, TIA+11, ZLS+15,CFIS+15, GPScF15, GJY+14]. Parallelism[KK19]. Parallelization [ZWcF17].Parallelized [HTLL12]. Parallelizing[GDWK+15]. Paralogous [ZZS18].Paramecium [iAOSS16]. Parameter[BBW18, BS11, BBK+12, BS07, CAW+19,DK17, FKLS07, GB10, HF12, MNND13,PK13, SGH12, WWLL16, ZWL+12, Gu16,HLW15, ZSY+14]. Parameter-Advising[DK17]. Parameter-Free [HF12].Parameterized[BN06, BvBF+11, SLH+06a, SCC+15].Parameterless [TK05]. Parameters[JSS+18, NSAH19, SNC+16, SMSZ17,TBRS13, XSS17, Zou13]. Parametric

43

[MSJP19, YAB13, FN14, KGK14]. Parasite[GAR+09]. Pareto[ACC+13, DK13, RM13, VGBK19].Pareto-Fronts [RM13]. parity [EES14].Parkinson [ZWS+18]. Parsimonious[CLH13, USMS19, MW16]. Parsimony[ACPR10, BFK17, BVD+10, BH06, DST07,GRH08, GE18, GM09, HZR+19, ICL11,JNST09, LLT+19, NNSZ07, SHI06, SLB+08,TBGL10, WMS09, vIKKS08, KO15].Parsing [RAA10]. Part [Cas06, Cas07,KJ04, LNY05b, LNY05a, KJ05]. Partial[BBK+07, HYY11, HDKS04, KK08, MMS10,ST19, STB+19, Smi09, TGGF10, WWC18,ZOZ10, MBS15]. Partially [SPA17, LV14].Particle [BU17, CYTY13, GSX+18,HKT+18, HGM18, NPD+17, NHTD17,SIK20, WZZ+18, XWF07, XAW07, ZwGC17,ZCR+17, GBLZ14, SPWF14]. Partition[Mai09, TC16]. Partition-Optimization[Mai09]. Partitioned [LWS+20].Partitioning [HKLN14, BM15]. PASA[JWZ+20]. Path[BCL13b, DNS19, HWPE17, HS08, LTL+19,ME19a, ME19c, SK19, Val11, WL19, ZD17,ZZRPZ19, BM14, ARZ+14, SVM14].Path-Difference [ME19a, ME19c, WL19].Pathogen [STD20, YBGB10]. Pathogenic[KZW+18]. Paths [MMS10, TGP+15].Pathway[AJD+12, BEQD19, CNM11, HHYH07,KDS+20, LLH18, PPM+13, PIPC18,RAM17, STD20, TP18, WGK16, YM20,YG19, ZW19, ZKW19, ED14, LYH+16].Pathway-Based [BEQD19, YG19].Pathway-Induced [TP18]. Pathways[ATA+17, AAH+18, AFMS19, DMD13,ED15, FKLS07, GLS+16, KCP19, KSN+12,SBRK11, UWLH15, ZZ13, ZZ18, GJPSV14].Patients[FLJS20, HEE+18, MFF+18, PvRV+20].Pattern [BHS+04, CLST+13, CLZ+18,GGJ+06, Han10, HPL+13, LSTW+17,LJK+12, LCW+18, MB16, RB16, STO06,

SHJL10, WMWA12, ZYW17, ZZN+11b,ZAZ11, ABH+14, KD15, MNA14].Pattern-Based [MB16]. Patterns[BLR08, CLW13, CLC+17, Gra04, MMH15,ML18, MB16, MCHT17, PG06, PCGS05,SB09, XL16, ZGC+05, CA14, GAVRRL15,KGK14, TYL+16, WL14]. PBN [MPSY18].PC [LHL+19a, TSMMG+13]. PCID[HZW+17]. PCR [Che16, YCYC12].PCR-RFLP [Che16, YCYC12]. PCs[LHL+19a]. PDZ [HZTP12]. Peak [PH10a,YLXS17, YHYY12, YLL+06, ZLW+11].Peak-Labeling [PH10a]. Peakbin[ASI+11]. pediatric [ZMP+14]. Pedigree[HWPE17, MYCW12, PVB+12]. Pedigrees[HWPE17, PG06, PBJ12]. Penalized[LW19b, PSIM17, ST05, ZZN+11b, LYH+16].Penalty [LNR+09, LLT10, YZG+17].Penetrating [WCLY20]. Pepsin [AHT+18].Peptide[AKR12, BBN19, IDD13, JXN+16, KNTB18,LZ18a, LMZL17, WM19a, WWT+20,YKW17, YMW+12, YHYY12, dAc17].Peptides[FWY19, JKN+12, VKS17, WCLY20].Percolation [BMH+16]. Percolator[YMW+12]. Perfect[BBSP08, BBCP07, GG11, HKM+18, KS14,SM08, SDB+07, vIKKS08]. Perform[ATA+17]. Performance [iAOSS16,BGS+12, BWRF12, CNM11, Dal16, HBH12,Jam18, LHG+16, Maz12, pD20].Performing [AKD17]. Periodic [AKMT12].periodicities [MEOL14]. Periodicity[KM20]. Permeation [KL11c].Permutation [Gru11, MTNH17, TW10].Permutation-Based [TW10].Permutations [GBD17, HZL19, XYYZ20].PerPAS [LLH18]. Personal[GSX+18, WAG19].Personal-Best-Position [GSX+18].Personalization [LHH19]. Personalized[Ano12a]. Perspective[CM13, YHY13, SRLR14]. Perturbation

44

[BDS12, FKB19, HAH13, RM18, WWLL16].Perturbed [ZZKW18]. Petri[BRS18, CNM11, RPBP18].Pharmacologic [SSK+20]. Phase[BCL+13a, RCM+19, ZCR+17]. Phasing[BZ08, GMP08, MW20, PVB+12, YXYC13].Phenomena [MNND13, NNM+12a].Phenotype [ABVD12, CSW11, DMJ+18,ED15, RLR20, WDX+15, ZPW+19].Phenotype-dependent [WDX+15].Phenotype-Specific [ABVD12].Phenotypes[BKKG19, HYL+20, WLHY19, TWZ+14].Phenotypic [PN17]. Phenotypically[QD12]. Phenotyping [CWT+19, ZDL+19].Phi [MPA15]. Phoshphorylation[XTL12c]. Phosphorylation[CRP12, XW16, LWG+14, TAL+15].Phylogenetic[BZ07, BG12, BS07, BGHM09, CRV09,CLRV09a, CLRV09b, CLRV09c, CW12,GH08a, GFS13, GJS11, HvIKS11, HDKS04,Hus09, Jam17, Jam18, JS12, JvI18, JNST09,KL11a, LFK16, LRM12, LHG+16, LCSW18,Mat09, MPKvH09, MNW+04, Mos07,Nak10, PAS+11, PB12b, RdMCBC13,Roc06, SNM08, SDB+07, SWH+12, SSS13b,WLMW+11, WBE13, Wil12, WMS09, ZM12,vIKK+09, vIJJ+20, DNR15, DS14, MW16,Nye14]. Phylogenetics[AR09, Gus09b, HMS09, MBKK18, TM11].Phylogenies [BCVS19]. Phylogenomic[KMSY20]. Phylogenomics[PR18, SZZ+19]. Phylogeny[BBSP08, BFM13, BM13, GG11, HKM+18,MR10, MS10, SM08, SLB+08, WYL07,vIKKS08, KS14]. Physarum[GLL+18, LGZ+17]. Physarum-Based[LGZ+17]. Physarum-Inspired [GLL+18].Physical[BCL13b, GLS+16, WRH+09, KSA16].Physicochemical [ADPH13].Physiologically [VdTVV19]. Piecewise[RBdJ11, ZHZ+20, dJP08].

Piecewise-Linear [RBdJ11, dJP08].Pigeon [ZD17]. Pigeon-Inspired [ZD17].Pipeline[GAJ+18, RAA20, LHN+14, ZMP+14].Pipelines [AL12, Jam13]. PIT [ZGDH16].Plagiarism [NSC17]. plaid [HM15].Planar [GGH+13, SNM12]. Planning[ZD17]. Plant [CWT+19, GPF+20,wTCAK+20, KKC+14, MZL15]. Planted[CW11, DBR07, Tan14]. Plants[DST15a, GF10]. Platform[HG16, PGF18, GMCB14, LLCZ15].Platforms [GLS+16]. Plausible[FHH+11, KP12]. Players [YFCM17].Plexus [WKE11]. Plots [TSMMG+13].PLS [PNP+18, TGGF10]. Pluribus[SLGK17]. Pneumatic [SNC+16]. Pockets[RTA+16]. Point[BCF+07, CW09a, CBM+20, FGKH11,HC07, KKI20, LFF18, RKZ16]. Points[IGA18, PS15, SKK14]. Poisson [WZA07].Poisson-Based [WZA07]. Polarity[GGH+13]. Policies [QD12]. PolyCluster[MW20]. Polymer [GZS12].polymorphisms [GBLZ14]. Polynomial[Gra04, Pol11, vIJJ+20]. Polynomial-Time[Gra04, vIJJ+20]. Polyploid [MW20].polytomy [DS14]. Pooling[Kur13, LLQ20, MDM13]. Pools [GKPS11].Population [CLS19, LLX+11, LHQ+18,LT07, NJMF19, PR18, SLH06b, TBRS11,VdTVV19, ZRK19, LAI+14].Population-Differentiation [ZRK19].Population-Structured [NJMF19].Populations [NGY+16, PPFG20, PN17,SHUP19, Wu10, Wu11]. Position[AH11, GSX+18, JLwC11, PRU11, RW07].Position-Specific [AH11, JLwC11].positional [KD16]. Positioning [CHN+18].Positions [CGZ15, GZGX14]. Positive[CZW+18, LCH19, UJ09]. Positives[HZTP12]. Possibilistic[SKD+07, YCCY20]. Possible [SLH06b].Post [PvRV+20, RCM+19, TSM14].

45

post-processing [TSM14]. Post-Sequence[RCM+19]. Post-Structuring [PvRV+20].Postcryopreservation [NFM+12].posteriori [CZWT15]. Postfix [HEK18].Potent [SYKS15]. Potential[AFAAW+11, HKS11, LH20, SB12, SMSZ17,KPB14, LLW+15]. potential-based[LLW+15]. Potentials [DZ11]. Power[ANR11, ALWG18, PBhL+11, LWM14].power-law [LWM14]. Powerful[AAP06, GDM12, VTGC16, IM14]. PPI[HC19, HC13, LCWZ13, LLW+15, LLNW17,LTRW19, OC13, TDZ+19, VBG+18]. PPIs[LZ18b, ZLZ+19]. pplacer [LFK16].Practical [DBR07, HLY+16, HvIKS11,ME19a, PVB+12]. Practice[SDB+07, BF14]. PRBP [MGXS15]. pre[SYKM17, TSM14, KTLM15]. pre-miRNA[SYKM17]. Pre-miRNAs [KTLM15].pre-processing [TSM14]. Precise[ZANN20]. Precision [SJZ19].Preclustering [HF07]. Precursor[YHYY12]. Pred [KNTB18]. Predator[ZD17]. Predator-Prey [ZD17]. Predict[LSY+20, LZZ+16, WCLY20, WWT+20,ZHG20, TW10]. Predictable [UWLH15].Predicted [CPM18, RSG18, Xu05].PredictFP2 [WWT+20]. Predicting[ATA+17, DZH16, DKDD10, EMDH11,FYSM12, FWY19, FPC20, GJPSV14,GLW12, GED+17, HZW+17, HC17,HLZ+17, HHL+20, HMK+07, JJH12, Jia10,JM12, JHXP15, KKI20, KTLM15, LWL+18,LNC+19, hLMBJ11, LWL+20, PLF12,PLCW17, QWC+16, RMV12, SDH20a,SBM15, TWZP14, TR07, WFD15, WMK16,WCC+18, WYHZ20, WXWL20, WWBZ19,WLL13, YWN+19, YZG+19, YKWK18,YHZ+19, YRD+15, YFWZ16, YFWZ18,ZGC+05, ZLZ+19, ZZH19, ZWXL20, ZXZ20,ZZBH20, ZZDW13, vBdRD+11, BDBH15,GZGX14, XG14, YDW+20]. Prediction[AFAAW+11, AL12, AM12, AAE11, BM17,BYZ+18, BS10a, BM20, CSW11, CC07,

CWL12, CHZ+16, CGW+16, CM16,CGPW06, CYTY13, CBF+18, DNS19,DPS+13, DCM20, DFM+11, DCVC11,EZW+17, FSDR16, FSX19, FB19, FWA10,GSC+18, GZR+18, HZZY16, HEE+18,HZTP12, HYC12, HCLS11, HHCY20,HRdR09, IDD13, JBP08, JLwC11, JQH+20,JKN+12, KCD+12, Kar12a, KS18, KNTB18,KZW+18, KAP+12, KY19, LSMF08,LQV+13, LPH18, LH20, LLRZ15, LLX+16,LYL+17, LC19, LZ18b, LHL+19b, LZQ+20,LBQ+13, LDL+17, LTRW19, MGL+12,MGXS15, MKG20, MP19, MK16, MLZ18,MPM11, MSS13b, MFF+18, NZR11, OM07,PI09, PS19, QL16, QL09, QBPEL12, RLR20,RFFB+20, RP13, SFMS18, SMRP15, STD20,SSS13a, SDH20b, SLRQ19, SYKM17,SWX+19, SWL19, TW10, Val11, WMK17,WL13b, WXS+19, WDH08, WHS04, WZ13a,WWL+17, XHY+18, XPXY11, YXS16,YL12, YRD+13, YSW+17, YWF+20].Prediction [ZLLZ17, ZLH+20, ZD12,ZLY+13, ZLPW16, ZLH+17, ZCG+18,ZZF+19, ZWM+20, ZWL11, ZG19, ZLX+20,ZHE19, ZL15, AJYT+15, AM15, BHW+14,CM15, FHRG14, HRHP16, SEC15, TYA15,WHZ14, YMT+14, YRD+14a, YRD+14b,YLH+15, ZHL+14]. Prediction-Based[BM20]. Predictions[BRZ+17, DPW12, KL11a, NSAH19].Predictive [ALWG18, HW07, LLX+11,VBG+18, AM15, CBN15]. Predictor[MGXS15]. Preferences [SDH20a]. Prefix[KK19]. premature [WDX+15]. PREMER[VBB18]. Preprocessing [ICL11, ZANN20].PreProPath [UWLH15]. Presence[MSG18, DYD15]. Preserve [BMM06].Preserves [RBdJ11]. Preserving[ANR11, BKP+19, BMM08, FZM20,HBM19, RTPM+19, SJNS19, ZDYH17].Pressures [CS15]. Preterm [FMA+20].Prey [ZD17]. Primary [YHZ+19]. Primer[Che16, YCYC12]. primers [CFIS+15].Principal [BKLS18, GPC+20, Han10,

46

dCAR11, LLH+14, Nye14]. Principle[BGHM09, CCYW12, ZWL11]. Principles[PR18, Tho16]. Prior[KB20, TAAP11, ZWHC19]. Prioritization[CM16, CPM18, GSC17, PBV+20].Prioritizing [XPH12, ZZRPZ19]. Priors[BEQD19, ED14]. Privacy [AJM18, ANT19,BBH+18, BKP+19, MZSL19, RCP+18,RTPM+19, SJNS19, WAG19].Privacy-Preserving[BKP+19, RTPM+19, SJNS19]. Private[BKLS18, GFG16, MZSL19]. pro [WFD15].pro-longevity [WFD15]. Probabilistic[BTTR11, BCFCC13, CHL+12, CMQ+16,DHC12, ED15, FFT16, HZZT14, JMA17,JZL13, JFN11, KC11, LEAK11, MHKR12,MPS18, MPSY18, MSS13b, NGY+16,SREK19, SSP+17, TMLI19, TZY11,TDK13a, TDK13b, WPL15, ZK16, FHRG14,GTDK15, PJN+14]. Probability[INT11, CZWT15]. Probe[CZ20, LEAK11, MSH+11]. Probes[HKS11]. Problem [AP07, AKR12, BE08,BEW09, BS11, BMM08, BBK+07, BS08,BODD20, CLH13, CCA12, CC09, CBF+18,DPS+13, GGP08, GRH08, GB10, GG11,HYW08, IMA13, LLT+19, MKS+17,NNSZ07, PHX+08, Pol12, QSJ+20, SZ11,SM08, SK19, SSS20a, WKLL12, Wan16,YHY13, ZW13, dDD18, dNG17, KD15,ARZ+14, Tan14, YHV+15, HBC+11].Problems [BBSP08, BN06, CW11, FM11,LGZ+17, LCC+11, RZMC17, UKV18,WBE13, vIKKS08, vIJJ+20, KS14].Procedure [ICL11, NSNA19, MBS15].Procedures [LGX10]. Process[CGZ15, GLS+16, RdlCGW09, RGCB05,TC13, YBGB10, PRZ+14]. Processes[AAF+13, ABVD12, NFM+12, RKZ16,ZC11, HM15, MCH+15]. Processing[Dem12, GSK13, HCQ14, OLS+13, SSD19,WYWX16, ZDL+19, CFIS+15, MM14a,TSM14]. Processivity [ZLS+19].Processor [RA16, XLZ+15]. Processors

[MTM+15]. Prodrug [MWD11]. Produce[DRS12]. producing [DR14]. Product[CP13, LTM+13, PKM06, SHS15].Production [LCH19]. Profile [HVG04,MGK08, TTWR13, ZZY+17, ZXZ20].Profile-Based [TTWR13]. Profile-Guided[ZZY+17]. profiler [CA14]. Profiles[BGS+12, CMMZ20, CGPW06, HHYH07,IVA11, JQH+20, KCCC15, MSS19a,PKRD12, POS+18, QV17, SSS13b, SB09,WPL15, YLY+12, YOKI09, YCY+14].Profiling[FSMJ05, HCA+10, KKK19, NS19].Profitable [UWLH15]. Prognosis[MCHT17, SZLL11, SWL19, ZLPW16].Programming[BBK+07, BH06, CLH13, CSSS16, CLR10,HT09, MIC+07, OC13, PI09, SLB+08,VKS17, VBG+18, WYL07, WCL11, LV14].Progression [CSSS16, PSS09, RB16, RM18,SSK+20, WGK16, ZLH+17, ZW19].Progressive [GRH08, HVG04]. Project[HLLO19]. Projection [RLV04, WCQ+19].prokaryotes [MBS15]. proline[AJYT+15, YMT+14]. Promising[MKKS20, WLG+14]. Promoter[CFOS06, FLW12, ZZCY10, HPH+15].promoter-RBS [HPH+15]. Promoters[LLTC19, LHL+19b]. Proof [HS08, Roc06].propagating [PRZ+14]. Propagation[HM13, GBLZ14]. Properties[AGGM11, DGY05, DR16, DBK18, KS18,NRV09, RBdJ11, TR13, WLL13]. property[KG15]. property-driven [KG15].Proposal [Pre04]. Prostate[FYZ+19, KCP18, XPH20, ZLXL19].Prostatic [ZLXL19]. Prosthetics[XLZ+15]. ProtDet [LL19]. ProtDet-CCH[LL19]. Protease [AFAAW+11, HHL+20].Protecting [RCP+18]. Protection[MZSL19]. Protein[ASJ+07, AC12, AM12, ADPH13, AAE11,BCS11, BM17, BWC17, BYZ+18, BSV10,BTYC13, BM12, BVN+11, BNV+13, Bro05,

47

CCA12, CLST+13, CC07, CWL12, CHZ+16,CZW+18, CDKT09, CGPW06, CBF+18,CHK17, DLT10, DKCM12, DZA+06, DNS19,DPS+13, DDS+17, DS19, DCVC11,DSCM20, ECK16, EMK18, ED15, FSDR16,FSX19, FJJ11, FMD18, FB19, FWA10,GSC+18, GBS11, GED+17, HBRU13, HK20,HLV+10, HCN+19, HZZY16, HYY11, HC18,HC19, HZL+20, HCLS11, HC13, HC17,HLDZ17, HLZ+17, HYL+19, HMK+07,mHB13, HRdR09, IQA18, IDD13, JJH12,JLwC11, JLYZ16, JM12, JDHL20, KCP19,KL19, KKI20, KAHK+10, KAP+12,KSK+18, LS10, LDS+07, LRM08,LSTW+17, LH20, LFF18, LLH+07, LBL12a,LZ18a, LNC+19, LW19a, LMZ+20, LSY+20,hLMBJ11, LZX20, LLW10, LLZ+13, LL19,LCGW19, LZQ+20, LCH19, LGB15, LCB17,MSZ19a, MGK08, MSJP19, MB20, Mam05].Protein [MK16, MMB+13, MPS18,MCCZC08, MKH11, MCDD12, MSKC19,MPM11, MSS13b, MDM13, NZR11,NHH+17, NLXS19, NWW19, ORCJ13,OM07, OYDZ15, PLF12, PLCW17, PR12,Pol11, Pol12, Pol13, PSN+15, QLZ16,RFFB+20, Roc11, dSRCT+11, RSG18,RSP08, RGN+09, SZ11, SYM+10, SDS18,SN12, SDH20a, SH11b, Shi10, STB+20,SLRQ19, SBM15, Str11, SSFW12, SSF18,TRBK08, TRBK09, Tsa12, VMD+08,VBG+18, WMK17, WLYZ+09, WLCP11,WSX11, WLMW+11, WL13b, WYHD17,WP08, WXS+19, WHKK07, WAK13,WLL13, WLPW16, WOYL17, WZ13b,XHY+18, XPXY11, XTL12c, XGWW19,YHYY12, YHY13, YDM+08, YSGZ20,YKWK18, YHZ+19, YRD+13, YRD+14a,YRD+14b, YFWZ16, ZD12, ZLY+12,ZDL12, ZLY+13, ZWcF17, ZZY+17, Zha18,ZZH19, ZWXL20, ZWM+20, ZZBH20, ZG19,ZWD+17, ZLX+20, ZZDY13, ZZDW13,ZDYH17, AM15, BDBH15, BF14, CWZW15,CR14, CM15, CXS15, DPL+14, DC15].protein [GJPSV14, GAVRRL15, HLW15,

KGK14, KD15, LMZ14, LHWL15, NYOL15,PSK+15, PWZW15, PWC+15, SCC+15,SEC15, TYA15, TAL+15, WL14, WHZ14,XG14, YTLL15, YLH+15, YRD+15, ZMT14,ZZ15, ZWL+14b, ZMC+14, SDH20b,WYHZ20, WSTL+15]. Protein-Binding[ZZDY13]. Protein-DNA[ASJ+07, CLST+13, HLZ+17, LSTW+17].Protein-Ligand [AM12, WLL13].Protein-Peptide [YHYY12].Protein-Protein[AC12, ADPH13, BCS11, BSV10, BVN+11,BNV+13, DSCM20, ECK16, FSDR16,GED+17, HLV+10, HMK+07, JLYZ16,KAHK+10, LSY+20, MB20, Mam05,MDM13, NWW19, OYDZ15, PR12, RSG18,SBM15, Tsa12, YKWK18, YHZ+19, ZLY+12,ZDL12, ZLY+13, ZZDW13, ZDYH17].Protein-RNA[KSK+18, LW19a, WYHZ20].protein-to-protein [XG14]. Proteins[CYJ+19, DBK18, FL18, GAR+09, HCA+10,HLG10, KNTB18, LYW20, LCWZ13,LLX+16, LYL+17, LLNW17, LNC+19,MGL+12, MGXS15, NLGG12, QL16,QWC+16, SKDA19, SP11, SSS+11, SSP+17,Tah18, TR07, WMK16, WBP+12, WLWP12,WKE11, WZ13a, YFWZ18, Zha18,ZXLZ18a, ZXLZ18b, ZXZ20, ZZDY13,ZBFK10, dAc17, DGRC15, GJK15,LLW+15, PWC+15, TWZP14]. Proteome[MSJP19]. Proteomic [MCC16, RLRH18].Proteomics [KBBD+17, PH10a]. Protocol[JHW+19]. prototype [EES14]. Protozoan[GAR+09]. Proximity [ASP20, JCF13].Prune [WM19b]. Prune-and-Regraft[WM19b]. PSAD [ZLXL19]. Pseudo[LLTC19, NLGG12]. Pseudogene [JZW17].Pseudoknot [CC11]. Pseudoknots[Jia10, MWL+12, RAA10, SW17, WHS04,WCLY12]. PSO [SSS+11, AV17, HYW+17,MM14b, ZWL+12]. PSO-based [MM14b].PSPEL [LYL+17]. Psychologically[TNQ08]. Pubcast [GTTR+17].

48

Publications [GTTR+17]. Publishing[Ano13e]. Pull [GZS12]. Pure[BVD+10, BH06, HVG04, ICL11]. Purely[MSKC19]. purification [CWZW15].purification/mass [CWZW15]. Push[HLN20]. Putative[CAN+08, LPH18, SSP+17, YCCM12].PyMut [LHDS18]. Python [CSZ+19].

QSAR [NSMH19, WB11]. Quadratic[FWY19, RFB20, RB14]. Quadruplexes[LBQ+13]. quadrupole [CZB+16].Qualitative [BDS12, INT11, Pau18].Quality [ANR11, BZ10, CLVT+20,GAJ+18, PvRV+20, SGR+17, WLG+14].Quantification [RCBB19, LCOMG14].Quantifying[FLW+14, GF10, SZL+20, ZLH12].Quantitative[AAF+13, ARM+19, BCMW15, BMZM15,CMC+12, FYSM12, IDD13, MVS+13,PLMV12, TRKRC13, RTWR15]. Quantum[Kar12b]. Quartet[BLS12, DLRW18, Rho20, WYL07].Quartet-Based [WYL07]. Quartets[GSB+13, SR10]. Quasi[CAW+19, Kar12a, LLW10, MMB+13].Quasi-Bicliques [LLW10, MMB+13].Quasi-Newton [CAW+19].Quasi-Supervised [Kar12a]. Queries[Jam18, SVM14]. Query[HHSC13, NSC17, PHX+08]. Query-Based[HHSC13]. Querying[BSV10, FPPR11, Jam17, MCC16, QKO18].Quest [DHCW18]. Question [MKS+17].QuickVina [HOS+12a, HOS+12b].Quorum [CZJ17, Kar12b].

r [SIM12, BBH12, VPB15]. R-based[VPB15]. R5 [LSMF08]. R5X4 [LSMF08].Radial [DM09]. Radiation[ZLL+20, SDAA+14]. Radiology[PvRV+20]. RAFP [KNTB18].RAFP-Pred [KNTB18]. Rafts [HBRU13].

Random [ALQ17, ABS17, CMSE+15,CSK+11, Cza18, Gru11, HCMB18, HBC+11,HLHAJ20, ISK18, LZHZ17, LWL+19,MGXS15, PGHT12, PLCW17, RW07,WL13b, WFY+19, WWL+17, XW16,XGWW19, YDW+20, YSW+17, YFWZ18,ZLZ+19, ZHE19, CWZW15, DGRC15,GGZZ14, SHK14, SPWF14, YLH+15].Randomized [AJYT+15, FWXZ19]. Range[HYW08, KL19, MK16, SSKH15]. RANGI[RSJK13]. Rank [CDB+16, HLN20, LC19,LCW+18, WLCX18, WLZ+19, XHQ+18,XLL+18, YZG+17, SFH+14]. Ranked[DRS12, DR14]. Ranking [AM12, DLT10,EFLA08, LJL+15, LL19, LGX10, RMV12,RV13, SPMB13, Tsa12, ZLZ06, ZWSX12].Rapid [PKA20, XLC+15]. rare [LLH+14].Rarely [LGW20]. Rate[AGMP09, GGP08, GCB+18, HLM+13,HZL+20, JS12, LKY+11, SS04, XSS17,YAB13, ZMT13, CWDS15, ZMT14]. Rates[EW04, HB11, GJY+14].Rates-across-Sites [EW04]. Ratio[SBW15, WM19a]. Ratios [KMSY20]. Raw[STB+19]. Ray [Str11]. RBioCloud[VPB15]. RBS [HPH+15]. RDCurve[LGX10]. Re [YLXS17]. Re-Mapping[YLXS17]. Reachability[GTDK15, Gos11, LT17]. Reaction[BBW18, FMRS18, FZWS17, HLM+13,HM13, LR20, MKKS20, MDPR18, TLSA18,TZP17, VSR+06, SYV14]. Reaction-Based[LR20]. Reaction-Diffusion [FZWS17].Reactions [BCFCC13, DB14, XLC+15].Reactive [GLS+16]. Read[AKLJ17, JZW17, AKD17, LKW+19,LLL+20, LWS+20, MTM+15, ML18,TED+12, TC16, CWLZ14, FSL+15].Readable [HLG10]. Reading[GGP08, LJ20]. Readmission [WCC+18].Reads [CBK20, KK19, LZL+20, LLBL20,PS11, STB+19, WLL+20, ZFZ+20, FSL+15].Real [GPC+20, HG16, LKW+19].Real-Time [GPC+20, HG16].

49

Rearrangement[BMM06, BFM13, CZF+05, FM11, HWS+18,MMS10, MS10, ZZS07].Rearrangement-Based [BFM13].Rearrangements[BG05, FM13, HBM19, BS15]. Reasoning[BDS12, BD19]. Reassortment[BJ10, BPJ12]. RecA [SB12].Recalibration [BM08]. Receiver[WLA+13]. Receptor [HBRU13, STT+14].receptor-ligand [STT+14]. Receptors[ISK18, KAL+17]. Recipe [LLX+11].Reciprocal [QLLX10]. Recognition[ASJ+07, AV17, FLW12, HLSR18, HGC+20,LJ20, LCGW19, TGLP16, VKS17, Xu05,ZZCY10, ZCWW19, DPL+14, HK15,MNA14]. Recombinant [Wu11].Recombination[BB04, NNSZ07, NLHL17, GJY+14].Recombinations [PBJ12]. Recommender[WLCX18]. Reconciliation[GET13, KB17, KB19, LCEMO18, LB19,USMS19, WHBM15, ZZ14].Reconciliations [DHC12, HZR+19].Reconciling [Wil09]. Reconstruct[AJD+12, BA18]. Reconstructibility[MNW+04]. Reconstructing[CW09b, HMW+12, HvIKS11, KP12,NNSZ07, SW09, TBRS11]. Reconstruction[BM13, CDB+16, CH11, CXW+13, GPF+20,HAK+12, HWPE17, IGA18, KSMT19,LHH13, LLZ+13, LCSW18, PKA20, Roc06,SDB+07, Str11, VMD+08, WYL07, CXS15,HZZT14]. record [Jam15]. Records[HXXJ18, SGR+17]. Recovering [YHCS19].Rectangular [GZS12]. Recurrence[SMRP15]. Recurrent [CC07, HB05,SDH20b, XL16, XLW20, XWF07].Recursive [LZX20, LHY+11, MT11].redesign [STT+14]. Redesigned[NLW+18]. Reduce [MTNH17, SSD19].Reduced [BPP+13, CLRV09c, HZTP12,Nak10, PB12a, SSS+11]. Reduced-Order[PB12a]. Reduction

[BHMA06, LRM08, MBKK18, Pau18,RBdJ11, ST05, SCCDK09, YLC20].Reduction-Based [ST05]. Redundancy[FW20, LLC+13, WSX11]. redundant[MM14b]. Reference [AAH+18, PS11].Referential [WL13a]. Refine [XLL19].Refined [LNC+19]. Refinement[LCLL10, MDPR18, PCDP18].Refinements [BvdGK+11]. Refining[WMS09, ZM12, ZZH18b]. Reformulated[GLS+16, SPMB13]. Reframed [GJZH17].Region [BdOS+18, MYCW12, OLS+13,SKDA19, GBTL14]. Regions[BTYC13, CRK+19, CAN+08, HHSC13,LZ18b, MK16, MCCZC08, PWT10, SSS20b,TWG+12, YNWC07, ZKP+07].Registration [MCRC17]. RegNetC[NCMCAR15]. Regraft [WM19b].Regression[AGGM11, AAT20, BTTR11, BEQD19,CSK+11, EMDH11, FYSM12, GCB+18,JHW+19, LW19b, MLZ18, PSIM17, PNP+18,QL09, ST05, SZLL11, TGGF10, WGX+17,WXWL20, WP08, YZG+17, YLH+15].Regular [ARM+19, SNM12, Wil11].Regularisation [DCM20, HLHAJ20].Regularization [JHX17, LCW+18,MHHJ20, ZYW+13, JHXP15]. Regularized[EZW+17, LWG+18, MLZ18, TGGF10,WLG+16, WCA+19, WLZ+19, ZDL12,ZLH+17, ZWXL20, CR14, Mir14].Regulating [MVW+13]. Regulation[BCL+13a, DS19, DBTB09, Gou06, KCCC15,LCH19, LLA19, PAAG07, WMWA12, KD16].Regulations [LCZN16]. Regulators[HL16]. Regulatory[ARK20, AOSN+18, AGAS18, APPG18,BGHC20, BMK11, BGS+12, BA18, CDB+16,CXW+13, CMMZ20, CHW+18, EAS13,FZWS17, FWXZ19, FKB19, FSD+11,GPZ20, GHL05, HL16, HLY+16, INT11,IBN19, IL18, JSS+18, JZS+18, KBNHD18,LL11, LCZN16, LT07, LHC18, MTSCO10,MSS19a, MPP+20, NRV09, NI07, NSNN12,

50

PB12a, PM20, PCDP18, PKA20, QD12,RC11, RST10, RRTB12, RMS15, SV16,SPA17, TAAP11, VRK12, WLL+09, XWF07,YCCM12, YGY+19, ZZKW18, ZM12,ZWZ16, ZWHC19, ZSD08, ZZH18b, dJP08,CZWT15, DYD15, GGZZ14, KKC+14,LLL16a, MM14a, RHH16, ZWC15].Regulon [OMAdG+12]. Reinforce[TDZ+19]. Reinforcement [IBN19]. Reject[QBPEL12]. Rejection [YBGB10]. Related[AC12, FFT16, HYR+19, JZSZ12, JZZQ19,MYCW12, PL17, PZH20, RYK+19, WWC18,XYYZ20, MFS+15, SFH+14, Tah14].Relation [ZYN+19]. Relational [KHO+20,RBdlVMPG16, SKD+07, GJPSV14].Relations [HL16, NAHT+20, HK15].Relationship [YNN+18]. Relationships[CCCY20, LHH13, LNC+05, PZWC20,YPS11, GJPSV14, LKLB14]. Relativity[CLH+15]. Relaxation [AKR12]. Relaxed[ZGDH16]. Relaxing [BCVS19]. Release[JLW17]. Relevance [MBGP12, MBP+19,RYK+19, SW17, BCLC15, LHWL15].Relevant[AGGM11, KTLM15, SDN+11, ZOZ10].Reliability [LEAK11]. Reliable[CBZ18, GJY+14, SDAA+14, WLCX18].Remodeling [PLMV12]. Remote [LL19,LCGW19, LGB15, LCB17, Sen19, DGRC15].Removal [HCLS11]. Removing[WSX11, ZZS07]. Renal [DCHW17].RENNSH [MRB12]. REPA [PIPC18].Repairing [CDB+16]. Repeat[KVX12, ZKP+07]. Repeated [PCGS05].Repeats [CW09b, SS06a, TDA+09].Replacement [MRK18]. Replicated[LLHF15, SVZ09, SGK12, ZAZ11].replicates [PJN+14]. replication[RB14, SSML15]. Reports [PvRV+20].Repositioning [LWL+19, RV13, WCQ+19].Representation[CZ20, CL08, HLDZ17, JLH16, JHX17,KY19, LCB17, LW13b, SSDN12, WLHY19,WLZ+19, WCLY20, XHQ+18, YXS16,

YZG+17, ZLW+11, ZZN+11a, SXL+14].Representations[DLRW18, SGR+17, ZYN+19].Representative [IMA13]. Represented[SSS+11]. representing [KGK14].Reproducibility [EFLA08].Reproducibility-Optimized [EFLA08].Reprogramming [MSP+19]. Repurposing[WLCX18]. requirement [DNR15].Reranking [YHYY12]. Resampling[LLHF15]. Rescue [DSZ+06]. rescuing[FSL+15]. Research [BPRZ11, CZ12,HMZ17, HLSR18, MPZ07, MPZ08, MPSZ09,MWZ13, MSZ19b, MNPZ10, MSS+13a,UBP+19, CEG14, SVM14]. Reserve [BS08].Residual [FSX19]. Residue[CD08, GBLZ14, MGXS15, MZS+16,TRBK08, TRBK09, ZG19, ZLX+20].Residue-specific [GBLZ14]. Residues[CWL12, CDKT09, GLW12, HLZ+17,KSK+18, LBL12b, MGL+12, WZ13a,YZG+19, ZCG+18, FLW+14]. Resistance[AHT+18, DCM20, KS18, MWZY17].Resistant [MWD11, FN14]. Resists[RKDR10]. Resolution [DPW12, HCLS11,LDS+07, MRB12, MKS+17, CV14].Resolving [MBJ19]. Resonance[AAG+18, WL07, CZB+16]. Resource[LHG+16, NSNA19, ZS18].Resource-Efficient [LHG+16]. Resources[XLL19]. Respect [RV13]. Respiratory[RSCX18, SNC+16, XHY+18]. Response[BMH+16, CCCY20, CRP12, GBB+11,RBdJ11, SdOD+12, SSD+16, TC13, UKV18,ZLL+20, GCC+14, HPH+15, MZL15].Responses [KG12, TWZ+14]. ResSeq[FSL+15]. Resting [JHZL19].Resting-State [JHZL19]. restricted[SHK14]. Resulting [SSS+11]. Results[JNST09, RZMC17]. Reticulate [CW12].Reticulation [vIJJ+20]. Reticulum[LLES18]. Retrieval[SK12, XLL+18, XLL19, CWDS15].Retrieving [MCDD12]. Retrospective

51

[ZLXL19]. Retroviral [AD12].Retroviruses [WWT+20]. Reusable[HT09]. Reveal [QTZ15, WL14]. Revealed[CBM+20]. revealing [MEOL14]. Reveals[LGN+19, WWL19, YCCY20, YCCM12].Reversal [BMM08, BODD20, MMS10].Reversals [BBCP07, BMM06, BSST08,DST07, GBD17, HZL19, Wan16]. Reverse[BGS+12, INT11, LLA19, RPB+13,SdOD+12, SYKS15, TSM14].reverse-complement [TSM14].Reverse-Engineering [INT11, LLA19].Reversible [GZS12]. Review [AMHH16,CSK+11, JDHL20, SGH12, KSM14].Reviewer [Ano10a, Xu14b]. Reviewers[Ano06a, Ano08b, Ano09a, Ano13a, KL11b,IEE05, IEE07, XTL12b, Ano16]. Revisited[DCVC11, Pre04]. Reviving [MPY18].Rewiring [TOYHZ19, XOYHZ18]. RF[ISK18, SDTK19]. RF-NR [ISK18]. RFCM[PM20]. RFE [TZH07]. RFLP[Che16, YCYC12]. Rhythm [KM20].Ribosome [MT12b, MT12a, RZMT15,ZMT13, ZMST18, ZMT14]. Rich[MP19, YSC13]. Ring [RZMT15]. Risk[JQH+20, MLZ18, LLRZ15]. RJMCMC[MBJ19]. RJMCMC-Based [MBJ19].RLIMS [TAL+15]. RLIMS-P [TAL+15].RMSD [WS08]. RNA[AM19, AS05, ABH+14, AALD17, BDD+10,CLC+17, CBK20, CZM+18, DBZ12,FSB+11, GzS11, HSTW06, HVG04, HS15,Jia10, KSK+18, LQV+13, LHTT11, LH20,LTaS13, LHN+14, LW19a, LHHL19,LXG+16, LZZ+16, LYY+19, LBQ+13,LTRW19, MGXS15, MIC+07, Mne09, NA11,NSAH19, RAA10, RP13, SW17, SDH20a,SDH20b, STB+19, Smi09, TW10, WS12,WYHZ20, WDH08, WHS04, YWW20,ZHEB05, ZZ20, ZWXL20, ZFZ+20].RNA-Binding [MGXS15]. RNA-Protein[SDH20b]. RNA-Seq[LXG+16, STB+19, WS12, ZFZ+20,LYY+19, LTRW19, CBK20, LHN+14].

RNA-Sequencing [YWW20, ZZ20]. RNAi[AAH+18, OC13]. RnaPredict [WDH08].RNAs [SLW15, WCLY12]. RNN [BA18].Roadmap [MPS18]. Robinson[CLRV09a, CBFB12]. Robots [TDY+18].Robust [BKKG19, GCL+18, GLG10,JZS+18, KNTB18, LT17, LZ18a, LZH18,LHZ+19, PLC+20, RFFB+20, SZ11, SJS19,SGK12, TGD+16, VdTVV19, VRK12,WZJH12, WLG+16, WCMB19, YM11,ZHJ17, MMSH14, RHH16, SXL+14].Robustness [ALWG18, KKC16, TC13,USMS19, Wil09, pD20, MG14]. ROC[Dal16]. ROC-Based [Dal16]. ROI[HYR+19]. Role[HBRU13, RBB+19, WWBZ19]. Root[MVW+13]. Rooted [GJS11, Hus09, SR06].Rosette [DST15a]. Rough [MP13, MZL15].Rough-Fuzzy [MP13]. Routing [GCL+18].RPCA [LXZ+15]. RPCA-based [LXZ+15].rRNA [LW13a]. RS [SHK14]. rSPR[CHNW20]. Rugged [RJNN18]. Rule[BU17, DMD13, FL18, HLG10, JRSS18,MC07, Val11, TAL+15, WSTL+15].Rule-Based [BU17, FL18, TAL+15]. Rules[AMGC16, GBB+11, NZR11, PAAG07,SDN+11, YL12]. Rumen [ZWDR20]. Run[QD12].

S [LWZ12]. S-System [LWZ12]. S2[BCMW15]. Safely [ST19]. SAFETY[SAM+19]. Sample[ALQ17, BB04, CLZ+18, HC07, LLH18,PH10a, PH10b, SLH06b, YHB12, GRDV14].Sampled [AGAS18, CSSS16].Sampled-Data [AGAS18]. Samples[CMQ+16, HKM+18, LWG+18, WLZ+19,XLW20, ZLZ06, ZHJ17, RHK14, XLWL15].Sampling[AM19, BO12, HLHAJ20, MMS10, MSS13b,RJNN18, SN12, TGLP16, TRBK09,ZZY+17, ZLZ+19, ZZZW19, SHK14].Sampling-Based [TGLP16]. Sapiens[LUdSCH10]. SARNA [TW10].

52

SARNA-Predict [TW10]. SAT [DT11].SAT-Based [DT11]. satisfying [TSM14].Saturation [ACP10]. SBML [CPQ08].Scaffold [JZSZ12, LJZZ13]. Scaffolding[LTL+19, LCSW18]. Scaffolds [RBB+19].Scalable [BZ08, GZG17, GMP08, KG20,PZS+20, SDAA+14]. Scale[ALR+13, BBH+18, DSHM08, DWSB11,FWXZ19, GJZH17, GSX+18, GHL05,HAK+12, HZW+17, JGBR15, JLYZ16,LFK16, LSY+20, MPA15, MKKS20, OC13,PZS+20, QBPEL12, SSS20a, SDH20b,TBRS13, YLL+06, ZZF+19, IM14, SHK14].Scale-Invariant [LSY+20].Scale-Space-Based [YLL+06]. Scaled[AC12]. Scales [SHUP19]. scaling[AMBK14]. Scalogram [NVSH18].Scattered [MZ17]. Schafer [RGI13].Schema [STB+20]. Scheme [HZL19,NHH+17, PPM+13, SSS13b, ZCG+18].Schemes [KK08, LRM08, OM07, ZWL14a].Schizophrenia [DHCW18, WHF+20].Schmidt [GZG17]. science [IM14].Scientific [HVD18]. SCJ [FM11, LLT+19].SCOP [AV12]. scope [HWK14]. Score[JNST09, Roc11, Tsa12, LJL+14]. Scores[CLST+13, SSK+20, WOYL17, XPH20,ZLLZ17]. Scoring [AM12, Csu04, GZFT15,JLwC11, JBgLS19, KK08, LLZ+20a,MSKC19, PSN+15, AM15, OFC+14, RB14].Screening [HF07, RAA20, SDTK19, UJ09,GCC+14, KKC+14]. Screens [STB+20].SCS [FLW12, ZZCY10]. SDE [MCH+15].SDMF [SB16]. Search [AKS13, ARP+16,BG05, Bro05, CCA12, CBFB12, DBR07,FLM+16, FS18, HZZY16, LFS06, LTaS13,ME19a, ME19c, MSS13b, MWSM12, NI07,PG12, SZ11, SS04, Smi09, SMSZ17, SJNS19,SB09, TDY+18, Zha07, ZWcF17, ZKW19,dJP08, CM15, DGRC15, KFHK14, LMZ14,SHK14, SSKH15, Tan14, YHV+15].Searches [BEW09, CW07, CWDS15].Searching [DWZ+15, GZC+17, KP12,MWL+12, RBdlVMPG16, TZY11, ZHEB05].

second [BCMW15]. Secondary[AS05, AL12, BRZ+17, CC07, CGPW06,HVG04, Jia10, KAP+12, LZZ+16, LBQ+13,NA11, NZR11, NSAH19, RP13, TW10,WDH08, WHS04, ARZ+14, SEC15].Secreted [SSS+11]. Secretion[RSCX18, SZCX19]. Secretory [DADF+10].Section [BLP18, BPW17, BPRZ11, Cas07,CZ12, FS12, FS13a, FJJ18, GH08b, GJH19,Gus09b, GM16, HMZ17, HBG16, HBG17,HBG18, HBG19, HBG20, HMS09, KJ04,KJ05, MPZ07, MPZ08, MPSZ09, MWZ13,MSZ19b, MNPZ10, MJ18, RZF07, TS17,TS18, TH18, WYWX16, WLWN17, YS17,ZC15, dSK13, CEG14, LW15, MKARB16,PR14, SA15, XHS15]. Sectional [WGK16].Secure[JHW+19, RTPM+19, SAM+19, SJNS19].SecureLR [JHW+19]. Security[AIS+16, AJM18, RCP+18, Sen19, KSA16,MKARB16, ANT19]. Seed[HAH13, LLH+17]. Seed-Extension[LLH+17]. Seeded [LPR+08]. Seeds[Bro05, RGN+09, TC16, Zha07]. Seeks[Ano12b]. SeeSite [LKLB14]. SEGA[MKH11]. Segment [Csu04, ZCWW19].Segmental [CGPW06, FM12].Segmentation[ALR+13, DPA+17, PWT10, DPL+14].segmentation-based [DPL+14].Segmentation-Free [ALR+13].Segmented [BJ10]. Segmenting[BdOS+18]. Segments [YXS16, NYOL15].Seizures [ZHG20]. Select[KCP18, LLZC12, WB11]. Selected [Cat17,HCQ14, Kim18, LC10, YGFC20, AS15].Selecting [HKS11, KTLM15, LLC+15].Selection[AV17, AWW18, AMHH16, AAT20, ASI+11,ACWW05, ACWW07, BHHMCL16, Bon07,BS08, BCL13b, BHP19, CLVT+20, FYSM12,GZG17, GCB+18, HYW+17, HLL+18a,HLN20, HDS+18, HC07, LTM+12, LH10,LLC+13, LW17, LDM18, LPH+13, LW19b,

53

LHH19, LSB+11, LHY+11, MT11, MCRC17,MCHT17, MBF+11, NPD+17, NO09,OLZ11, PGHT12, PBhL+11, RM13,SMRP15, SLX+18, SIM12, SZLL11, TZH07,TZ16, WSX11, WL13b, WLG+16, WXS+19,WWC18, YM11, YZG+19, YHB12, ZLPW16,ZwGC17, ZCR+17, ZRK19, ZKL18,ZWY+10, BCLC15, HRHP16, HLW15,LLRZ15, LJL+14, MZL15, MMSH14,WFD15, YCY+14]. Selectivity [VKS17].Self [CMC+12, GF10, LYL+17, WZA07,WMWA12, XHQ+18, YWK+07, YMW+12].Self-Adaptive [YWK+07]. Self-Assembly[CMC+12]. Self-Boosted [YMW+12].Self-Interacting [LYL+17].Self-Nestedness [GF10]. Self-Organizing[WZA07]. Self-Regulation [WMWA12].Self-Training [XHQ+18]. Semantic[CLH+15, DKDD10, DBK18, GM16, IQA18,JZL13, MCC16, SSP+05, XLL19, YFWZ16,HK15, JC15, SLS+14]. Semantic-Based[GM16]. semantically [Tah14]. Semantics[FMRS18, GzS11, HS09b]. Semi [AMHH16,DGV+17, HF12, JM12, KL11c, YCY+14].Semi-Automated [DGV+17].Semi-Markov [KL11c]. Semi-Supervised[AMHH16, HF12, JM12, YCY+14].Semiglobal [COW20, MKH11].Semisupervised[FSMJ05, KC11, LHLY11, LTL+07, XAW07].Sense [HVD18]. Sensing[CZJ17, Kar12b, MDM13, GFG16].Sensitive [HB11, MKG20, Wan12,WCC+18, WZ13a, LJL+14]. sensitivities[SYV14]. Sensitivity [ATA+17, HYW+17,PSIM17, WXWL20, XZG+18, BHW+14].Sensitivity-Based [XZG+18]. Sentence[NAHT+20]. Separability [MT11, UC10].Separable [LWZ12]. Separated [Pol13].Seq [LYY+19, LTRW19, CBK20, LHN+14,AALD17, CZM+18, LXG+16, STB+19,WS12, ZGDH16, ZFZ+20]. Seq2seq[KKI20]. SeqDB [How13]. Sequence[AH11, AGMP09, BAK06, COW20,

CCYW12, CLW13, CHZ+16, CWLS15,CGPW06, DSZ+06, DK17, DK13, FS18,HB05, HZTP12, HT09, HPL+13, HLZ+17,HYZ16, HLG10, IGM+07, IQA18, JL10,KPP19, KCD+12, KS18, KK08, Kuk13,KMG+05, LN17, LPH18, cLWA07, LCGW19,MWL+12, MGL+12, NNSZ07, NP13,NSZK15, PLF12, PS11, POS+18, PT09,RW07, RCM+19, dSRCT+11, SLH+06a,WLMW+11, WYHD17, WXS+19, WZ13a,WCXL18, XHY+18, YZG+19, YHZ+19,YH13, ZANN20, ZWcF17, ZLX+20, CV14,GJPSV14, MBS15, PSK+15, STT+14,SPWF14, YTLL15]. Sequence-Based[CHZ+16, HLZ+17, LPH18, MGL+12,WXS+19, WZ13a]. sequence-independent[PSK+15]. Sequence-Order [LCGW19].Sequence-Specific [AH11]. Sequences[Bi09, CW07, CZ20, CFOS06, CWLS15,CLS19, CAN+08, CHK17, DSVMM18,FM12, HC17, HLDZ17, HLH11, JDHL20,Kar12a, KWL07, KC11, KT07, LPH18,LLW+11, LYL+17, MRK18, MIC+07,PFJ+19, RH05, RFFB+20, RLV04, RA16,SIK20, SLH06b, TED+12, WL13a, WKLL12,Wan12, WCLY20, Wu11, ZWZS16, ZGZ+20,CR14, DKS+15, GAVRRL15, LZGZ14,WL14, YlCW+15]. Sequencing [AKR12,BBN18, CH11, FS13b, HG16, AKD17,KSS15, Kur13, LMZL17, ML18, OLS+13,PNP+18, Pre04, TWW+20, WM19a,WPL15, YKW17, YWW20, YWW+18,ZZ20, FSL+15, WLC+15, XZY+14].Sequencing-by-Hybridization [Pre04].Sequential [AKV16, KCZ+15, MSP+19,WL07, YLL+06, ZWZS16]. Serial [WZA07].Series [BMK11, EAS13, HAH13, KSB12,KMG+05, LLL15, MTSCO10, PH10b,RMS15, SC11, WLL+09, WGP11, ZZKW18].Serum [RTA+16]. Server[XYYZ20, LBL+10]. Services [KPP19]. Set[AFAAW+11, BGHC20, BSV10, DRS12,FLAM15, HYY11, HMK+07, LZH18,NLGG12, SMSZ17, WYL07, XLZ+15, YSC13,

54

YNN+18, BM15, DB14, MZL15, WLG+14].Sets [AJD+12, BKP+19, BMHS13,BNV+13, Csu04, Cza18, DK17, DG19,GLG10, HS08, HC07, KNS+05, KBSCZ12,LWS+20, OMWX09, PAS+11, Pol13,RBdlVMPG16, RGCB05, SSS+11, SMK+12,UC10, WZZ+18, WCQ+19, YC08, ZWW17].Several [FM11]. Shannon [DGH+06].Shape [ADPH11, ADPH13, ARP+16,DZA+06, GAGM11, Mat07, Str11].Shape-Structure [DZA+06]. Shaped[AKS20, BG13]. Share [LBL12b]. Sharing[NGY+16, WAG19]. Shaving[GLG10, SDCW11]. Sheet [AAE11, DNS19].Shewanella [DS19]. Shifting [AMBK14].Shifting-and-scaling [AMBK14]. Shock[CRP12]. Shoot [GPF+20, TRKRC13].Shorelines [vIKKS08]. Short[AKLJ17, GBD17, JL10, KK19, LEAK11,LKW+19, LL19, MTM+15, Roc06, SC11,SSS20b, TR07, TED+12, WLL+09,WCLY20, ZLX+20, FSL+15]. Short-Read[LKW+19, TED+12, FSL+15]. Short-Term[LL19, TR07, ZLX+20]. shortest [ARZ+14].Shotgun [ZKP+07]. Show [SYKS15].Shrinkage [MRS09, WDS+12]. Shuffled[HDS+18]. Side[AD12, JQH+20, LBL12b, GBLZ14].Side-Chain [LBL12b, GBLZ14].Side-Effect [JQH+20]. Sided [QSJ+20].Sigma [LHL+19b]. Sigma-54 [LHL+19b].Sigma70 [LLTC19]. Signal[BZ10, FLW12, HCQ14, Kar12b, LZL+19,TP18, WPL15, ZZCY10, SB16]. Signaling[AJD+12, AAH+18, ED15, FKLS07,HAK+12, KKC16, LLZ+13, OC13, RAM17,YOGY11, ZZ13, CXS15, LP15]. Signalling[HLLO19, LCH19]. Signals[HLH11, RH05, MEOL14]. Signature[CBZ18, SMRP15, KGF+14]. Signatures[DST15a, PN17]. Signed[Gru11, HZL19, LNW20, OYDZ15].Significance [AH11, MS17, PBV+20, WS12,ZLZ06, FLW+14]. Significant

[PRU11, YNWC07, Tah14]. Significantly[AAP06]. Silico[DMD13, LYL+17, PG12, VDS+20, SYKS15].SimBioNeT [DFTC12]. Similar[AFJ12, LBL12b, MP13, PB19, WL13a].Similarities [CWLS15, LWL+18, VSKJ11,YWN+19, YDW+20]. Similarity [ARP+16,CC11, CLW13, DBK18, FS18, HC14b,HLDZ17, HYZ16, IQA18, KPW13, MS17,NWZ+20, NWW19, PKM06, RBdlVMPG16,SZZ+19, STD20, SSP+05, WLYZ+09,ZHJ17, ZKW19, ZDYH17, BM14, CM15,JC15, KFHK14, LMZ14, SLS+14, YTLL15].Similarity-Based [STD20].Similarity-Constrained [NWW19].Simple[GDM12, MWL+12, PK13, GJPSV14, IM14].Simpler [CMS12]. Simplification [WZ13b].Simplified [BBK+07, FS18]. Simplifies[FM11]. Simulated [BA18, TW10].Simulating [BBH+18, SH11a]. Simulation[BU17, CP13, CHC+05, GLS+16, GPZ20,JGBR15, KAL+17, LKW+19, LZZ+16,MS11, MBGP12, PTM+19, PZS+20, SJZ19,TZP17, ADTAQ16]. Simulations[ACCT20, CNM11, Dem12, LR20, RTA+16,SCM19, KD16]. Simulator[DFTC12, VdTVV19]. Simultaneous[CDW12, THL11]. SINE [AD12]. Single[ABS15, BFM13, CSSS16, CBM+20, GGP08,Gou06, KBND19, KKI20, LLH18, SSS20a,WWLL16, XWC15, ZLXL19, ZZ20, SXL+14].Single-Cell[CSSS16, CBM+20, KBND19, ZZ20].Single-Center [ZLXL19].Single-Cut-or-Join [BFM13].Single-Dimensional [WWLL16]. singleton[KH14]. Singular[FWXZ19, LLL16b, XL16, YWK+07].Siphon [BRS18]. siRNA [QL09]. Site[CHZ+16, JFR+19, JLW17, KCD+12,KL11a, MWZY17, WLL13]. Sites[BYZ+18, BCVS19, EW04, GLW12,HHL+20, Kar12a, LPH18, LFF18, NHH+17,

55

PLF12, QWC+16, SDH20b, SBM15,WXS+19, WHKK07, WPL15, Wu10, XW16,ZZH19, PSK+15, RB14]. Situ [LHCL20].Sixth [FJJ18]. Size[ALQ17, LLH+17, RRTB12].Skeletonization [ALR+13]. Sketch [GK19].Sketch-Based [GK19]. Sleep [SGP+20].Slice [AAG+18]. Slice-based [AAG+18].Slide [XPH20]. SLIDER [BVN+11].Sliding [dSRCT+11]. Slowly [MMS10]. SM[LZL+19]. Small [ALQ17, AFAAW+11,HC07, LYK07, LLT+19, NNSZ07]. Smallest[GJS11]. Smoking [WQY18].Smoking-Induced [WQY18]. Smoldyn[Dem12]. Smolign [SSFW12]. Smooth[ZmCXS17]. smoothed [MEOL14].SMT-based [KH14]. SNP[CSK+11, Che16, DWZ+15, FYSM12,GGP08, LLC+15, Wu11, XZY+14, YCYC12,YLCC13]. SNPs [LLC+13, LLZC12]. Soft[LCB17, MDH11, RP13, FHRG14].Software [Ano13b, Ano13c, CM15, GSK13,AKD17, MZ17, XHS15]. sofware [Ano13d].Solid [KHP12]. Solution [BSST08,HLM+13, SSS20a, LV14, XLC+15, SAM+19].Solutions [AM19, BLS12, ST19, WOYL17].Solvent [GSC+18]. Solving [BMM08,LGZ+17, ARZ+14, PHX+08, TGP+15].Somatic [KCZ+15]. Some [BvdGK+11].Sorting [BBCP07, BSST08, BS15, EH06,GBD17, HZL19, HBM19, MR10, QLLX10,Wan16, dDD18, ZZ14]. sound [BCMW15].Source [PSPM20, YSW+17].Source-Target [PSPM20]. Sources[JSA08, LZHZ17, RM18]. SP [ADPH13].SP-Dock [ADPH13]. spa [AKNB07]. Space[AKS13, BPV+11, BSST08, DKCM12,DHC12, GLS+16, HZR+19, HZZY16, LR20,Nak10, NSNN12, OP11, YLL+06, ZZY+17,LHS16, SHK14, BU17]. space-efficient[LHS16]. Spaced [Zha07, LMZ14]. Spaces[DSZ+06, HEF17, YDM+08]. Spanning[HEF17]. Sparse[BBH12, CCCY20, CDB+16, Che10, CZX19,

FYSM12, GCB+18, HYR+19, JFN11,KSN+12, LDM18, LLT10, LXG+16, MLZ18,SdOD+12, TP18, WHXS17, WHF+20, XL16,YXS16, YCCM12, YZG+17, ZDL12,ZmCXS17, ZRK19, ZZN+11a, SXL+14].Sparsity [NSNN12, MMSH14].sparsity-inducing [MMSH14]. Spartan[ATA+17]. Spatial[BU17, CSZT19, HKT+18, JL10,LUdSCH10, LW18, LMZ+20, LCOMG14,RKZ16, SSFW12, ZHZ+20, ZYF+18].Spatial-Temporal [ZYF+18]. spatially[ZMC+14]. Spatio [SDA+06].Spatio-Temporal [SDA+06]. Special[Ano09c, Ano12a, Ano13d, Ano13b, Ano13c,BLP18, BPW17, BPRZ11, Cas06, CZ12,FS12, FS13a, FJJ18, GH08b, GJH19,Gus09b, GM16, HMZ17, HBG16, HBG17,HBG18, HBG19, HBG20, HMS09, KJ04,KJ05, MPZ08, MPSZ09, MWZ13, MSZ19b,MNPZ10, MJ18, TS17, TS18, TH18,WYWX16, WLWN17, WH11, YS17, ZC15,dSK13, CEG14, LW15, MKARB16, PR14,SA15, XHS15, Ano05b, Cas07, LNY05b,LNY05a, MPZ07, RZF07]. Speciation[ZZS18]. Species[ADR18, DRS12, DR16, DHC12, KHO+20,LB19, MSG18, SRM18, VRJ+10, Zha11,wTCAK+20, DR14, HWK14].Species-Based [VRJ+10]. Species-VOC[KHO+20]. Specific [AH11, ABVD12,CSS11, JLwC11, MSQ18, MSS+19b, MB16,RB16, XLZ+15, YKWK18, ZCG+18, ZHE19,GBLZ14, MZS+16, MEOL14]. Specificities[LLX+16]. Specificity [FW20]. Specified[ZWL11]. Spectra[BM08, BKR11, LMZL17, OG11, SLL+19,YKW17, ZGC+05, ZGB+12, DST+15b].Spectral [FLAM15, SSDN12, SH11b,WNT+17, YLY+12, ZHJ17, ZYW+13].Spectrometry [ASI+11, BBN19, HYY11,KSS15, PH10a, SN12, YMW+12, ZLW+11,CWZW15, KGF+14, SHK14].Spectrometry-Based [SN12].

56

spectroscopy [CZB+16]. Spectrum[KSS15, Pre04, SVdSS+18]. Speed[BE08, TC16, WYHZ20]. Speed-Up [BE08].SpeedHap [GGP08]. SPF [HKT+18].SPF-CellTracker [HKT+18]. Spike[HLL18b]. Spin [AAG+18]. Splice[KCD+12, LKLB14]. Spliced [RLRH18].splicing [LKLB14]. Spline[ZXB11, ZSY+14]. Split [BG12, MPKvH09,PB12b, SNM08, SNM12, BCMW15]. Splits[ADR18, DH04]. Spots[LZX20, SP11, ZLZ+19]. SPR [CCLS13].Spreadsheet [VSR+06]. Spring [DABV17].Spurious [ZZDW13, ZDYH17]. Square[Cza18]. Squared [CD08]. Squares[FYSM12, LN13, WWC18, MBS15].Squares-Based [WWC18]. Stability[CXW+13, FZWS17, HLG10, KKI20, LFK16,LGX10, MT12b, ZLH12, ZWZ16, ZL15,ZWC15]. Stability-Based [CXW+13].Stabilization [AGAS18]. Stable[CBZ18, LCH19, SMRP15, Wig15, YHB12].Stacking [SSD+16]. Stacks [MCRC17].Stadiums [Cza18]. Stage[HLL+18a, HHYH07, HGC+20, KKK19,TZH07, ZWM+20]. Stage-Dependent[KKK19]. Stages [DCHW17, SGP+20].Staphylococcus [AKNB07]. STAR[ADR18]. Start [IGM+07]. Starvation[RBdJ11]. State[CHW+18, Gus05, Gus06b, Gus07c,HLM+13, HGC+20, JHZL19, KBNHD18,LR20, MT12a, MKKS20, MPY18, NSNN12,SH11a, SW17, SBRK11, ZZKW18, ZMT13,ZWL+12, EES14, Gu16, SYV14].State-of-the-Art [SW17]. State-Space[NSNN12]. States[BFK17, FPC20, PPM+13, dJP08]. Static[GBJ08, MKS+17]. Stationary [APPG18].Statistic [EFLA08]. Statistical[AH11, AGMP09, CW09a, CBN15,DADF+10, HSTW06, KSN+12, NJMF19,RCBB19, RSP08, YOGY11, ZZS18, BMM14,WSTL+15, XLC+15]. Statistically

[YNWC07]. Statistics [HCQ14, Mat07,NU06, SBW15, WLL+20, ZPW+19]. Steady[HLM+13, MT12a, MKKS20, PPM+13,SBRK11, ZZKW18, ZMT13, dJP08, SYV14].Steady-State [HLM+13, MT12a, MKKS20,ZMT13, SYV14]. Steering [PPM+13].Stem [GBTW16, GBTL14, YHV+15]. Step[PBhL+11]. Stepwise [DCM20]. Stilbene[NSMH19]. Stochastic[BBW18, CP13, CAW+19, GzS11, JLW17,KG12, MS11, MDPR18, NA11, PTM+19,SS04, TZP17, DGRC15, MCH+15]. Storage[SK12]. Strand [JBP08]. Strategies[CMC+12, HLY+16, LHL+19b, OMAdG+12,QV17, VRJ+10, YNWC07]. Strategy[BPP+13, BKKG19, Bon07, SSS13a, SJS19,TZH07, TDY+18, ZZZW19]. Strengthened[WXWL20]. stress [MZL15]. String[CW11, Kuk13, SLRQ19, SJNS19]. Strings[BO12]. Stroke [MFF+18]. Strongly[HKT+18]. Strongly-Correlated[HKT+18]. Structural[AV12, AKS20, BM12, CWG+18, DPS+13,GF10, HSS18, HZTP12, JWZ+20, JQH+20,KL19, KS18, LCTS08, LDS+07, LFF18,MCD+11, MSKC19, NRV09, SSFW12,SSF18, VSKJ11, WLHY19, WHKK07,WCLY12, YB08, DGRC15, DPL+14, DC15,GZGX14, LP15, YLH+15]. Structure[AS05, AL12, BWC17, BRZ+17, BTYC13,BKR11, BM12, CSZT19, CSZ+19, CCA12,CC07, CC11, CHL+12, CLW13, CMQ+16,CDKT09, CGPW06, CBF+18, DZA+06,DBZ12, DCVC11, ED15, FLW12, FSDR16,FSB+11, FMD18, GSC+18, HZZY16, HS09a,HVG04, HCLS11, KAP+12, LQV+13,LBL12a, LZ18b, LZZ+16, LHQ+18, LBQ+13,MP19, MPS18, MKH11, MSS13b, NA11,NZR11, NSAH19, NLW+18, ORCJ13, Pol11,Pol12, Pol13, QTZ15, RP13, RM18, SH11b,SLH+06a, SK12, SLL+19, SSF18, TMLI19,TW10, WS08, WSX11, WDH08, WAK13,WWL+17, ZZCY10, ZCG+18, ZWM+20,HS15, LAI+14, ARZ+14, PWZW15, SEC15,

57

Vog15]. Structure-Based[CCA12, DBZ12, MKH11, ZCG+18].Structure-Guided [MPS18].Structure-Redesigned-Based [NLW+18].Structure-Sequence [SLH+06a].Structured [CFOS06, GSK13, LW19b,NJMF19, TBKH05, VdTVV19, MMSH14].Structures [AJD+12, BDD+10, HXXJ18,Jia10, KL19, MCDD12, Mne09, Ozy12,Shi10, VMD+08, WLYZ+09, WHS04,YHCS19, ABH+14, NYOL15, ZMC+14].Structuring [PvRV+20]. Studies[EFLA08, FMA+20, IYA12, KAL+17,LEAK11, LRM08, LZW20, LLZC12, RGI13,SYKS15, SJZ19, VTGC16, WYY+13].Study[AVD+12, CSSS16, CLZ+18, DS19, GSC17,KAP+12, LW18, LNC+05, MSB19, NSMH19,OMAdG+12, SCCDK09, SKK14, WHF+20,WWBZ19, WAG19, WB11, WLPW16,WLA+13, XYYZ20, ZLXL19, ZWW17,ZBFK10, BMM14, LCOMG14, TWZ+14].Studying [HBRU13, LHTT11, MWLS18].Sub [AM19]. Sub-Optimal [AM19].Subcellular [hLMBJ11, LZQ+20, MGK08,OM07, QWC+16, SLX+18, TR07, WL13b,XPXY11, YL12, ZXZ20, ZHE19].Subchloroplast [WMK17]. subclones[XLWL15]. Subdivided [Wu10]. Subgraph[BG17, CLC+17, SKDA19, ZLY+12].Subgraphs [MSS+19b]. Submodels [JS12].Submodular [BBN19]. Subnetworks[SAE+20]. Subsequence [BVD+07].Subset [MT11, RGN+09]. subsets[SQZA14]. Subspace [CHWY19, LCW+18,SY09, XHQ+18, AJYT+15]. Substitution[AH11, DFM+11]. Substitutions [SGC07].Substrate [LLX+16]. Substrates[HHL+20]. Substring [CW11].Substructural [CLC+17]. Substructure[TBRS11]. Subtilis [NPBD16, SSDN12].Subtree [BN06, WM19b]. Subtrees[SCPS12]. Subtype [GXSZ17, WZJH12].Subtyping [ZY20]. Subunit [KAL+17].

Sufficient [Son06]. Suffix[SLGK17, LHS16]. Suitable [RAA10]. suite[CM15]. Sum [CD08, JZS+18, LL11].Sum-Squared [CD08]. Summarizing[MSH+11]. Summary [DLRW18]. Super[DDS+17, GBD17, HDKS04, YNN+18].Super-Networks [HDKS04].Super-Thresholding [DDS+17].superbubbles [SSS+15]. Supercomputer[PCY+19, PZS+20]. Superfamily [AV12].Superiority [Zha07]. Supermatrix[WBE13]. SuperMIC [WDL+17].Supernetworks [GSB+13]. Superposition[FGKH11, HS15]. Superpositioning[LFF18]. SuperQ [GSB+13]. Supertree[DLRW18, GB10, WBE13, Wil09, BM15,LCEMO18]. Supertrees[CBFB12, CEFBS06]. Supervised[AMHH16, BCLC15, DDS+17, HF12, JM12,Kar12a, MKG20, SFMS18, ZZBH20,YCY+14]. Support [LLX+11, LLX+16,LLT10, MNR09, MSKC19, QL09, RTA+16,SZLL11, TNQ08, WLL13, WZ13a].Supported [DM09]. Supporting[CLVT+20, RSG18]. Suppressed[YNBM05]. Suppression [NVSH18].Surface[GAGM11, GPF+20, HCA+10, MCD+11].Surface-Based [GAGM11]. Surfaces[DM09, ZXB11]. Survey[ECK16, IYA12, AKD17, LUdSCH10,LTM+12, LWG+18, MO04, MSS+13a, RG16,RHAK13, TV11, BMM14]. Survival[CKWY12, PGHT12, SAE+20].Susceptibility [YLCC13]. SVM[DLT10, JXN+16, MGK08, SBM15, TZH07].SVM-Based [DLT10, JXN+16].SVM-RFE [TZH07]. SVMs[HLZ+17, ZYW17]. Swarm[ALWG18, CYTY13, GSX+18, HGM18,KP12, LYW20, NPD+17, NHTD17, SIK20,TS17, TS18, TDY+18, WZZ+18, XWF07,XAW07, ZwGC17, SPWF14].Swarm-Based [TS18]. Swine [BPJ12].

58

Swine-Origin [BPJ12]. Switch[KG12, WLY15]. Switch-Like [KG12].Switched [LLA19, ZWL15]. Switching[ZWL+12]. Symbiont [USMS19].Symbiosis [NHTD17]. Symbiosis-Based[NHTD17]. Symmetric [MHHJ20].Symmetry [WHWP12]. Symposium[SA15]. Synaptic [KAL+17].Synchronization [ZWL14a, ZWL15].Synchronous [DT11]. Syndrome[XHY+18]. Syndrome-Coronavirus[XHY+18]. Synonymous [SGC07].SynPAM [SGC07]. Syntenic [SZZ+19].Synthesis [BBK+12, CL15, ZMST18].synthesizing [CL14]. Synthetic[LWL+20, ZLZ+19, KG15]. System[AAG+18, CWT+19, CLM10, CHZ+16,FJJ18, LWZ12, LGZ+17, LBL+10, MIC+07,MWD11, RSCX18, SYM+10, STD20, SJS19,TNQ08, WMWA12, WLCX18, XTL12c,CWLZ14, GRDV14, MZL15, TYA15,TAL+15]. Systematic[BDS12, HPH+15, MBP+19, MM14a, ZZ13].Systematically [WLHY19]. Systems[ACCT20, BLP18, BMZM15, CSW11, CN12,DGV+17, FS12, FS13a, FKLS07, GDWK+15,GJH19, JGBR15, JFN11, LR20, LLH+07,MZ17, MS11, Maz12, MVS+13, MPKvH09,MDM13, PFJ+19, PB12b, SH11a, SdOD+12,SJZ19, SNM08, SGH12, TC13, Wig15,WH11, Zha16, GPScF15, Gu16, JZCZ15,KSA16, KG15, SYV14, WLY15, ZSY+14].

T [YBGB10]. T-Cell [YBGB10]. Tables[FS18, PHX+08]. Tabu [CCA12]. tag[LLC+15]. Tailed [NVSH18]. Taking[MSH+11]. TAME [MGKG17]. Taming[MPQY19]. Tandem [BBN19, BG05,BKR11, CW09b, HCMB18, KSS15, SS06a,ZGC+05, ZWD+17, CWZW15, YMW+12].Tangible [dNG17]. Tanglegrams[MBKK18, VASG10]. Tardiness [SSS20a].Target[CGW+16, CWG+18, EZW+17, GZR+18,

IGM+07, LH20, LC19, MKG20, PSPM20,SFMS18, SSP+17, VKS17, DB14, FHRG14].Targetability [MSJP19]. Targeted[DMD13, FYZ+19, WLCX18]. Targeting[PG12]. Targets[KCP19, SPMB13, TDY+18]. Task[CLM10, FB19, LS10, ZYW17, CR14].Task-load [ZYW17]. taxa [BM15].Taxonomic [CHL+12, LW13a]. Taxonomy[CBK20, QTZ15]. TBC [ZC15]. TBR[BE08]. TCBB [Ano09b, Ano10b, Ano13d,Ano13b, Ano13c, Gus09b, KL11b, SA15].TCGA [GZR+18]. TCLUST [DWSB11].TD [SPA17]. Teaching[Che16, GAVRRL15].Teaching-Learning-Based [Che16]. Team[WL11, WKLL12, WLY14]. Teams [WL11].Technique [HEK18, WXS+19, ZLZ+19].Techniques [CMSE+15, GAR+09, HSS18,HC07, LTM+12, RHAK13, ZL19].telomerase [KPB14]. Temporal[ATA+17, KCCC15, LMZ+20, MSS19a,MCHT17, RdMCBC13, SDA+06, TRKRC13,ZYF+18, KD16]. Tensor[MGKG17, ZGDH16]. Tensor-Based[MGKG17]. Term[LL19, LHH19, TR07, YKWK18, ZLX+20].Term-Based [LHH19]. Terms[Ano12b, BM17, CLH+15, XLL19, SLS+14].Tertiary [BM12, MCDD12]. Test[EFLA08, KM20, YBGB10, ZS19]. Testing[FLAM15]. Tests [MTNH17, BMM14].Tetrameric [CMC+12]. Text[BMHS13, DLT10, HLV+10, JLH16,KAHK+10, LS10, LNC+05, SYM+10].Texts [HVD18, NAHT+20]. tgMC[LHG+16]. thaliana[MVW+13, TRKRC13, WWL19]. Their[DADF+10, LCTS08, LLZC12, MHKR12,RYK+19, VASG10, Wil11, FKLS07]. Theme[Gus09b]. Theoretic [BRS18, BLR08,GBS11, GLW12, VRK12, ZSD08, CA14].Theoretical [BCL13b, CHK17, MWD11].Theory [BDP11, BD19, LQV+13, NWZ+20,

59

SK19, SDB+07, BF14, MZL15].Therapeutic [RV13]. therapeutics [JR14].Therapies [BRS18, MPF12, NTCO07].Therapy[SSK+20, VDS+20, WLCX18, KPB14].There [DFM+11]. Thermodynamic[DPW12, TSM14, ZL15]. Thinning[ZWS+18]. Third [MVVR19]. Thomas[KSB12]. Thread [LZL+20]. Three[CHC+05, DZA+06, PLCW17, TZY11,WRH+09, WWL+17, ZD17, BF14, ZZ15,ZMC+14]. Three-Color [TZY11].Three-Dimensional[CHC+05, DZA+06, WRH+09, WWL+17,ZD17, BF14, ZMC+14]. Threshold[BMH+16]. Thresholded [HAH13].Thresholding [DDS+17]. Thresholds[PAAG07]. Throughput [HF07, How13,Kur13, LW18, LJL+15, MJPP20, MDM13,YP13, ZZH18a, GCC+14, XZY+14]. Tianhe[PCY+19, PZS+20]. Tianhe-2[PCY+19, PZS+20]. Tight [BS08, LCH19].Tikhonov [DCM20, Mir14]. Tiling[BCL13b, HKS11, SK08]. Time [AKV16,BBH+18, BEW09, BMK11, DST15a, EAS12,EAS13, FZWS17, Gra04, GPC+20, HAH13,HG16, IVA11, JSS+18, JZS+18, JNST09,KCCC15, KSB12, KMG+05, LCZN16,LLL15, LCC+11, MTSCO10, OMAdG+12,PTH+18, PH10b, PRU11, Pol11, PKA20,RFB20, RMS15, SH11a, SCSS05, SC11,SHUP19, TZP17, Vis18, WLL+09, WGP11,YC08, ZZKW18, ZWHC19, vIJJ+20,CZWT15, GM14, SSS+15, WLY14, ZWC15].Time-Course [EAS12]. Time-Courses[SCSS05]. Time-Delay [JSS+18].Time-Delayed [JZS+18, LCZN16, LLL15].Time-Dependent [AKV16]. time-lagged[GM14]. Time-Lapse [DST15a].Time-Series [EAS13, LLL15, PH10b,RMS15, SC11, ZZKW18]. Time-Varying[FZWS17, PKA20, YC08, ZWHC19,CZWT15, ZWC15]. Times [EW04]. Tissue[BMT17, JGBR15, LZQ+20, YLXJ04,

ZHE19]. Tissue-Specific [ZHE19]. Tissues[MMH15, SCM19]. ToBio [ZKW19]. toggle[WLY15]. Tool [BMZM15, CYJ+19, GPZ20,IL18, JKN+12, LTaS13, LMPT15, LZL+20,LHDS18, MBKK18, VSKJ11, VBB18,ZLW+11, MCH+15, SSML15]. Toolbox[MPSY18]. Tools [CBK20, LKW+19, MZ17].Top [AFJ12, SIM12, OFC+14]. Top-[AFJ12]. Top-r [SIM12]. Topic[BLP+12, CHL+12, WXWL20]. Topological[BG05, BGHM09, DGY05, DBK18, HC13,RB16, Rho20, Wil09, ZKW19].Topologically [ZHZ+20]. Topologies[MSJP19, Wu11]. Topology[BRZ+17, DNS19, DFTC12, FW20, KL11a,LLH18, MBGP12, Roc11, TDK13a,WWL+17, ZXLZ18a, ZXLZ18b, ZXZ20,BDBH15, DST+15b, LLW+15].Topology-Based [LLH18]. Torsion[FSX19]. Total[KMSY20, SSS20a, SMSZ17, ZYW+13].Touring [DKCM12]. Toxicity [BPP+13].Toxicogenomics [SWX+19]. TP53[MBP+19]. Trace [LZH18]. Trace-Norm[LZH18]. Traces [FL18]. Tracking[BM20, HKT+18, LHQ+18, MBJ19].Tractability[BS11, GB10, SHI06, vIKKS08]. Tractable[BS07, KO15, Lab06, PK13]. Trade[PH10b]. Trade-Off [PH10b]. Train[HLL18b]. Training [XHQ+18, YSC13].trait [HRHP16]. Traits[FYSM12, MTNH17]. Trajectories[KBNHD18, KBND19]. Trajectory[CBM+20, CGLF12]. TraM [AFJ12]. Trans[PHX+08, AJYT+15, YMT+14].Trans-Genomic [PHX+08]. Transaction[Gus05]. Transactional [XPH12].Transactions[Ano09c, Ano12b, Gus04b, Tit16].Transcript [CM13]. Transcriptase[SYKS15]. Transcription[BPP+13, LPH18, PIPC18, WPL15].Transcriptional [BBN18, CXW+13, DS19,

60

Gou06, KMG+05, LHH13, LLA19, WP08,ZWHC19, KD16, NCMCAR15].Transcriptome[CLVT+20, CS15, FS13b, GAJ+18, ZFZ+20].Transcriptomic [YLXS17]. Transcripts[AALD17, STB+19]. Transduction[LZL+19, LDL+17]. Transductive[WNT+17, WMK17, HRHP16]. Transfer[HZR+19, HXXJ18, KB17, KB19, MSG18,SSV+19, SLRQ19, ZM12, ZS18].Transfer-Based [ZS18]. Transfers[CDW12, THL11]. Transform[KK19, KVX12, LSY+20, Mat09, MCCZC08,SP11, TED+12, LHS16, YTLL15, LKY+11,TZY11, ZLLS17]. Transformation[AFMS19, ED15, XPH12]. Transient[PB12a, Pau18]. Transition[MPS18, RCM+19]. Translation[CPQ08, ZMT13, ZK16, ZMT14].Translational[BYZ+18, RKDR10, RKDR11].Translocation [CWZL08]. Translocations[QLLX10]. Transmembrane[WWL+17, YXS16]. Transmission [PG06].Transport [FVP+20, KHP12, LLX+16].Transporter [DGV+17]. Transposable[WQL+16]. Transposition[BODD20, Lab06]. Transpositions[EH06, HZL19]. transposon [DI15].Transreversals [HZL19]. Trapping[MBP+18]. Travel [GAGM11]. Traversal[UAH16]. Treating [MWD11]. Treatment[MWZY17]. Tree[APRS11, ADR18, BWC17, BPV+11, BN06,BS09, CRV09, DHC12, GZFT15, GRH08,GET13, GE18, GM09, GJS11, HYR+19,HEF17, JRSS18, JvI18, KVX12, LCEMO18,LNR+09, LPR+08, Mat07, NSNA19, OP11,QTZ15, Rho20, Roc06, SLGK17, STO06,SRM18, Son06, SDB+07, TBRS11, Wu11,Zha11, ZLW+11, ZRK19, GE15, LAI+14,WLY14, ZZ14]. Tree-Based [JvI18].Tree-Child [CRV09]. Tree-Guided[HYR+19]. Tree-Like [HEF17, NSNA19].

tree-reconciliation-based [ZZ14].Tree/Species [DHC12]. TreeDT [STO06].Treelength [LNR+09]. Trees[BG05, BG12, BS07, CLRV11, CW12,DLRW18, DRS12, DR16, GF10, HSlSM11,HW13, HDKS04, KB17, KB19, LRM12,LS09, ME19a, ME19b, ME19c, Mat09,Mos07, MG19, PK13, Rho20, SN12, Smi09,SR06, VASG10, WL11, Wil11, WMS09,Zha11, DR14, LV14, Mat15, MW16].Treespace [WYH17, Nye14]. Treespaces[GFS13]. trends [MKARB16]. TRIAL[VSKJ11]. Triangular [MGKG17]. Trigger[HLL+18a, JRN+18]. Triggered [ZZ13].Trimming [LLZ+20a]. Trios [BZ08]. Triple[YLY+12]. Triplets[CLRV09b, GJS11, vIKK+09]. True[ALR+13, MKKS20, Val11]. Trypanosoma[GAR+09]. Trypsinized [dAc17].Tuberculosis [SKS+19]. Tumor[BCVS19, HKM+18, KHP12, LHHL19,LCW+18, SMPS20, SJS19, SCM19, SSS13b,WZJH12, WLZ+19, XLW20, YCY+13,ZZN+11a, LXZ+15, XLWL15, YCY+14].Tumor-Associated [LHHL19].Tumor-Immune [SJS19]. Tumorgenesis[KCZ+15]. Tumors [DGY05, SMPS20].tunnels [PSK+16]. Twin [HCLS11]. Two[APRS11, BS07, HLL+18a, HHYH07,HGC+20, LTaS13, LLC+13, MPY18,PBhL+11, PK13, SC11, SY09, TZH07,Wan12, XWC15, ZCR+17, ZWM+20].Two-Dimensional [LTaS13]. Two-Locus[LLC+13, XWC15]. Two-Phase [ZCR+17].Two-Stage [HLL+18a, HHYH07, HGC+20,TZH07, ZWM+20]. Two-State [MPY18].Two-Step [PBhL+11]. Two-Tree[APRS11]. Two-Way [SY09]. txCoords[YLXS17]. Type[CLZ+18, UKV18, WCLY20, ZZ13]. Types[WMK16]. Typing [AKNB07, BBSP08].

uAnalyze [DPW12]. Ubiquitination[NHH+17]. UDoNC [PWC+15]. Ultra

61

[ZKL18]. Ultra-High [ZKL18]. Ultrasound[FYZ+19]. Unbalanced [PLCW17].Uncertain [BMZM15, MDD18, ZWL+14b].Uncertainties [SJS19]. Uncertainty[Dal16, RCBB19, RdlCGW09, UWLH15,DI15, DYD15]. Uncertainty-Aware[UWLH15]. Unconstrained [GPE17].Uncorrelated [YLXJ04]. Uncovering[LLX+11, PSIM17, PAS+11].Underestimation [HZZY16].Underrepresented [XYYZ20].Understand [ACCT20]. Understanding[NZR11]. Undirected [SM08, TRBK09].Unfold [Qiu14]. Unicyclic [SS06b].Unidentifiable [EW04]. Unified[CLST+13, GET13, LYY+19, SYM+10,SW09, WCXL18]. Uniform [RLV04]. unify[LLC+15]. Uninhabited [ZD17]. Uniquely[Wil11]. Unit [SDH20b]. United [LLNW17].Units [Dem12, IMA13, CFIS+15]. Universe[PBV+20]. Unknown [LBM+18].Unlabeled [CZW+18]. Unparametrized[KSB12]. Unravel [JZZQ19, HM15].Unravelling [dNG17]. Unrelated [BZ08].Unrooted[ADR18, BG12, CBFB12, GET13, WM19b].Unscented [MNND13]. Unsigned[CWZL08]. Unsupervised[AMHH16, AV12, JLH16, KL19, LW17,LHKL17, Mam05, NO09, SFMS18, Vog15,ZWSX12, LZGZ14]. Untangling [VASG10].update [ZWL14a]. Updates [HT09]. upon[CSW11, KKI20]. upstream [MBS15].Usage [LSMF08, MNR09]. Use [ALWG18].Used [Pol11]. Using[AKNB07, AH11, AV17, AOSN+18, ALR+13,ACCT20, AGGM11, AFJ12, AFAAW+11,AV12, AAT20, ASI+11, AD12, ADPH13,BBN18, BGS+12, BHMA06, BFM13,BMHS13, BSV10, BS10a, BHHMCL16,BM12, BM20, BWRF12, BBH12, CP13,CZ20, COW20, CC11, CLC+17, CWLS15,CLH+15, CD08, CKWY12, CWZ08,CYTY13, CSS11, CAN+08, DGH+06,

DSHM08, DNS19, DMJ+18, DM09,DKDD10, DABV17, DBK18, EMDH11,FWXZ19, FSX19, FJJ11, FWY19, FSB+11,GZG17, GK08, GPMH16, GLW12, GED+17,GPC+20, HEK18, HOS+12a, HOS+12b,HZZY16, HZTP12, HYY11, HS08, HYC12,HKT+18, HCLS11, HPL+13, HLSR18,HDS+18, HGC+20, HC07, HMK+07, HF12,HGM18, INT11, IQA18, IBN19, KMSY20,KSMT19, Kar12a, KNTB18, KCP18, KK19,KAHK+10, KVX12, LCEMO18, LFK16,LLX+11, LLH+17, LYL+17, LW19a,LMZ+20, LSY+20, cLWA07, LZH18, LWZ12,LHKL17, LHQ+18, LNW20]. Using[LLL15, LT07, MNR09, MGXS15,MTSCO10, MTNH17, MSB19, MK16,MBP+18, MCCZC08, MIC+07, MSKC19,MFF+18, MWSM12, MGS17, MDM13,NSAH19, NWW19, OC13, PGHT12, PI09,PR18, PLCW17, PPFG20, PGF18, PN17,QBPEL12, RLR20, RM13, RTA+16,RFFB+20, RdlCGW09, RP13, RKZ16,RBdJ11, RA16, SKDA19, SP11, SLGK17,SMRP15, SB12, SBW15, SSV+19, SYZ+13,SRM18, ST05, SDH20a, SDCW11, SSD+16,SSP+17, SKD+07, SR06, SZLL11, SGH12,TIA+11, TGGF10, TZY11, TED+12, TW10,TAI+19, TWZW16, UAH16, Vis18, WS12,WCX07, WZJH12, WFY+19, WHF+20,WWBZ19, WRH+09, WXS+19, WB11,WLL13, WDS+12, WZ13a, WW19, XWF07,XAW07, XLL+18, XLL19, YCYC12,YLCC13, YLXJ04, YNBM05, YBGB10,YOKI09, ZLLZ17, ZHEB05, ZHSS07,ZLPW16, ZLH+17, ZZY+17, ZCG+18,ZPW+19, ZLXL19, ZZF+19, ZWXL20,ZSD08, ZWW17, ZSC+10, ZYF+18,ZWY+10, ZZDY13, ZGDH16, ZDYH17,ZCWW19]. Using[ZHE19, ZL15, vBdRD+11, wTCAK+20,CWDS15, CR14, CZB+16, DGRC15, EES14,GGZZ14, GZGX14, GAVRRL15, HC14a,HLHAJ20, HS15, HWK14, HK15, JZCZ15,JHXP15, KGK14, KD15, LJL+14, LP15,

62

LXZ+15, MZL15, MEOL14, MMSH14,ARZ+14, NI07, PWZW15, PRZ+14, RHH16,SHK14, SSS20a, SLS+14, SXL+14,WSTL+15, XZY+14, YRD+13, YRD+14a,YRD+15, ZSY+14]. uSPR [BS10b].Utilization [ED15]. Utilizing[DSCM20, FMA+20, HC13, NSC17].

V [ZLS+19]. Vaccine [SSP+17]. Validation[BG13, CBZ18, GZR+18, GHL05, JCF13,MBF+11, VDS+20, ZLLZ17]. Validity[SMK+12, FN14]. Value [FWXZ19,WCA+19, XL16, YWK+07, YPS11]. Valued[LW13b]. Values [VTGC16, KS14].Variability [LKY+11, MSH+11, PPFG20].Variable [BG17, EAS13, RFFB+20, SS06a,ZKL18, MM14b]. Variable-Length[RFFB+20]. Variables [ALQ17]. Variance[SYZ+13]. Variant [PR18, TWW+20].Variants[JWZ+20, KB20, LQY+20, NLGG12,WHXS17, ZmCXS17, ZRK19, LLH+14].Variation [TBRS13, ZYW+13, LWM14].variational [BCLC15]. Variations [CW09a,CSK+11, ZANN20, dNG17, PV16, SB16].Variety [ZGZ+20]. VARUN [ACP10].Varying [FZWS17, PKA20, YC08,ZWHC19, CZWT15, ZWC15].Vascularization [UBP+19]. VCF[LQY+20]. VCF-Based [LQY+20]. VCV[SZCX19]. Vector[BM17, CCYW12, LLX+11, LLX+16, LLT10,MNR09, MSKC19, QL09, RTA+16, SZLL11,WLL13, WZ13a, JHXP15]. Vectors[CZ20, Kar12a, YH13]. Vehicle[GCL+18, ZD17]. Vein [wTCAK+20].Ventilated [RSCX18]. Ventilator[SZCX19]. Verified [SFB+08]. versus[SDN+11, TSM14]. Vertex [BSV10].Vertices [MSS+19b]. verticillioides[KZW+18]. Very [WCX07, SYV14].Vesicles [DADF+10]. via [CWZW15,CCCY20, CSSS16, CZF+05, CHNW20,DLM12, DKS+15, GAJ+18, GBLZ14,

GPScF15, GFG16, HYR+19, HLN20, HF07,HYL+19, JHW+19, KSN+12, LYH+16,LDM18, LFZ+19, LCW+18, LWL+20,NSNN12, PS15, QD12, RdMCBC13,SdOD+12, SDH20b, SGR+17, TYL+16,TK05, TC13, VF09, VM18, WLL+09,WL13b, WYHD17, WCC+18, WCL11,WOYL17, XL16, XW16, YHCS19, YFCM17,YHB12, YFWZ16, YWF+20, ZZKW18,ZDL12, ZHZ+20, ZYW+13, ZZDW13].Video [DST15a, ZHG20]. Videos[GBTW16]. View[BCF+07, LC19, SSF18, ZHJ17]. Views[WRH+09]. Vignette [WAG19]. Vimentin[CMC+12]. Vina [HOS+12a, HOS+12b].Virulent [NLGG12]. Virus[LLW+11, MBP+18, RAA20, ZZ13].Virus-Triggered [ZZ13]. Viruses [BJ10].Vision [CWT+19, GPF+20]. Visual[Jam17, LTwG+11, MBB+17, WRH+09,GCC+14]. Visualization[CMS12, GLG10, RWH+10, SW17].Visualizing [RdlCGW09]. Visually[Jam13]. Vitiligo [MSJP19]. Vitro [XSS17].VOC [KHO+20]. Vocabulary [BMHS13].Vogtmann [WYH17]. Vol [Tit16]. Volume[SSK+20]. Voting [PI09]. Voxel [CBES11].

WABI [Cas07, KJ04, KJ05]. Walk[LZHZ17, LWL+19, PLCW17, XW16,XGWW19, YDW+20, YSW+17, CWZW15].Walking [ABS17]. Walks[CCLS13, GFS13, YFWZ18]. Warning[TP18]. Watermarking [HEK18].Wavefronts [MBF+13]. Wavelet [KVX12,MK16, MCCZC08, NVSH18, SJNS19,ZZDY13, GZGX14, YTLL15, MSS+13a].wavelet-based [GZGX14]. Way [SY09].Weakly [ZZBH20]. Weakly-Supervised[ZZBH20]. web[MCH+15, CYJ+19, DPW12, KPP19, LZ18a,LHDS18, XYYZ20, YLXS17]. web-based[MCH+15, DPW12]. WeCoMXP [MB20].Weight [DNS19, PRU11, VPB15].

REFERENCES 63

Weighted [AMGC16, HK20, HBM19,LSY+20, LLT+19, MB20, SMB12, SSS20a,TGP+15, WS08, XGWW19, dCAR11,dDD18, PWZW15, TWZP14]. Weightedly[HLZ+17]. Weighting[AWW18, CHWY19, YHB12, LZGZ14].Weights [HRdR09]. Welcome[Gus07a, Gus07b, Wil04b]. Wheeler[KK19, KVX12, LHS16, NTR16, TED+12].Which [iAOSS16, SSS+11]. Whole[HKS11, LN17, NLHL17, PH10a, SSS13b,TGLP16, TWW+20, XPH20, ZZS18].Whole-Exome [TWW+20].Whole-Genome [HKS11, TGLP16].Whole-Sample [PH10a]. Wide[BGS+12, DGV+17, FLW12, FMA+20,GZC+17, KMSY20, LW18, LW19a, LZW20,MK16, NPK+07, PIPC18, SKS+19, TIA+11,Val11, VTGC16, WYY+13, ZZCY10,ZHG20, ZAZ11, TYL+16, WHZ14].Wide-Range [MK16]. Widely [Pol11].Wild [PCGS05]. Window[MK16, dSRCT+11, SSS13a]. Wing[GGH+13]. Wise[GCB+18, HZL+20, ZGDH16]. within[BEQD19, PWT10]. Without[JZS+18, BBSP08, MYCW12, ZWS+18].Women [FMA+20]. Word[HVD18, HLL+18a, JLH16, LLQ+16].Workflow[AAF+13, HVD18, LBL+10, MZ17, BF14].Workflow-Enabling [LBL+10]. Workshop[AJM18, ANT19, HCQ14, Kim18].Workshop/International [Kim18].Wrapper [LH10]. Wrong [LNR+09].

X [Str11, YMW+12]. X-Ray [Str11]. X4[LSMF08]. XDR [SKS+19]. Xeon [MPA15].XGBoost [OW20]. XlnR [OMAdG+12].XML [LLZ+20b]. XML-Based [LLZ+20b].Xor [BVD+10].

Y-Ion [WM19a]. YamiPred [KTLM15].Year [Gus09a]. Yeast

[CAW+19, CS15, ZACS09].

Zassenhaus [CP13]. zebrafish [GCC+14].Zero [YNBM05, ZW13]. Zero-Suppressed[YNBM05]. Zika [RAA20]. ZoomOut[ABS15].

ReferencesAydin:2011:BMA

[AAE11] Zafer Aydin, Yucel Altun-basak, and Hakan Erdogan.Bayesian models and algo-rithms for protein β-sheetprediction. IEEE/ACMTransactions on Computa-tional Biology and Bioinfor-matics, 8(2):395–409, March2011. CODEN ITCBCY.ISSN 1545-5963 (print),1557-9964 (electronic).

Abate:2013:GLB

[AAF+13] Francesco Abate, AndreaAcquaviva, Elisa Ficarra,Roberto Piva, and EnricoMacii. Gelsius: a literature-based workflow for determin-ing quantitative associationsbetween genes and biologi-cal processes. IEEE/ACMTransactions on Computa-tional Biology and Bioinfor-matics, 10(3):619–631, May2013. CODEN ITCBCY.ISSN 1545-5963 (print),1557-9964 (electronic).

Alazmi:2018:SBD

[AAG+18] Meshari Alazmi, Ahmed Ab-bas, Xianrong Guo, MingFan, Lihua Li, and Xin Gao.

REFERENCES 64

A slice-based 13c-detectedNMR spin system form-ing and resonance assign-ment method. IEEE/ACMTransactions on Computa-tional Biology and Bioin-formatics, 15(6):1999–2008,November 2018. CODENITCBCY. ISSN 1545-5963(print), 1557-9964 (elec-tronic).

Alim:2018:CSP

[AAH+18] Md Abdul Alim, Ahmet Ay,Md Mahmudul Hasan, My T.Thai, and Tamer Kahveci.Construction of signalingpathways with RNAi dataand multiple reference net-works. IEEE/ACM Trans-actions on ComputationalBiology and Bioinformatics,15(4):1079–1091, July 2018.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Azofeifa:2017:AAA

[AALD17] Joseph G. Azofeifa, Mary A.Allen, Manuel E. Lladser,and Robin D. Dowell. An an-notation agnostic algorithmfor detecting nascent RNAtranscripts in GRO-Seq.IEEE/ACM Transactionson Computational Biologyand Bioinformatics, 14(5):1070–1081, September 2017.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Abul:2006:PAE

[AAP06] Osman Abul, Reda Alhajj,and Faruk Polat. A pow-erful approach for effectivefinding of significantly dif-ferentially expressed genes.IEEE/ACM Transactions onComputational Biology andBioinformatics, 3(3):220–231, July 2006. CODENITCBCY. ISSN 1545-5963(print), 1557-9964 (elec-tronic).

Arabameri:2020:DCC

[AAT20] Abazar Arabameri, DavudAsemani, and Pegah Tey-mourpour. Detection ofcolorectal carcinoma basedon microbiota analysis usinggeneralized regression neuralnetworks and nonlinear fea-ture selection. IEEE/ACMTransactions on Computa-tional Biology and Bioin-formatics, 17(2):547–557,March 2020. CODENITCBCY. ISSN 1545-5963(print), 1557-9964 (elec-tronic). URL https://dl.acm.org/doi/abs/10.1109/TCBB.2018.2870124.

Amit:2014:LEP

[ABH+14] Mika Amit, Rolf Backofen,Steffen Heyne, Gad M.Landau, Mathias Mohl,Christina Otto, and Se-bastian Will. Local ex-act pattern matching fornon-fixed RNA structures.IEEE/ACM Transactions onComputational Biology and

REFERENCES 65

Bioinformatics, 11(1):219–230, January 2014. CODENITCBCY. ISSN 1545-5963(print), 1557-9964 (elec-tronic).

Athanasiadis:2015:ZAM

[ABS15] Emmanouil I. Athanasiadis,Marilena M. Bourdakou,and George M. Spyrou.ZoomOut: Analyzing multi-ple networks as single nodes.IEEE/ACM Transactionson Computational Biologyand Bioinformatics, 12(5):1213–1216, September 2015.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Athanasiadis:2017:DMR

[ABS17] Emmanouil Athanasiadis,Marilena Bourdakou, andGeorge Spyrou. D-Map:Random walking on genenetwork inference maps to-wards differential avenue dis-covery. IEEE/ACM Trans-actions on ComputationalBiology and Bioinformatics,14(2):484–490, March 2017.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Ansari:2012:DPS

[ABVD12] Nadeem A. Ansari, RiyueBao, Calin Voichita, andSorin Draghici. Detect-ing phenotype-specific in-teractions between biologi-cal processes from microar-ray data and annotations.

IEEE/ACM Transactionson Computational Biologyand Bioinformatics, 9(5):1399–1409, September 2012.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Ambert:2012:IGS

[AC12] Kyle H. Ambert and Aaron M.Cohen. k-informationgain scaled nearest neigh-bors: a novel approach toclassifying protein-proteininteraction-related docu-ments. IEEE/ACM Transac-tions on Computational Bi-ology and Bioinformatics, 9(1):305–310, January 2012.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Angione:2013:POO

[ACC+13] Claudio Angione, GiovanniCarapezza, Jole Costanza,Pietro Lio, and GiuseppeNicosia. Pareto optimality inorganelle energy metabolismanalysis. IEEE/ACM Trans-actions on ComputationalBiology and Bioinformatics,10(4):1032–1044, July 2013.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Alden:2020:UEE

[ACCT20] Kieran Alden, Jason Cos-grove, Mark Coles, and JonTimmis. Using emulationto engineer and understandsimulations of biological sys-

REFERENCES 66

tems. IEEE/ACM Transac-tions on Computational Bi-ology and Bioinformatics, 17(1):302–315, January 2020.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic). URL https://dl.acm.org/doi/abs/10.1109/TCBB.2018.2843339.

Apostolico:2010:VDE

[ACP10] Alberto Apostolico, MatteoComin, and Laxmi Parida.VARUN: Discovering exten-sible motifs under satura-tion constraints. IEEE/ACMTransactions on Computa-tional Biology and Bioinfor-matics, 7(4):752–762, Octo-ber 2010. CODEN ITCBCY.ISSN 1545-5963 (print),1557-9964 (electronic).

Alon:2010:AMP

[ACPR10] Noga Alon, Benny Chor,Fabio Pardi, and AnatRapoport. Approximatemaximum parsimony andancestral maximum likeli-hood. IEEE/ACM Transac-tions on Computational Bi-ology and Bioinformatics, 7(1):183–187, January 2010.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Au:2005:ACG

[ACWW05] Wai-Ho Au, Keith C. C.Chan, Andrew K. C. Wong,and Yang Wang. At-tribute clustering for group-ing, selection, and classi-

fication of gene expressiondata. IEEE/ACM Trans-actions on ComputationalBiology and Bioinformat-ics, 2(2):83–101, April 2005.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Au:2007:CAC

[ACWW07] Wai-Ho Au, Keith C. C.Chan, Andrew K. C. Wong,and Yang Wang. Correc-tion to “Attribute Clusteringfor Grouping, Selection, andClassification of Gene Ex-pression Data”. IEEE/ACMTransactions on Computa-tional Biology and Bioin-formatics, 4(1):157, January2007. CODEN ITCBCY.ISSN 1545-5963 (print),1557-9964 (electronic).

Ashlock:2012:DER

[AD12] Wendy Ashlock and SuprakashDatta. Distinguishing en-dogenous retroviral LTRsfrom SINE elements us-ing features extracted fromevolved side effect machines.IEEE/ACM Transactionson Computational Biologyand Bioinformatics, 9(6):1676–1689, November 2012.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Axenopoulos:2011:SDF

[ADPH11] Apostolos Axenopoulos, Pet-ros Daras, Georgios Pa-padopoulos, and Elias Houstis.

REFERENCES 67

A shape descriptor forfast complementarity match-ing in molecular docking.IEEE/ACM Transactionson Computational Biologyand Bioinformatics, 8(6):1441–1457, November 2011.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Axenopoulos:2013:SDP

[ADPH13] Apostolos Axenopoulos, Pet-ros Daras, Georgios E.Papadopoulos, and EliasHoustis. SP-Dock: Protein-protein docking using shapeand physicochemical com-plementarity. IEEE/ACMTransactions on Computa-tional Biology and Bioin-formatics, 10(1):135–150,January 2013. CODENITCBCY. ISSN 1545-5963(print), 1557-9964 (elec-tronic).

Allman:2018:STI

[ADR18] Elizabeth S. Allman, James H.Degnan, and John A.Rhodes. Species tree in-ference from gene splitsby unrooted STAR meth-ods. IEEE/ACM Transac-tions on Computational Bi-ology and Bioinformatics, 15(1):337–342, January 2018.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Al-Dalky:2016:AMC

[ADTAQ16] Rami Al-Dalky, Kamal

Taha, Dirar Al Homouz,and Murad Qasaimeh. Ap-plying Monte Carlo simula-tion to biomedical literatureto approximate genetic net-work. IEEE/ACM Trans-actions on ComputationalBiology and Bioinformatics,13(3):494–504, May 2016.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Andonie:2011:FAP

[AFAAW+11] Razvan Andonie, LeventeFabry-Asztalos, Christo-pher B. Abdul-Wahid, SarahAbdul-Wahid, Grant I.Barker, and Lukas C. Mag-ill. Fuzzy ARTMAP pre-diction of biological ac-tivities for potential HIV-1 protease inhibitors us-ing a small molecular dataset. IEEE/ACM Transac-tions on Computational Bi-ology and Bioinformatics,8(1):80–93, January 2011.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Amin:2012:TSG

[AFJ12] Mohammad Shafkat Amin,Russell L. Finley, Jr., andHasan M. Jamil. Top-k sim-ilar graph matching usingTraM in biological networks.IEEE/ACM Transactionson Computational Biologyand Bioinformatics, 9(6):1790–1804, November 2012.CODEN ITCBCY. ISSN

REFERENCES 68

1545-5963 (print), 1557-9964(electronic).

Andersen:2019:CTM

[AFMS19] Jakob L. Andersen, ChristophFlamm, Daniel Merkle, andPeter F. Stadler. Chemi-cal transformation motifs —modelling pathways as inte-ger hyperflows. IEEE/ACMTransactions on Computa-tional Biology and Bioin-formatics, 16(2):510–523,March 2019. CODENITCBCY. ISSN 1545-5963(print), 1557-9964 (elec-tronic). URL https://dl.acm.org/doi/abs/10.1109/TCBB.2017.2781724.

Ali:2018:SDS

[AGAS18] M. Syed Ali, N. Gu-nasekaran, Choon Ki Ahn,and Peng Shi. Sampled-data stabilization for fuzzygenetic regulatory networkswith leakage delays. IEEE/ACM Transactions on Com-putational Biology and Bioin-formatics, 15(1):271–285,January 2018. CODENITCBCY. ISSN 1545-5963(print), 1557-9964 (elec-tronic).

Ambroise:2011:IRP

[AGGM11] Jerome Ambroise, JoachimGiard, Jean-Luc Gala, andBenoit Macq. Identificationof relevant properties for epi-topes detection using a re-gression model. IEEE/ACMTransactions on Computa-

tional Biology and Bioin-formatics, 8(6):1700–1707,November 2011. CODENITCBCY. ISSN 1545-5963(print), 1557-9964 (elec-tronic).

Arribas-Gil:2009:SAS

[AGMP09] Ana Arribas-Gil, Dirk Met-zler, and Jean-Louis Plouhinec.Statistical alignment witha sequence evolution modelallowing rate heterogene-ity along the sequence.IEEE/ACM Transactions onComputational Biology andBioinformatics, 6(2):281–295, April 2009. CODENITCBCY. ISSN 1545-5963(print), 1557-9964 (elec-tronic).

Agrawal:2011:PSS

[AH11] Ankit Agrawal and Xiao-qiu Huang. Pairwise sta-tistical significance of lo-cal sequence alignment us-ing sequence-specific andposition-specific substitu-tion matrices. IEEE/ACMTransactions on Computa-tional Biology and Bioinfor-matics, 8(1):194–205, Jan-uary 2011. CODEN ITCBCY.ISSN 1545-5963 (print),1557-9964 (electronic).

Anders:2018:IPR

[AHT+18] Gerd Anders, Ulrich Has-siepen, Stephan Theisgen,Stephan Heymann, LionelMuller, Tania Panigada,Daniel Huster, and Sergey A.

REFERENCES 69

Samsonov. The intrin-sic pepsin resistance ofinterleukin-8 can be ex-plained from a combinedbioinformatical and exper-imental approach. IEEE/ACM Transactions on Com-putational Biology and Bioin-formatics, 15(1):300–308,January 2018. CODENITCBCY. ISSN 1545-5963(print), 1557-9964 (elec-tronic).

Ali:2016:SAC

[AIS+16] Sk Subidh Ali, MohamedIbrahim, Ozgur Sinanoglu,Krishnendu Chakrabarty,and Ramesh Karri. Se-curity assessment of cyber-physical digital microfluidicbiochips. IEEE/ACM Trans-actions on ComputationalBiology and Bioinformatics,13(3):445–458, May 2016.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Acharya:2012:GCA

[AJD+12] Lipi Acharya, Thair Judeh,Zhansheng Duan, MichaelRabbat, and Dongxiao Zhu.GSGS: a computational ap-proach to reconstruct sig-naling pathway structuresfrom gene sets. IEEE/ACMTransactions on Computa-tional Biology and Bioinfor-matics, 9(2):438–450, March2012. CODEN ITCBCY.ISSN 1545-5963 (print),1557-9964 (electronic).

Ayday:2018:GIW

[AJM18] Erman Ayday, XiaoqianJiang, and Bradley Malin.GenoPri’16: Internationalworkshop on genome privacyand security. IEEE/ACMTransactions on Computa-tional Biology and Bioin-formatics, 15(5):1403–1404,September 2018. CODENITCBCY. ISSN 1545-5963(print), 1557-9964 (elec-tronic).

Al-Jarrah:2015:RSL

[AJYT+15] Omar Y. Al-Jarrah, Paul D.Yoo, Kamal Taha, SamiMuhaidat, Abdallah Shami,and Nazar Zaki. Randomizedsubspace learning for prolinecis–trans isomerization pre-diction. IEEE/ACM Trans-actions on ComputationalBiology and Bioinformatics,12(4):763–769, July 2015.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Kawam:2017:SSH

[AKD17] Ahmad Al Kawam, SunilKhatri, and AniruddhaDatta. A survey of softwareand hardware approaches toperforming read alignment innext generation sequencing.IEEE/ACM Transactionson Computational Biologyand Bioinformatics, 14(6):1202–1213, November 2017.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

REFERENCES 70

Arram:2017:LFA

[AKLJ17] James Arram, Thomas Ka-plan, Wayne Luk, and Peiy-ong Jiang. Leveraging FP-GAs for accelerating shortread alignment. IEEE/ACMTransactions on Computa-tional Biology and Bioinfor-matics, 14(3):668–677, May2017. CODEN ITCBCY.ISSN 1545-5963 (print),1557-9964 (electronic).

Akutsu:2012:FPA

[AKMT12] Tatsuya Akutsu, Sven Ko-sub, Avraham A. Melk-man, and Takeyuki Tamura.Finding a periodic attrac-tor of a Boolean network.IEEE/ACM Transactionson Computational Biologyand Bioinformatics, 9(5):1410–1421, September 2012.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Agius:2007:TSA

[AKNB07] Phaedra Agius, Barry Kreiswirth,Steve Naidich, and KristinBennett. Typing Staphylo-coccus aureus using the spagene and novel distance mea-sures. IEEE/ACM Transac-tions on Computational Bi-ology and Bioinformatics, 4(4):693–704, October 2007.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Andreotti:2012:ALR

[AKR12] Sandro Andreotti, Gun-nar W. Klau, and KnutReinert. Antilope — aLagrangian relaxation ap-proach to the de novopeptide sequencing prob-lem. IEEE/ACM Transac-tions on Computational Bi-ology and Bioinformatics, 9(2):385–394, March 2012.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Ahirwal:2013:EEA

[AKS13] M. K. Ahirwal, A. Kumar,and G. K. Singh. EEG/ERPadaptive noise canceller de-sign with Controlled SearchSpace (CSS) approach incuckoo and other optimiza-tion algorithms. IEEE/ACMTransactions on Computa-tional Biology and Bioin-formatics, 10(6):1491–1504,November 2013. CODENITCBCY. ISSN 1545-5963(print), 1557-9964 (elec-tronic).

Azuma:2020:SBA

[AKS20] Shun-Ichi Azuma, Toshim-itsu Kure, and ToshiharuSugie. Structural bistabil-ity analysis of flower-shapedand chain-shaped Booleannetworks. IEEE/ACMTransactions on Computa-tional Biology and Bioin-formatics, 17(6):2098–2106,November 2020. CODENITCBCY. ISSN 1545-5963

REFERENCES 71

(print), 1557-9964 (elec-tronic). URL https://dl.acm.org/doi/10.1109/TCBB.2019.2917196.

Ancherbak:2016:TDG

[AKV16] Sergiy Ancherbak, Ercan E.Kuruoglu, and Martin Vin-gron. Time-dependentgene network modelling bysequential Monte Carlo.IEEE/ACM Transactionson Computational Biologyand Bioinformatics, 13(6):1183–1193, November 2016.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Armano:2012:EII

[AL12] Giuliano Armano and Fil-ippo Ledda. Exploitingintrastructure informationfor secondary structure pre-diction with multifacetedpipelines. IEEE/ACMTransactions on Computa-tional Biology and Bioinfor-matics, 9(3):799–808, May2012. CODEN ITCBCY.ISSN 1545-5963 (print),1557-9964 (electronic).

Adl:2017:DPI

[ALQ17] Amin Ahmadi Adl, Hye-Seung Lee, and XiaoningQian. Detecting pairwiseinteractive effects of con-tinuous random variablesfor biomarker identificationwith small sample size.IEEE/ACM Transactionson Computational Biology

and Bioinformatics, 14(6):1265–1275, November 2017.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

AlNasr:2013:IBS

[ALR+13] Kamal Al Nasr, ChunmeiLiu, Mugizi Rwebangira,Legand Burge, and JingHe. Intensity-based skele-tonization of CryoEM gray-scale images using a truesegmentation-free algorithm.IEEE/ACM Transactionson Computational Biologyand Bioinformatics, 10(5):1289–1298, September 2013.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Alves:2018:MSE

[ALWG18] Pedro Alves, Shuang Liu,Daifeng Wang, and MarkGerstein. Multiple-swarmensembles: Improving thepredictive power and robust-ness of predictive models andits use in computational bi-ology. IEEE/ACM Trans-actions on ComputationalBiology and Bioinformatics,15(3):926–933, May 2018.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Ashtawy:2012:CAR

[AM12] Hossam M. Ashtawy and Ni-har R. Mahapatra. A com-parative assessment of rank-ing accuracies of conven-

REFERENCES 72

tional and machine-learning-based scoring functions forprotein-ligand binding affin-ity prediction. IEEE/ACMTransactions on Computa-tional Biology and Bioin-formatics, 9(5):1301–1313,September 2012. CODENITCBCY. ISSN 1545-5963(print), 1557-9964 (elec-tronic).

Ashtawy:2015:CAP

[AM15] Hossam M. Ashtawy and Ni-har R. Mahapatra. A com-parative assessment of pre-dictive accuracies of conven-tional and machine learningscoring functions for protein–ligand binding affinity pre-diction. IEEE/ACM Trans-actions on ComputationalBiology and Bioinformatics,12(2):335–347, March 2015.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Ahmed:2019:GMS

[AM19] Syed Ali Ahmed and SaadMneimneh. Gibbs/MCMCsampling for multiple RNAinteraction with sub-optimalsolutions. IEEE/ACMTransactions on Computa-tional Biology and Bioinfor-matics, 16(3):703–712, May2019. CODEN ITCBCY.ISSN 1545-5963 (print),1557-9964 (electronic).

Ahmed:2014:SSC

[AMBK14] Hasin Afzal Ahmed, Priyak-

shi Mahanta, Dhruba Ku-mar Bhattacharyya, and Ju-gal Kumar Kalita. Shifting-and-scaling correlation basedbiclustering algorithm. IEEE/ACM Transactions on Com-putational Biology and Bioin-formatics, 11(6):1239–1252,November 2014. CODENITCBCY. ISSN 1545-5963(print), 1557-9964 (elec-tronic).

Agapito:2016:ECO

[AMGC16] Giuseppe Agapito, Mari-anna Milano, Pietro Hi-ram Guzzi, and Mario Can-nataro. Extracting cross-ontology weighted associa-tion rules from gene ontologyannotations. IEEE/ACMTransactions on Computa-tional Biology and Bioin-formatics, 13(2):197–208,March 2016. CODENITCBCY. ISSN 1545-5963(print), 1557-9964 (elec-tronic).

Ang:2016:SUS

[AMHH16] Jun Chin Ang, Andri Mirzal,Habibollah Haron, and HazaNuzly Abdull Hamed. Su-pervised, unsupervised, andsemi-supervised feature se-lection: a review on gene se-lection. IEEE/ACM Trans-actions on ComputationalBiology and Bioinformat-ics, 13(5):971–989, Septem-ber 2016. CODEN ITCBCY.ISSN 1545-5963 (print),1557-9964 (electronic).

REFERENCES 73

Anonymous:2004:AI

[Ano04a] Anonymous. Annual in-dex. IEEE/ACM Transac-tions on Computational Bi-ology and Bioinformatics, 1(4):191–192, October 2004.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Anonymous:2004:INA

[Ano04b] Anonymous. Introductionof new Associate Editor.IEEE/ACM Transactionson Computational Biologyand Bioinformatics, 1(2):65, April 2004. CODENITCBCY. ISSN 1545-5963(print), 1557-9964 (elec-tronic).

Anonymous:2005:AI

[Ano05a] Anonymous. 2005 annual in-dex. IEEE/ACM Transac-tions on Computational Bi-ology and Bioinformatics, 2(4):380–384, October 2005.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Anonymous:2005:CPS

[Ano05b] Anonymous. Call for papersfor Special Issue on Com-putational Intelligence Ap-proaches in ComputationalBiology and Bioinformat-ics. IEEE/ACM Trans-actions on ComputationalBiology and Bioinformat-ics, 2(3):271, July 2005.CODEN ITCBCY. ISSN


Anonymous:2006:RL

[Ano06a] Anonymous. 2005 review-ers list. IEEE/ACM Trans-actions on ComputationalBiology and Bioinformatics,3(1):95–96, January 2006.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Anonymous:2006:AI

[Ano06b] Anonymous. Annual in-dex. IEEE/ACM Trans-actions on ComputationalBiology and Bioinformat-ics, 3(4):??, October 2006.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Anonymous:2008:AI

[Ano08a] Anonymous. 2007 annual in-dex. IEEE/ACM Transac-tions on Computational Bi-ology and Bioinformatics, 5(1):148–158, January 2008.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Anonymous:2008:RL

[Ano08b] Anonymous. 2007 reviewerslist. IEEE/ACM Transac-tions on Computational Bi-ology and Bioinformatics, 5(1):146–147, January 2008.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

REFERENCES 74

Anonymous:2008:CAE

[Ano08c] Anonymous. Call for appli-cations for Editor-in-Chief.IEEE/ACM Transactionson Computational Biologyand Bioinformatics, 5(1):159, January 2008. CODENITCBCY. ISSN 1545-5963(print), 1557-9964 (elec-tronic).

Anonymous:2009:RL

[Ano09a] Anonymous. 2008 reviewerslist. IEEE/ACM Transac-tions on Computational Bi-ology and Bioinformatics, 6(1):171–173, January 2009.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Anonymous:2009:TAI

[Ano09b] Anonymous. 2009 TCBBannual index. IEEE/ACMTransactions on Computa-tional Biology and Bioinfor-matics, 6(4):Not in Print,October 2009. CODENITCBCY. ISSN 1545-5963(print), 1557-9964 (elec-tronic).

Anonymous:2009:CPS

[Ano09c] Anonymous. Call for pa-pers: Special issue of trans-actions in computational bi-ology and bioinformatics:Special issue on BioCreativeII.5. IEEE/ACM Trans-actions on ComputationalBiology and Bioinformat-ics, 6(4):703, October 2009.

CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Anonymous:2010:RL

[Ano10a] Anonymous. 2009 reviewer’slist. IEEE/ACM Transac-tions on Computational Bi-ology and Bioinformatics, 7(1):188–190, January 2010.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Anonymous:2010:TAI

[Ano10b] Anonymous. 2010 TCBBannual index. IEEE/ACMTransactions on Computa-tional Biology and Bioinfor-matics, 7(4):763–767, Octo-ber 2010. CODEN ITCBCY.ISSN 1545-5963 (print),1557-9964 (electronic).

Anonymous:2010:EN

[Ano10c] Anonymous. Editor’s note.IEEE/ACM Transactionson Computational Biologyand Bioinformatics, 7(1):1, January 2010. CODENITCBCY. ISSN 1545-5963(print), 1557-9964 (elec-tronic).

Anonymous:2012:CPS

[Ano12a] Anonymous. Call for papers:Special issue on ‘-omics’based companion diagnosticsfor personalized medicine.IEEE/ACM Transactions onComputational Biology andBioinformatics, 9(6):1855,November 2012. CODEN

REFERENCES 75

ITCBCY. ISSN 1545-5963(print), 1557-9964 (elec-tronic).

Anonymous:2012:IAT

[Ano12b] Anonymous. IEEE/ACMTransactions on Computa-tional Biology and Bioin-formatics seeks new Edi-tor in Chief for 2013–2014terms. IEEE/ACM Trans-actions on ComputationalBiology and Bioinformat-ics, 9(3):942, May 2012.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Anonymous:2013:RL

[Ano13a] Anonymous. 2012 reviewerslist. IEEE/ACM Transac-tions on Computational Bi-ology and Bioinformatics, 10(1):240–243, January 2013.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Anonymous:2013:CPSb

[Ano13b] Anonymous. Call for pa-pers: Special issue onsoftware and databases inTCBB. IEEE/ACM Trans-actions on ComputationalBiology and Bioinformat-ics, 10(3):816, May 2013.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Anonymous:2013:CPSc

[Ano13c] Anonymous. Call for pa-pers: Special issue on

software and databases inTCBB. IEEE/ACM Trans-actions on ComputationalBiology and Bioinformat-ics, 10(4):1086, July 2013.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Anonymous:2013:CPSa

[Ano13d] Anonymous. Call for pa-pers: Special issue onsofware and databases inTCBB. IEEE/ACM Trans-actions on ComputationalBiology and Bioinformat-ics, 10(2):544, March 2013.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Anonymous:2013:IOA

[Ano13e] Anonymous. IEEE open ac-cess publishing. IEEE/ACMTransactions on Computa-tional Biology and Bioinfor-matics, 10(5):1344, Septem-ber 2013. CODEN ITCBCY.ISSN 1545-5963 (print),1557-9964 (electronic).

Anonymous:2016:RL

[Ano16] Anonymous. 2015 reviewerslist. IEEE/ACM Transac-tions on Computational Bi-ology and Bioinformatics, 13(1):168–171, January 2016.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

REFERENCES 76

Aharoni:2011:QPD

[ANR11] Ehud Aharoni, Hani Neu-virth, and Saharon Ros-set. The quality preserv-ing database: a computa-tional framework for encour-aging collaboration, enhanc-ing power and controllingfalse discovery. IEEE/ACMTransactions on Computa-tional Biology and Bioin-formatics, 8(5):1431–1437,September 2011. CODENITCBCY. ISSN 1545-5963(print), 1557-9964 (elec-tronic).

Ayday:2019:GIW

[ANT19] Erman Ayday, Muham-mad Naveed, and HaixuTang. GenoPri’17: In-ternational Workshop onGenome Privacy and Secu-rity. IEEE/ACM Transac-tions on Computational Bi-ology and Bioinformatics, 16(4):1322–1323, July 2019.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Al-Ouran:2018:DGR

[AOSN+18] Rami Al-Ouran, RobertSchmidt, Ashwini Naik, Jef-frey Jones, Frank Drews,David Juedes, Laura Elnit-ski, and Lonnie Welch. Dis-covering gene regulatory ele-ments using coverage-basedheuristics. IEEE/ACMTransactions on Computa-tional Biology and Bioin-formatics, 15(4):1290–1300,

July 2018. CODEN ITCBCY.ISSN 1545-5963 (print),1557-9964 (electronic).

Alekseyev:2007:CBG

[AP07] Max A. Alekseyev andPavel A. Pevzner. Col-ored de Bruijn graphs andthe genome halving prob-lem. IEEE/ACM Transac-tions on Computational Bi-ology and Bioinformatics, 4(1):98–107, January 2007.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Awdeh:2018:DEA

[APKP18] Aseel Awdeh, Hilary Phenix,Mads Karn, and Theodore J.Perkins. Dynamics in epis-tasis analysis. IEEE/ACMTransactions on Computa-tional Biology and Bioinfor-matics, 15(3):878–891, May2018. CODEN ITCBCY.ISSN 1545-5963 (print),1557-9964 (electronic).

Avcu:2018:ACM

[APPG18] Neslihan Avcu, Nihal Peker-gin, Ferhan Pekergin, andCuneyt Guzelis. Aggregationfor computing multi-modalstationary distributions in1-D gene regulatory net-works. IEEE/ACM Trans-actions on ComputationalBiology and Bioinformatics,15(3):813–827, May 2018.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

REFERENCES 77

Allman:2011:ITT

[APRS11] Elizabeth S. Allman, SonjaPetrovic, John A. Rhodes,and Seth Sullivant. Iden-tifiability of two-tree mix-tures for group-based mod-els. IEEE/ACM Trans-actions on ComputationalBiology and Bioinformat-ics, 8(3):710–722, May/June2011. CODEN ITCBCY.ISSN 1545-5963 (print),1557-9964 (electronic).

Allman:2009:ICM

[AR09] Elizabeth S. Allman andJohn A. Rhodes. The identi-fiability of covarion models inphylogenetics. IEEE/ACMTransactions on Computa-tional Biology and Bioinfor-matics, 6(1):76–88, January2009. CODEN ITCBCY.ISSN 1545-5963 (print),1557-9964 (electronic).

Ahmed:2020:AEC

[ARK20] Syed Sazzad Ahmed, SwarupRoy, and Jugal Kalita. As-sessing the effectiveness ofcausality inference meth-ods for gene regulatory net-works. IEEE/ACM Trans-actions on ComputationalBiology and Bioinformatics,17(1):56–70, January 2020.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic). URL https://dl.acm.org/doi/abs/10.1109/TCBB.2018.2853728.

Abbas:2019:QRE

[ARM+19] Houssam Abbas, AlenaRodionova, KonstantinosMamouras, Ezio Bartocci,Scott A. Smolka, and RaduGrosu. Quantitative regu-lar expressions for arrhyth-mia detection. IEEE/ACMTransactions on Computa-tional Biology and Bioin-formatics, 16(5):1586–1597,September 2019. CODENITCBCY. ISSN 1545-5963(print), 1557-9964 (elec-tronic).

Axenopoulos:2016:SSF

[ARP+16] Apostolos Axenopoulos, Dim-itrios Rafailidis, GeorgiosPapadopoulos, Elias N.Houstis, and Petros Daras.Similarity search of flexible3D molecules combining lo-cal and global shape descrip-tors. IEEE/ACM Trans-actions on ComputationalBiology and Bioinformat-ics, 13(5):954–970, Septem-ber 2016. CODEN ITCBCY.ISSN 1545-5963 (print),1557-9964 (electronic).

Aparicio:2017:EAG

[ARS17] David Aparicio, Pedro Ri-beiro, and Fernando Silva.Extending the applicabilityof graphlets to directed net-works. IEEE/ACM Trans-actions on ComputationalBiology and Bioinformatics,14(6):1302–1315, November2017. CODEN ITCBCY.

REFERENCES 78

ISSN 1545-5963 (print),1557-9964 (electronic).

Nasr:2014:SSS

[ARZ+14] Kamal Al Nasr, Desh Ran-jan, Mohammad Zubair, LinChen, and Jing He. Solv-ing the secondary struc-ture matching problem incryo-EM de novo model-ing using a constrained K-shortest path graph algo-rithm. IEEE/ACM Trans-actions on ComputationalBiology and Bioinformatics,11(2):419–430, March 2014.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Allali:2005:NDH

[AS05] Julien Allali and Marie-France Sagot. A new dis-tance for high level RNAsecondary structure compar-ison. IEEE/ACM Trans-actions on ComputationalBiology and Bioinformat-ics, 2(1):3–14, January 2005.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Aluru:2015:GEI

[AS15] Srinivas Aluru and Donna K.Slonim. Guest Editors’introduction: selected pa-pers from ACM-BCB 2013.IEEE/ACM Transactions onComputational Biology andBioinformatics, 12(1):2–3,January 2015. CODENITCBCY. ISSN 1545-5963

(print), 1557-9964 (elec-tronic).

Armananzas:2011:PSM

[ASI+11] Ruben Armananzas, YvanSaeys, Inaki Inza, MiguelGarcia-Torres, Concha Bielza,Yves van de Peer, and Pe-dro Larranaga. Peakbin se-lection in mass spectrom-etry data using a consen-sus approach with estimationof distribution algorithms.IEEE/ACM Transactionson Computational Biologyand Bioinformatics, 8(3):760–774, May/June 2011.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Aeling:2007:DDE

[ASJ+07] Kimberly A. Aeling, Nicholas R.Steffen, Matthew John-son, G. Wesley Hatfield,Richard H. Lathrop, andDonald F. Senear. DNAdeformation energy as anindirect recognition mecha-nism in protein-DNA inter-actions. IEEE/ACM Trans-actions on ComputationalBiology and Bioinformatics,4(1):117–125, January 2007.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Acharya:2020:MFG

[ASP20] Sudipta Acharya, SriparnaSaha, and Prasanna Prad-han. Multi-factored gene-gene proximity measures ex-

REFERENCES 79

ploiting biological knowl-edge extracted from geneontology: Application ingene clustering. IEEE/ACMTransactions on Computa-tional Biology and Bioin-formatics, 17(1):207–219,January 2020. CODENITCBCY. ISSN 1545-5963(print), 1557-9964 (elec-tronic). URL https://dl.acm.org/doi/abs/10.1109/TCBB.2018.2849362.

Alden:2017:EAS

[ATA+17] Kieran Alden, Jon Timmis,Paul S. Andrews, HenriqueVeiga-Fernandes, and MarkColes. Extending and ap-plying spartan to performtemporal sensitivity analy-ses for predicting changesin influential biological path-ways in computational mod-els. IEEE/ACM Transac-tions on Computational Bi-ology and Bioinformatics,14(2):431–442, March 2017.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Angadi:2012:SSS

[AV12] Ulavappa B. Angadi andM. Venkatesulu. Struc-tural SCOP superfamilylevel classification using un-supervised machine learn-ing. IEEE/ACM Transac-tions on Computational Bi-ology and Bioinformatics, 9(2):601–608, March 2012.CODEN ITCBCY. ISSN


Akkasi:2017:IBN

[AV17] Abbas Akkasi and EkremVaroglu. Improving bio-chemical named entity recog-nition using PSO classifierselection and Bayesian com-bination methods. IEEE/ACM Transactions on Com-putational Biology and Bioin-formatics, 14(6):1327–1338,November 2017. CODENITCBCY. ISSN 1545-5963(print), 1557-9964 (elec-tronic).

Abate:2012:MMS

[AVD+12] Alessandro Abate, StephaneVincent, Roel Dobbe, Al-berto Silletti, Neal Mas-ter, Jeffrey D. Axelrod, andClaire J. Tomlin. A mathe-matical model to study thedynamics of epithelial cellu-lar networks. IEEE/ACMTransactions on Computa-tional Biology and Bioin-formatics, 9(6):1607–1620,November 2012. CODENITCBCY. ISSN 1545-5963(print), 1557-9964 (elec-tronic).

An:2018:LNN

[AWW18] Shuai An, Jun Wang,and Jinmao Wei. Local-nearest-neighbors-based fea-ture weighting for gene se-lection. IEEE/ACM Trans-actions on ComputationalBiology and Bioinformatics,

REFERENCES 80

15(5):1538–1548, September2018. CODEN ITCBCY.ISSN 1545-5963 (print),1557-9964 (electronic).

Biswas:2018:BOR

[BA18] Surama Biswas and SriyankarAcharyya. A bi-objectiveRNN model to reconstructgene regulatory network:a modified multi-objectivesimulated annealing ap-proach. IEEE/ACM Trans-actions on ComputationalBiology and Bioinformatics,15(6):2053–2059, November2018. CODEN ITCBCY.ISSN 1545-5963 (print),1557-9964 (electronic).

Bilu:2006:FAO

[BAK06] Yonatan Bilu, Pankaj K.Agarwal, and Rachel Kolodny.Faster algorithms for optimalmultiple sequence alignmentbased on pairwise compar-isons. IEEE/ACM Transac-tions on Computational Bi-ology and Bioinformatics, 3(4):408–422, October 2006.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Bafna:2004:NRE

[BB04] Vineet Bafna and VikasBansal. The number ofrecombination events in asample history: Conflictgraph and lower bounds.IEEE/ACM Transactionson Computational Biologyand Bioinformatics, 1(2):78–

90, April 2004. CODENITCBCY. ISSN 1545-5963(print), 1557-9964 (elec-tronic).

Bandyopadhyay:2011:BIM

[BB11] Sanghamitra Bandyopad-hyay and Malay Bhat-tacharyya. A biologically in-spired measure for coexpres-sion analysis. IEEE/ACMTransactions on Computa-tional Biology and Bioinfor-matics, 8(4):929–942, July2011. CODEN ITCBCY.ISSN 1545-5963 (print),1557-9964 (electronic).

Berard:2007:PSR

[BBCP07] Severine Berard, Anne Berg-eron, Cedric Chauve, andChristophe Paul. Perfectsorting by reversals is not al-ways difficult. IEEE/ACMTransactions on Computa-tional Biology and Bioinfor-matics, 4(1):4–16, January2007. CODEN ITCBCY.ISSN 1545-5963 (print),1557-9964 (electronic).

Bustamam:2012:FPM

[BBH12] Alhadi Bustamam, KevinBurrage, and Nicholas A.Hamilton. Fast paral-lel Markov clustering inbioinformatics using mas-sively parallel computingon GPU with CUDA andELLPACK-R sparse for-mat. IEEE/ACM Trans-actions on ComputationalBiology and Bioinformat-

REFERENCES 81

ics, 9(3):679–692, May 2012.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Backes:2018:SLS

[BBH+18] Michael Backes, PascalBerrang, Mathias Humbert,Xiaoyu Shen, and VerenaWolf. Simulating the large-scale erosion of genomic pri-vacy over time. IEEE/ACMTransactions on Computa-tional Biology and Bioin-formatics, 15(5):1405–1412,September 2018. CODENITCBCY. ISSN 1545-5963(print), 1557-9964 (elec-tronic).

Blazewicz:2007:SPD

[BBK+07] Jacek Blazewicz, EdmundBurke, Marta Kasprzak,Alexandr Kovalev, andMikhail Kovalyov. Sim-plified partial digest prob-lem: Enumerative and dy-namic programming algo-rithms. IEEE/ACM Trans-actions on ComputationalBiology and Bioinformatics,4(4):668–680, October 2007.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Barnat:2012:PSP

[BBK+12] Jiri Barnat, Lubos Brim,Adam Krejci, Adam Streck,David Safranek, Martin Ve-jnar, and Tomas Vejpustek.On parameter synthesisby parallel model check-

ing. IEEE/ACM Trans-actions on ComputationalBiology and Bioinformat-ics, 9(3):693–705, May 2012.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Bahadorinejad:2018:OFD

[BBN18] Arghavan Bahadorinejadand Ulisses M. Braga-Neto. Optimal fault de-tection and diagnosis intranscriptional circuits us-ing next-generation sequenc-ing. IEEE/ACM Transac-tions on Computational Bi-ology and Bioinformatics,15(2):516–525, March 2018.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Bai:2019:SGM

[BBN19] Wenruo Bai, Jeffrey Bilmes,and William S. Noble. Sub-modular generalized match-ing for peptide identificationin tandem mass spectrome-try. IEEE/ACM Transac-tions on Computational Bi-ology and Bioinformatics, 16(4):1168–1181, July 2019.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Barzuza:2008:CPP

[BBSP08] Tamar Barzuza, Jacques S.Beckmann, Ron Shamir, andItsik Pe’er. Computationalproblems in perfect phy-logeny haplotyping: Typ-

REFERENCES 82

ing without calling the al-lele. IEEE/ACM Transac-tions on Computational Bi-ology and Bioinformatics, 5(1):101–109, January 2008.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Backenkohler:2018:MBP

[BBW18] Michael Backenkohler, LucaBortolussi, and Verena Wolf.Moment-based parameter es-timation for stochastic re-action networks in equilib-rium. IEEE/ACM Transac-tions on Computational Bi-ology and Bioinformatics, 15(4):1180–1192, July 2018.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Blin:2007:CGD

[BCF+07] Guillaume Blin, CedricChauve, Guillaume Fertin,Romeo Rizzi, and StephaneVialette. Comparing genomeswith duplications: a compu-tational complexity point ofview. IEEE/ACM Transac-tions on Computational Bi-ology and Bioinformatics, 4(4):523–534, October 2007.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Braz:2013:PMC

[BCFCC13] Fernando A. F. Braz, Jader S.Cruz, Alessandra C. Faria-Campos, and Sergio V. A.Campos. Probabilistic model

checking analysis of paly-toxin effects on cell en-ergy reactions of the Na+/K+-ATPase. IEEE/ACMTransactions on Computa-tional Biology and Bioin-formatics, 10(6):1530–1541,November 2013. CODENITCBCY. ISSN 1545-5963(print), 1557-9964 (elec-tronic).

Bernardini:2013:GRN

[BCL+13a] Camilla Bernardini, Feder-ica Censi, Wanda Lattanzi,Giovanni Calcagnini, andAlessandro Giuliani. Generegulation networks in earlyphase of Duchenne muscu-lar dystrophy. IEEE/ACMTransactions on Computa-tional Biology and Bioin-formatics, 10(2):393–400,March 2013. CODENITCBCY. ISSN 1545-5963(print), 1557-9964 (elec-tronic).

Bozdag:2013:GTA

[BCL13b] Serdar Bozdag, Timothy J.Close, and Stefano Lonardi.A graph-theoretical ap-proach to the selection of theminimum tiling path from aphysical map. IEEE/ACMTransactions on Computa-tional Biology and Bioin-formatics, 10(2):352–360,March 2013. CODENITCBCY. ISSN 1545-5963(print), 1557-9964 (elec-tronic).

REFERENCES 83

Boareto:2015:SVR

[BCLC15] Marcelo Boareto, JonatasCesar, Vitor B. P. Leite,and Nestor Caticha. Su-pervised variational rele-vance learning, an analyticgeometric feature selectionwith applications to omicdatasets. IEEE/ACM Trans-actions on ComputationalBiology and Bioinformatics,12(3):705–711, May 2015.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Barma:2015:QMS

[BCMW15] Shovan Barma, Bo-WeiChen, Ka Lok Man, andJhing-Fa Wang. Quantita-tive measurement of splitof the second heart sound(S2). IEEE/ACM Trans-actions on ComputationalBiology and Bioinformatics,12(4):851–860, July 2015.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Bajaj:2011:FFP

[BCS11] Chandrajit L. Bajaj, RezaulChowdhury, and Vinay Sid-dahanavalli. F 2Dock: FastFourier protein-protein dock-ing. IEEE/ACM Transac-tions on Computational Bi-ology and Bioinformatics,8(1):45–58, January 2011.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Bonizzoni:2019:DRI

[BCVS19] Paola Bonizzoni, Simone Ci-ccolella, Gianluca Della Ve-dova, and Mauricio Soto.Does relaxing the infinitesites assumption give bettertumor phylogenies? An ILP-based comparative approach.IEEE/ACM Transactionson Computational Biologyand Bioinformatics, 16(5):1410–1423, September 2019.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Biane:2019:CRB

[BD19] Celia Biane and Franck De-laplace. Causal reasoningon Boolean control networksbased on abduction: The-ory and application to cancerdrug discovery. IEEE/ACMTransactions on Computa-tional Biology and Bioin-formatics, 16(5):1574–1585,September 2019. CODENITCBCY. ISSN 1545-5963(print), 1557-9964 (elec-tronic).

Birlutiu:2015:BFC

[BDBH15] Adriana Birlutiu, FlorenceD’Alche-Buc, and Tom Hes-kes. A Bayesian frame-work for combining pro-tein and network topol-ogy information for predict-ing protein–protein interac-tions. IEEE/ACM Trans-actions on ComputationalBiology and Bioinformatics,12(3):538–550, May 2015.

REFERENCES 84


Blin:2010:ARS

[BDD+10] Guillaume Blin, Alain Denise,Serge Dulucq, Claire Her-rbach, and Heleene Touzet.Alignments of RNA struc-tures. IEEE/ACM Trans-actions on ComputationalBiology and Bioinformatics,7(2):309–322, April 2010.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Bao:2018:AAC

[BDD18] Feng Bao, Yue Deng, andQionghai Dai. ACID: As-sociation correction for im-balanced data in GWAS.IEEE/ACM Transactions onComputational Biology andBioinformatics, 15(1):316–322, January 2018. CODENITCBCY. ISSN 1545-5963(print), 1557-9964 (elec-tronic).

Borges:2018:RGS

[BdOS+18] Vinicius R. P. Borges, MariaCristina F. de Oliveira,Thais Garcia Silva, ArmandoAugusto Henriques Vieira,and Bernd Hamann. Re-gion growing for segment-ing green microalgae im-ages. IEEE/ACM Transac-tions on Computational Bi-ology and Bioinformatics, 15(1):257–270, January 2018.CODEN ITCBCY. ISSN


Benso:2011:CMG

[BDP11] Alfredo Benso, Stefano DiCarlo, and Gianfranco Poli-tano. A cDNA microarraygene expression data clas-sifier for clinical diagnos-tics based on graph theory.IEEE/ACM Transactionson Computational Biologyand Bioinformatics, 8(3):577–591, May/June 2011.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Badaloni:2012:QRB

[BDS12] Silvana Badaloni, BarbaraDi Camillo, and FrancescoSambo. Qualitative reason-ing for biological networkinference from systematicperturbation experiments.IEEE/ACM Transactionson Computational Biologyand Bioinformatics, 9(5):1482–1491, September 2012.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Bansal:2008:STH

[BE08] Mukul S. Bansal and OliverEulenstein. An Ω(n2/ log n)speed-up of TBR heuris-tics for the gene-duplicationproblem. IEEE/ACM Trans-actions on ComputationalBiology and Bioinformatics,5(4):514–524, October 2008.CODEN ITCBCY. ISSN

REFERENCES 85


Boluki:2019:CPB

[BEQD19] Shahin Boluki, Moham-mad Shahrokh Esfahani,Xiaoning Qian, and Ed-ward R. Dougherty. Con-structing pathway-based pri-ors within a Gaussian mix-ture model for Bayesianregression and classifica-tion. IEEE/ACM Trans-actions on ComputationalBiology and Bioinformatics,16(2):524–537, March 2019.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic). URL https://dl.acm.org/doi/abs/10.1109/TCBB.2017.2778715.

Bansal:2009:GDP

[BEW09] Mukul S. Bansal, Oliver Eu-lenstein, and Andre Wehe.The gene-duplication prob-lem: Near-linear time algo-rithms for NNI-based localsearches. IEEE/ACM Trans-actions on ComputationalBiology and Bioinformatics,6(2):221–231, April 2009.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Bitar:2014:BPC

[BF14] Maina Bitar and Gloria ReginaFranco. A basic protein com-parative three-dimensionalmodeling methodologicalworkflow theory and prac-tice. IEEE/ACM Transac-

tions on Computational Bi-ology and Bioinformatics,11(6):1052–1065, November2014. CODEN ITCBCY.ISSN 1545-5963 (print),1557-9964 (electronic).

Boes:2017:LBN

[BFK17] Olivier Boes, Mareike Fis-cher, and Steven Kelk. Alinear bound on the num-ber of states in optimalconvex characters for max-imum parsimony distance.IEEE/ACM Transactions onComputational Biology andBioinformatics, 14(2):472–477, March 2017. CODENITCBCY. ISSN 1545-5963(print), 1557-9964 (elec-tronic).

Biller:2013:RBP

[BFM13] Priscila Biller, Pedro Fei-jao, and Joao Meidanis.Rearrangement-based phy-logeny using the single-cut-or-join operation. IEEE/ACM Transactions on Com-putational Biology and Bioin-formatics, 10(1):122–134,January 2013. CODENITCBCY. ISSN 1545-5963(print), 1557-9964 (elec-tronic).

Bertrand:2005:TRL

[BG05] Denis Bertrand and OlivierGascuel. Topological rear-rangements and local searchmethod for tandem dupli-cation trees. IEEE/ACMTransactions on Computa-

REFERENCES 86

tional Biology and Bioinfor-matics, 2(1):15–28, January2005. CODEN ITCBCY.ISSN 1545-5963 (print),1557-9964 (electronic).

Bogdanowicz:2012:MSD

[BG12] Damian Bogdanowicz andKrzysztof Giaro. Match-ing split distance for un-rooted binary phylogenetictrees. IEEE/ACM Transac-tions on Computational Bi-ology and Bioinformatics, 9(1):150–160, January 2012.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Baya:2013:HMC

[BG13] Ariel E. Baya and Pablo M.Granitto. How many clus-ters: a validation indexfor arbitrary-shaped clus-ters. IEEE/ACM Transac-tions on Computational Bi-ology and Bioinformatics,10(2):401–414, March 2013.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Bonnici:2017:VOS

[BG17] Vincenzo Bonnici and Ros-alba Giugno. On thevariable ordering in sub-graph isomorphism algo-rithms. IEEE/ACM Trans-actions on ComputationalBiology and Bioinformat-ics, 14(1):193–203, January2017. CODEN ITCBCY.


Bakhteh:2020:IMS

[BGHC20] Somayeh Bakhteh, AlirezaGhaffari-Hadigheh, and NaderChaparzadeh. Identifica-tion of minimum set ofmaster regulatory genes ingene regulatory networks.IEEE/ACM Transactions onComputational Biology andBioinformatics, 17(3):999–1009, May 2020. CODENITCBCY. ISSN 1545-5963(print), 1557-9964 (elec-tronic). URL https://dl.acm.org/doi/10.1109/TCBB.2018.2875692.

Bordewich:2009:CTM

[BGHM09] Magnus Bordewich, OlivierGascuel, Katharina T. Hu-ber, and Vincent Moulton.Consistency of topologicalmoves based on the balancedminimum evolution princi-ple of phylogenetic infer-ence. IEEE/ACM Transac-tions on Computational Bi-ology and Bioinformatics, 6(1):110–117, January 2009.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Belcastro:2012:REA

[BGS+12] Vincenzo Belcastro, FrancescoGregoretti, Velia Siciliano,Michele Santoro, GiovanniD’Angelo, Gennaro Oliva,and Diego di Bernardo. Re-verse engineering and anal-ysis of genome-wide gene

REFERENCES 87

regulatory networks fromgene expression profiles us-ing high-performance com-puting. IEEE/ACM Trans-actions on ComputationalBiology and Bioinformat-ics, 9(3):668–678, May 2012.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Brown:2006:IPA

[BH06] Daniel G. Brown and Ian M.Harrower. Integer program-ming approaches to haplo-type inference by pure par-simony. IEEE/ACM Trans-actions on ComputationalBiology and Bioinformatics,3(2):141–154, April 2006.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Bonilla-Huerta:2016:HFU

[BHHMCL16] Edmundo Bonilla-Huerta,Alberto Hernandez-Montiel,Roberto-Morales Caporal,and Marco Arjona Lopez.Hybrid framework usingmultiple-filters and an em-bedded approach for an ef-ficient selection and classi-fication of microarray data.IEEE/ACM Transactions onComputational Biology andBioinformatics, 13(1):12–26,January 2016. CODENITCBCY. ISSN 1545-5963(print), 1557-9964 (elec-tronic).

Berger:2006:JAG

[BHMA06] John A. Berger, SampsaHautaniemi, Sanjit K. Mi-tra, and Jaakko Astola.Jointly analyzing gene ex-pression and copy numberdata in breast cancer us-ing data reduction mod-els. IEEE/ACM Trans-actions on ComputationalBiology and Bioinformat-ics, 3(1):2–16, January 2006.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Brankovic:2019:DFS

[BHP19] Aida Brankovic, MarjanHosseini, and Luigi Piroddi.A distributed feature selec-tion algorithm based on dis-tance correlation with anapplication to microarrays.IEEE/ACM Transactionson Computational Biologyand Bioinformatics, 16(6):1802–1815, November 2019.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic). URL https://dl.acm.org/doi/abs/10.1109/TCBB.2018.2833482.

Bannai:2004:ADO

[BHS+04] Hideo Bannai, Heikki Hyyro,Ayumi Shinohara, MasayukiTakeda, Kenta Nakai, andSatoru Miyano. An O(N 2)algorithm for discoveringoptimal Boolean patternpairs. IEEE/ACM Transac-tions on Computational Bi-ology and Bioinformatics, 1

REFERENCES 88

(4):159–170, October 2004.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Berlow:2014:IAA

[BHW+14] Noah Berlow, Saad Haider,Qian Wan, Mathew Geltzeiler,Lara E. Davis, CharlesKeller, and Ranadip Pal.An integrated approach toanti-cancer drug sensitiv-ity prediction. IEEE/ACMTransactions on Computa-tional Biology and Bioin-formatics, 11(6):995–1008,November 2014. CODENITCBCY. ISSN 1545-5963(print), 1557-9964 (elec-tronic).

Bi:2009:MCE

[Bi09] Chengpeng Bi. A MonteCarlo EM algorithm forDe Novo Motif discoveryin biomolecular sequences.IEEE/ACM Transactions onComputational Biology andBioinformatics, 6(3):370–386, July 2009. CODENITCBCY. ISSN 1545-5963(print), 1557-9964 (elec-tronic).

Bokhari:2010:RNI

[BJ10] Shahid H. Bokhari andDaniel Janies. Reassortmentnetworks for investigatingthe evolution of segmentedviruses. IEEE/ACM Trans-actions on ComputationalBiology and Bioinformatics,7(2):288–298, April 2010.


Bulteau:2013:IED

[BJ13] Laurent Bulteau and MinghuiJiang. Inapproximabilityof ((1, 2))-exemplar distance.IEEE/ACM Transactionson Computational Biologyand Bioinformatics, 10(6):1384–1390, November 2013.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Biswas:2019:RIM

[BKKG19] Ashis Kumer Biswas, Dong-Chul Kim, Mingon Kang,and Jean X. Gao. Robustinductive matrix completionstrategy to explore associa-tions between LincRNAs andhuman disease phenotypes.IEEE/ACM Transactionson Computational Biologyand Bioinformatics, 16(6):2066–2077, November 2019.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic). URL https://dl.acm.org/doi/abs/10.1109/TCBB.2018.2844816.

Bogdanov:2018:IEA

[BKLS18] Dan Bogdanov, Liina Kamm,Sven Laur, and Ville Sokk.Implementation and evalua-tion of an algorithm for cryp-tographically private princi-pal component analysis ongenomic data. IEEE/ACMTransactions on Computa-

REFERENCES 89

tional Biology and Bioin-formatics, 15(5):1427–1432,September 2018. CODENITCBCY. ISSN 1545-5963(print), 1557-9964 (elec-tronic).

Baker:2019:PPL

[BKP+19] Dixie B. Baker, Bartha M.Knoppers, Mark Phillips,David van Enckevort, PetraKaufmann, Hanns Lochmuller,and Domenica Taruscio.Privacy-preserving linkage ofgenomic and clinical datasets. IEEE/ACM Transac-tions on Computational Bi-ology and Bioinformatics, 16(4):1342–1348, July 2019.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Bocker:2011:DGS

[BKR11] Sebastian Bocker, BirteKehr, and Florian Rasche.Determination of glycanstructure from tandem massspectra. IEEE/ACM Trans-actions on ComputationalBiology and Bioinformat-ics, 8(4):976–986, July 2011.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Bicego:2012:ITM

[BLP+12] Manuele Bicego, Pietro Lo-vato, Alessandro Perina,Marianna Fasoli, MassimoDelledonne, Mario Pezzotti,Annalisa Polverari, and Vit-torio Murino. Investigating

topic models’ capabilities inexpression microarray dataclassification. IEEE/ACMTransactions on Computa-tional Biology and Bioin-formatics, 9(6):1831–1836,November 2012. CODENITCBCY. ISSN 1545-5963(print), 1557-9964 (elec-tronic).

Bartocci:2018:GEI

[BLP18] Ezio Bartocci, Pietro Lio,and Nicola Paoletti. Guesteditors’ introduction to thespecial section on the 14thInternational Conference onComputational Methods inSystems Biology CMSB2016. IEEE/ACM Transac-tions on Computational Bi-ology and Bioinformatics, 15(4):1122–1123, July 2018.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Boscolo:2008:ITE

[BLR08] Riccardo Boscolo, James C.Liao, and Vwani P. Roy-chowdhury. An informa-tion theoretic exploratorymethod for learning pat-terns of conditional gene co-expression from microarraydata. IEEE/ACM Trans-actions on ComputationalBiology and Bioinformatics,5(1):15–24, January 2008.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

REFERENCES 90

Basu:2015:EIF

[BLR15] Saurav Basu, Chi Liu, andGustavo Kunde Rohde. Ex-traction of individual fil-aments from 2D confocalmicroscopy images of flatcells. IEEE/ACM Trans-actions on ComputationalBiology and Bioinformatics,12(3):632–643, May 2015.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Bonet:2012:CFM

[BLS12] Maria Luisa Bonet, Si-mone Linz, and Kather-ine St. John. The com-plexity of finding multi-ple solutions to between-ness and quartet compati-bility. IEEE/ACM Transac-tions on Computational Bi-ology and Bioinformatics, 9(1):273–285, January 2012.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Bocker:2008:CAM

[BM08] Sebastian Bocker and VeliMakinen. Combinatorial ap-proaches for mass spectrarecalibration. IEEE/ACMTransactions on Computa-tional Biology and Bioinfor-matics, 5(1):91–100, January2008. CODEN ITCBCY.ISSN 1545-5963 (print),1557-9964 (electronic).

Bonnel:2012:LFP

[BM12] Nicolas Bonnel and Pierre-Francois Marteau. LNA:Fast protein structural com-parison using a Laplaciancharacterization of tertiarystructure. IEEE/ACMTransactions on Computa-tional Biology and Bioin-formatics, 9(5):1451–1458,September 2012. CODENITCBCY. ISSN 1545-5963(print), 1557-9964 (elec-tronic).

Bordewich:2013:AGP

[BM13] Magnus Bordewich andRadu Mihaescu. Accuracyguarantees for phylogenyreconstruction algorithmsbased on balanced mini-mum evolution. IEEE/ACMTransactions on Computa-tional Biology and Bioinfor-matics, 10(3):576–583, May2013. CODEN ITCBCY.ISSN 1545-5963 (print),1557-9964 (electronic).

Bandyopadhyay:2014:NPB

[BM14] Sanghamitra Bandyopad-hyay and Koushik Mallick. Anew path based hybrid mea-sure for gene ontology simi-larity. IEEE/ACM Transac-tions on Computational Bi-ology and Bioinformatics, 11(1):116–127, January 2014.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

REFERENCES 91

Bhattacharyya:2015:CCS

[BM15] Sourya Bhattacharyya andJayanta Mukherjee. COSPEDTree:couplet supertree by equiv-alence partitioning of taxaset and DAG formation.IEEE/ACM Transactions onComputational Biology andBioinformatics, 12(3):590–603, May 2015. CODENITCBCY. ISSN 1545-5963(print), 1557-9964 (elec-tronic).

Bandyopadhyay:2017:NFV

[BM17] Sanghamitra Bandyopad-hyay and Koushik Mallick.A new feature vector basedon gene ontology terms forprotein–protein interactionprediction. IEEE/ACMTransactions on Computa-tional Biology and Bioinfor-matics, 14(4):762–770, July2017. CODEN ITCBCY.ISSN 1545-5963 (print),1557-9964 (electronic).

Boukari:2020:ACT

[BM20] Fatima Boukari and SokratisMakrogiannis. Automatedcell tracking using mo-tion prediction-based match-ing and event handling.IEEE/ACM Transactions onComputational Biology andBioinformatics, 17(3):959–971, May 2020. CODENITCBCY. ISSN 1545-5963(print), 1557-9964 (elec-tronic). URL https://dl.acm.org/doi/10.1109/TCBB.2018.2875684.

Bahlouli:2016:FBP

[BMH+16] S. Bahlouli, A. Mokaddem,F. Hamdache, H. Riane, andM. Kameche. Fractal behav-ior of the pancreatic β-cellnear the percolation thresh-old: Effect of the KATP chan-nel on the electrical response.IEEE/ACM Transactions onComputational Biology andBioinformatics, 13(1):112–121, January 2016. CODENITCBCY. ISSN 1545-5963(print), 1557-9964 (elec-tronic).

Bleik:2013:TCB

[BMHS13] Said Bleik, Meenakshi Mishra,Jun Huan, and Min Song.Text categorization of biomed-ical data sets using graphkernels and a controlledvocabulary. IEEE/ACMTransactions on Computa-tional Biology and Bioin-formatics, 10(5):1211–1217,September 2013. CODENITCBCY. ISSN 1545-5963(print), 1557-9964 (elec-tronic).

Barker:2011:LGR

[BMK11] Nathan A. Barker, Chris J.Myers, and Hiroyuki Kuwa-hara. Learning genetic reg-ulatory network connectiv-ity from time series data.IEEE/ACM Transactions onComputational Biology andBioinformatics, 8(1):152–165, January 2011. CODENITCBCY. ISSN 1545-5963

REFERENCES 92


Bernt:2006:GRB

[BMM06] Matthias Bernt, DanielMerkle, and Martin Midden-dorf. Genome rearrange-ment based on reversalsthat preserve conserved in-tervals. IEEE/ACM Trans-actions on ComputationalBiology and Bioinformat-ics, 3(3):275–288, July 2006.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Bernt:2008:SPR

[BMM08] Matthias Bernt, DanielMerkle, and Martin Midden-dorf. Solving the preserv-ing reversal median prob-lem. IEEE/ACM Trans-actions on ComputationalBiology and Bioinformat-ics, 5(3):332–347, July 2008.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Bandyopadhyay:2014:SCS

[BMM14] Sanghamitra Bandyopad-hyay, Saurav Mallik, andAnirban Mukhopadhyay. Asurvey and comparativestudy of statistical tests foridentifying differential ex-pression from microarraydata. IEEE/ACM Transac-tions on Computational Bi-ology and Bioinformatics, 11(1):95–115, January 2014.CODEN ITCBCY. ISSN


Becker:2017:MTL

[BMT17] Matthias Becker and NadiaMagnenat-Thalmann. Mus-cle tissue labeling of hu-man lower limb in multi-channel mDixon MR imag-ing: Concepts and applica-tions. IEEE/ACM Trans-actions on ComputationalBiology and Bioinformatics,14(2):290–299, March 2017.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Bordon:2015:FLC

[BMZM15] Jure Bordon, Miha Moskon,Nikolaj Zimic, and MihaMraz. Fuzzy logic as a com-putational tool for quanti-tative modelling of biologi-cal systems with uncertainkinetic data. IEEE/ACMTransactions on Computa-tional Biology and Bioin-formatics, 12(5):1199–1205,September 2015. CODENITCBCY. ISSN 1545-5963(print), 1557-9964 (elec-tronic).

Berry:2006:IPC

[BN06] Vincent Berry and FrancoisNicolas. Improved param-eterized complexity of themaximum agreement subtreeand maximum compatibletree problems. IEEE/ACMTransactions on Computa-tional Biology and Bioinfor-

REFERENCES 93

matics, 3(3):289–302, July2006. CODEN ITCBCY.ISSN 1545-5963 (print),1557-9964 (electronic).

Boyen:2013:MMM

[BNV+13] Peter Boyen, Frank Neven,Dries Van Dyck, FelipeValentim, and Aalt vanDijk. Mining minimal mo-tif pair sets maximally cover-ing interactions in a protein-protein interaction network.IEEE/ACM Transactions onComputational Biology andBioinformatics, 10(1):73–86,January 2013. CODENITCBCY. ISSN 1545-5963(print), 1557-9964 (elec-tronic).

Boucher:2012:HCS

[BO12] Christina Boucher and Mo-hamed Omar. On thehardness of counting andsampling center strings.IEEE/ACM Transactionson Computational Biologyand Bioinformatics, 9(6):1843–1846, November 2012.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Brito:2020:HRT

[BODD20] Klairton Lima Brito, An-dre Rodrigues Oliveira,Ulisses Dias, and ZanoniDias. Heuristics for the re-versal and transposition dis-tance problem. IEEE/ACMTransactions on Computa-tional Biology and Bioinfor-

matics, 17(1):2–13, January2020. CODEN ITCBCY.ISSN 1545-5963 (print),1557-9964 (electronic). URLhttps://dl.acm.org/doi/abs/10.1109/TCBB.2019.2945759.

Bontempi:2007:BSI

[Bon07] Gianluca Bontempi. Ablocking strategy to improvegene selection for classifi-cation of gene expressiondata. IEEE/ACM Trans-actions on ComputationalBiology and Bioinformatics,4(2):293–300, April 2007.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Bokhari:2012:RNE

[BPJ12] Shahid H. Bokhari, Laura W.Pomeroy, and Daniel A. Ja-nies. Reassortment networksand the evolution of pan-demic H1N1 swine-origin in-fluenza. IEEE/ACM Trans-actions on ComputationalBiology and Bioinformatics,9(1):214–227, January 2012.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Bach:2013:SND

[BPP+13] Christian Bach, Prabir Pa-tra, Jani M. Pallis, WilliamSherman, and Hassan Ba-jwa. Strategy for naturelikedesigner transcription fac-tors with reduced toxicity.IEEE/ACM Transactions

REFERENCES 94

on Computational Biologyand Bioinformatics, 10(5):1340–1343, September 2013.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Borodovsky:2011:GEI

[BPRZ11] Mark Borodovsky, Teresa M.Przytycka, Sanguthevar Ra-jasekaran, and Alexander Ze-likovsky. Guest Editors’introduction to the spe-cial section on bioinformat-ics research and applica-tions. IEEE/ACM Trans-actions on ComputationalBiology and Bioinformat-ics, 8(4):865–866, July 2011.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Battagliero:2011:EAA

[BPV+11] Simone Battagliero, Giu-seppe Puglia, Saverio Vi-cario, Francesco Rubino,Gaetano Scioscia, and PietroLeo. An efficient algorithmfor approximating geodesicdistances in tree space.IEEE/ACM Transactionson Computational Biologyand Bioinformatics, 8(5):1196–1207, September 2011.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Basu:2017:GEI

[BPW17] Mitra Basu, Yi Pan, andJianxin Wang. Guest Ed-itors introduction to the

special section on ISBRA2014. IEEE/ACM Trans-actions on ComputationalBiology and Bioinformatics,14(2):314–315, March 2017.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Barragan:2017:COA

[BRF17] Sandra Barragan, CristinaRueda, and Miguel A. Fer-nandez. Circular order ag-gregation and its applicationto cell-cycle genes expres-sions. IEEE/ACM Trans-actions on ComputationalBiology and Bioinformatics,14(4):819–829, July 2017.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Brown:2005:OMS

[Bro05] Daniel G. Brown. Opti-mizing multiple seeds forprotein homology search.IEEE/ACM Transactions onComputational Biology andBioinformatics, 2(1):29–38,January 2005. CODENITCBCY. ISSN 1545-5963(print), 1557-9964 (elec-tronic).

Behinaein:2018:PNS

[BRS18] Behnam Behinaein, KarenRudie, and Waheed San-grar. Petri net siphon analy-sis and graph theoretic mea-sures for identifying com-bination therapies in can-cer. IEEE/ACM Transac-

REFERENCES 95

tions on Computational Bi-ology and Bioinformatics, 15(1):231–243, January 2018.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Biswas:2017:ECM

[BRZ+17] Abhishek Biswas, Desh Ran-jan, Mohammad Zubair,Stephanie Zeil, Kamal AlNasr, and Jing He. An effec-tive computational methodincorporating multiple sec-ondary structure predic-tions in topology deter-mination for cryo-EM im-ages. IEEE/ACM Trans-actions on ComputationalBiology and Bioinformatics,14(3):578–586, May 2017.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Bordewich:2007:CHN

[BS07] Magnus Bordewich andCharles Semple. Comput-ing the hybridization num-ber of two phylogenetic treesis fixed-parameter tractable.IEEE/ACM Transactions onComputational Biology andBioinformatics, 4(3):458–466, July 2007. CODENITCBCY. ISSN 1545-5963(print), 1557-9964 (elec-tronic).

Bordewich:2008:NRS

[BS08] Magnus Bordewich andCharles Semple. Nature re-serve selection problem: a

tight approximation algo-rithm. IEEE/ACM Trans-actions on ComputationalBiology and Bioinformatics,5(2):275–280, April 2008.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Bryant:2009:CDT

[BS09] David Bryant and MikeSteel. Computing the dis-tribution of a tree met-ric. IEEE/ACM Trans-actions on ComputationalBiology and Bioinformat-ics, 6(3):420–426, July 2009.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Bogdanov:2010:MFP

[BS10a] Petko Bogdanov and Am-buj K. Singh. Molecu-lar function prediction us-ing neighborhood features.IEEE/ACM Transactions onComputational Biology andBioinformatics, 7(2):208–217, April 2010. CODENITCBCY. ISSN 1545-5963(print), 1557-9964 (elec-tronic).

Bonet:2010:CUD

[BS10b] Maria Luisa Bonet andKatherine St.John. On thecomplexity of uSPR dis-tance. IEEE/ACM Trans-actions on ComputationalBiology and Bioinformat-ics, 7(3):572–576, July 2010.CODEN ITCBCY. ISSN

REFERENCES 96


Bansal:2011:NFP

[BS11] Mukul S. Bansal and RonShamir. A note on the fixedparameter tractability of thegene-duplication problem.IEEE/ACM Transactionson Computational Biologyand Bioinformatics, 8(3):848–850, May/June 2011.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Braga:2015:SLG

[BS15] Marılia D. V. Braga andJens Stoye. Sorting lin-ear genomes with rearrange-ments and indels. IEEE/ACM Transactions on Com-putational Biology and Bioin-formatics, 12(3):500–506,May 2015. CODEN ITCBCY.ISSN 1545-5963 (print),1557-9964 (electronic).

Boscolo:2005:GFN

[BSLR05] Riccardo Boscolo, ChiaraSabatti, James C. Liao, andVwani P. Roychowdhury. Ageneralized framework fornetwork component analy-sis. IEEE/ACM Transac-tions on Computational Bi-ology and Bioinformatics, 2(4):289–301, October 2005.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Braga:2008:ESS

[BSST08] Marılia D. V. Braga, Marie-France Sagot, Celine Scor-navacca, and Eric Tan-nier. Exploring the solu-tion space of sorting by re-versals, with experimentsand an application to evo-lution. IEEE/ACM Trans-actions on ComputationalBiology and Bioinformat-ics, 5(3):348–356, July 2008.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Blin:2010:QGP

[BSV10] Guillaume Blin, FlorianSikora, and Stephane Vialette.Querying graphs in protein-protein interactions net-works using feedback vertexset. IEEE/ACM Transac-tions on Computational Bi-ology and Bioinformatics, 7(4):628–635, October 2010.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Befekadu:2011:PMR

[BTTR11] Getachew K. Befekadu,Mahlet G. Tadesse, Tsung-Heng Tsai, and Habtom W.Ressom. Probabilistic mix-ture regression models foralignment of LC-MS data.IEEE/ACM Transactionson Computational Biologyand Bioinformatics, 8(5):1417–1424, September 2011.CODEN ITCBCY. ISSN

REFERENCES 97


Blumenthal:2013:IIR

[BTYC13] Seth Blumenthal, YishengTang, Wenjie Yang, andBrian Chen. Isolating in-fluential regions of electro-static focusing in protein andDNA structure. IEEE/ACMTransactions on Computa-tional Biology and Bioin-formatics, 10(5):1188–1198,September 2013. CODENITCBCY. ISSN 1545-5963(print), 1557-9964 (elec-tronic).

Bittig:2017:MSH

[BU17] Arne T. Bittig and Adelinde M.Uhrmacher. ML-Space: Hy-brid spatial Gillespie andparticle simulation of multi-level rule-based models incell biology. IEEE/ACMTransactions on Computa-tional Biology and Bioin-formatics, 14(6):1339–1349,November 2017. CODENITCBCY. ISSN 1545-5963(print), 1557-9964 (elec-tronic).

Betzler:2011:PAF

[BvBF+11] Nadja Betzler, Rene vanBevern, Michael R. Fellows,Christian Komusiewicz, andRolf Niedermeier. Pa-rameterized algorithmicsfor finding connected mo-tifs in biological networks.IEEE/ACM Transactionson Computational Biology

and Bioinformatics, 8(5):1296–1308, September 2011.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Bonizzoni:2007:ELC

[BVD+07] Paola Bonizzoni, Gian-luca Della Vedova, Ric-cardo Dondi, GuillaumeFertin, Raffaella Rizzi, andStephane Vialette. Exem-plar longest common subse-quence. IEEE/ACM Trans-actions on ComputationalBiology and Bioinformatics,4(4):535–543, October 2007.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Bonizzoni:2010:PPX

[BVD+10] Paola Bonizzoni, Gian-luca Della Vedova, Ric-cardo Dondi, Yuri Pirola,and Romeo Rizzi. Pureparsimony xor haplotyp-ing. IEEE/ACM Transac-tions on Computational Bi-ology and Bioinformatics, 7(4):598–610, October 2010.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Buhrman:2011:SMR

[BvdGK+11] Harry Buhrman, Peter T. S.van der Gulik, Steven M.Kelk, Wouter M. Koolen,and Leen Stougie. Somemathematical refinementsconcerning error minimiza-tion in the genetic code.

REFERENCES 98


Boyen:2011:SGM

[BVN+11] Peter Boyen, Dries VanDyck, Frank Neven, RoelandC. H. J. van Ham, and AaltD. J. van Dijk. SLIDER: ageneric metaheuristic for thediscovery of correlated motifsin protein-protein interac-tion networks. IEEE/ACMTransactions on Computa-tional Biology and Bioin-formatics, 8(5):1344–1357,September 2011. CODENITCBCY. ISSN 1545-5963(print), 1557-9964 (elec-tronic).

Bao:2017:CPS

[BWC17] Wenzheng Bao, Dong Wang,and Yuehui Chen. Clas-sification of protein struc-ture classes on flexible neu-tral tree. IEEE/ACM Trans-actions on ComputationalBiology and Bioinformatics,14(5):1122–1133, September2017. CODEN ITCBCY.ISSN 1545-5963 (print),1557-9964 (electronic).

Burkitt:2012:CCB

[BWRF12] Mark Burkitt, Dawn Walker,Daniella M. Romano, andAlireza Fazeli. Constructingcomplex 3D biological envi-

ronments from medical imag-ing using high performancecomputing. IEEE/ACMTransactions on Computa-tional Biology and Bioinfor-matics, 9(3):643–654, May2012. CODEN ITCBCY.ISSN 1545-5963 (print),1557-9964 (electronic).

Biyani:2005:JCP

[BWS05] Pravesh Biyani, Xiaolin Wu,and Abhijit Sinha. Jointclassification and pairingof human chromosomes.IEEE/ACM Transactions onComputational Biology andBioinformatics, 2(2):102–109, April 2005. CODENITCBCY. ISSN 1545-5963(print), 1557-9964 (elec-tronic).

Bao:2018:MFP

[BYZ+18] Wenzheng Bao, Chang-An Yuan, Youhua Zhang,Kyungsook Han, Asoke K.Nandi, Barry Honig, andDe-Shuang Huang. Mutli-features prediction of pro-tein translational modifi-cation sites. IEEE/ACMTransactions on Computa-tional Biology and Bioin-formatics, 15(5):1453–1460,September 2018. CODENITCBCY. ISSN 1545-5963(print), 1557-9964 (elec-tronic).

Bereg:2007:PNB

[BZ07] Sergey Bereg and YuanyiZhang. Phylogenetic net-

REFERENCES 99

works based on the molecu-lar clock hypothesis. IEEE/ACM Transactions on Com-putational Biology and Bioin-formatics, 4(4):661–667, Oc-tober 2007. CODENITCBCY. ISSN 1545-5963(print), 1557-9964 (elec-tronic).

Brinza:2008:SPM

[BZ08] Dumitru Brinza and Alexan-der Zelikovsky. 2SNP: Scal-able phasing method fortrios and unrelated individ-uals. IEEE/ACM Trans-actions on ComputationalBiology and Bioinformatics,5(2):313–318, April 2008.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Bergemann:2010:SQM

[BZ10] Tracy L. Bergemann andLue Ping Zhao. Sig-nal quality measurementsfor cDNA microarray data.IEEE/ACM Transactions onComputational Biology andBioinformatics, 7(2):299–308, April 2010. CODENITCBCY. ISSN 1545-5963(print), 1557-9964 (elec-tronic).

Comin:2014:FEP

[CA14] Matteo Comin and MorrisAntonello. Fast entropic pro-filer: an information theo-retic approach for the discov-ery of patterns in genomes.IEEE/ACM Transactions on

Computational Biology andBioinformatics, 11(3):500–509, May 2014. CODENITCBCY. ISSN 1545-5963(print), 1557-9964 (elec-tronic).

Congdon:2008:EIC

[CAN+08] Clare Bates Congdon, Joseph C.Aman, Gerardo M. Nava,H. Rex Gaskins, and Car-olyn J. Mattingly. An eval-uation of information con-tent as a metric for theinference of putative con-served noncoding regionsin DNA sequences usinga genetic algorithms ap-proach. IEEE/ACM Trans-actions on ComputationalBiology and Bioinformat-ics, 5(1):1–14, January 2008.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Casadio:2006:GEI

[Cas06] Rita Casadio. Guest Edi-tor’s introduction to the spe-cial issue on computationalbiology and bioinformatics –part 1. IEEE/ACM Transac-tions on Computational Bi-ology and Bioinformatics, 3(4):321–322, October 2006.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Casadio:2007:GEI

[Cas07] Rita Casadio. Guest Edi-tor’s introduction to the Spe-cial Section on Computa-

REFERENCES 100

tional Biology and Bioin-formatics (WABI) – part2. IEEE/ACM Transactionson Computational Biologyand Bioinformatics, 4(1):3, January 2007. CODENITCBCY. ISSN 1545-5963(print), 1557-9964 (elec-tronic).

Catalyurek:2017:GEI

[Cat17] Umit V. Catalyurek. GuestEditor’s introduction: Se-lected papers from ACM-BCB 2014. IEEE/ACMTransactions on Computa-tional Biology and Bioin-formatics, 14(5):1000–1001,September 2017. CODENITCBCY. ISSN 1545-5963(print), 1557-9964 (elec-tronic).

Chen:2019:QNS

[CAW+19] Minghan Chen, Brandon D.Amos, Layne T. Watson,John J. Tyson, YoungCao, Clifford A. Shaffer,Michael W. Trosset, CihanOguz, and Gisella Kakoti.Quasi-Newton stochastic op-timization algorithm for pa-rameter estimation of astochastic model of thebudding yeast cell cycle.IEEE/ACM Transactions onComputational Biology andBioinformatics, 16(1):301–311, January 2019. CODENITCBCY. ISSN 1545-5963(print), 1557-9964 (elec-tronic).

Cortes:2011:EMM

[CBES11] Juan Cortes, Sophie Barbe,Monique Erard, and ThierrySimeon. Encoding molecu-lar motions in voxel maps.IEEE/ACM Transactions onComputational Biology andBioinformatics, 8(2):557–563, March 2011. CODENITCBCY. ISSN 1545-5963(print), 1557-9964 (elec-tronic).

Correa:2018:MAP

[CBF+18] Leonardo Correa, BrunoBorguesan, Camilo Farfan,Mario Inostroza-Ponta, andMarcio Dorn. A memeticalgorithm for 3D proteinstructure prediction prob-lem. IEEE/ACM Transac-tions on Computational Bi-ology and Bioinformatics,15(3):690–704, May 2018.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Chaudhary:2012:FLS

[CBFB12] Ruchi Chaudhary, J. Gor-don Burleigh, and DavidFernandez-Baca. Fast lo-cal search for unrootedRobinson–Foulds supertrees.IEEE/ACM Transactions onComputational Biology andBioinformatics, 9(4):1004–1013, July 2012. CODENITCBCY. ISSN 1545-5963(print), 1557-9964 (elec-tronic).

REFERENCES 101

Chowdhury:2020:DEA

[CBK20] Hussain Ahmed Chowd-hury, Dhruba Kumar Bhat-tacharyya, and Jugal Ku-mar Kalita. Differential ex-pression analysis of RNA-seq reads: Overview, taxon-omy, and tools. IEEE/ACMTransactions on Computa-tional Biology and Bioin-formatics, 17(2):566–586,March 2020. CODENITCBCY. ISSN 1545-5963(print), 1557-9964 (elec-tronic). URL https://dl.acm.org/doi/abs/10.1109/TCBB.2018.2873010.

Chen:2020:BPD

[CBM+20] Ziwei Chen, Xiangqi Bai,Liang Ma, Xiawei Wang, Xi-uqin Liu, Yuting Liu, Luo-nan Chen, and Lin Wan. Abranch point on differentia-tion trajectory is the bifur-cating event revealed by dy-namical network biomarkeranalysis of single-cell data.IEEE/ACM Transactions onComputational Biology andBioinformatics, 17(2):366–375, March 2020. CODENITCBCY. ISSN 1545-5963(print), 1557-9964 (elec-tronic). URL https://dl.acm.org/doi/abs/10.1109/TCBB.2018.2847690.

Chen:2015:SDI

[CBN15] Ting Chen and Ulisses M.Braga-Neto. Statistical de-tection of intrinsically mul-tivariate predictive genes.

IEEE/ACM Transactions onComputational Biology andBioinformatics, 12(4):951–963, July 2015. CODENITCBCY. ISSN 1545-5963(print), 1557-9964 (elec-tronic).

Chlis:2018:ISB

[CBZ18] Nikolaos-Kosmas Chlis, Eka-terini S. Bei, and MichalisZervakis. Introducing astable bootstrap validationframework for reliable ge-nomic signature extraction.IEEE/ACM Transactions onComputational Biology andBioinformatics, 15(1):181–190, January 2018. CODENITCBCY. ISSN 1545-5963(print), 1557-9964 (elec-tronic).

Chen:2007:CBR

[CC07] Jinmiao Chen and Naren-dra Chaudhari. Cascadedbidirectional recurrent neu-ral networks for proteinsecondary structure predic-tion. IEEE/ACM Transac-tions on Computational Bi-ology and Bioinformatics, 4(4):572–582, October 2007.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Chen:2009:AAM

[CC09] Xin Chen and Yun Cui.An approximation algorithmfor the minimum break-point linearization prob-lem. IEEE/ACM Trans-

REFERENCES 102

actions on ComputationalBiology and Bioinformat-ics, 6(3):401–409, July 2009.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Chen:2011:FAP

[CC11] Qingfeng Chen and Yi-Ping Phoebe Chen. Functionannotation for pseudoknotusing structure similarity.IEEE/ACM Transactionson Computational Biologyand Bioinformatics, 8(6):1535–1544, November 2011.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Cavuslar:2012:TSA

[CCA12] Gizem Cavuslar, BulentCatay, and Mehmet SerkanApaydin. A tabu search ap-proach for the NMR pro-tein structure-based assign-ment problem. IEEE/ACMTransactions on Computa-tional Biology and Bioin-formatics, 9(6):1621–1628,November 2012. CODENITCBCY. ISSN 1545-5963(print), 1557-9964 (elec-tronic).

Cai:2020:IMM

[CCCY20] Jiulun Cai, Hongmin Cai, Ji-azhou Chen, and Xi Yang.Identifying “many-to–many”relationships between gene-expression data and drug-response data via sparse bi-nary matching. IEEE/ACM

Transactions on Computa-tional Biology and Bioin-formatics, 17(1):165–176,January 2020. CODENITCBCY. ISSN 1545-5963(print), 1557-9964 (elec-tronic). URL https://dl.acm.org/doi/abs/10.1109/TCBB.2018.2849708.

Choudhury:2019:HAE

[CCE19] Olivia Choudhury, AnkushChakrabarty, and Scott J.Emrich. Highly accurate andefficient data-driven meth-ods for genotype imputa-tion. IEEE/ACM Transac-tions on Computational Bi-ology and Bioinformatics, 16(4):1107–1116, July 2019.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Caceres:2013:WSN

[CCLS13] Alan Joseph J. Caceres,Juan Castillo, Jinnie Lee,and Katherine St. John.Walks on SPR neighbor-hoods. IEEE/ACM Transac-tions on Computational Bi-ology and Bioinformatics, 10(1):236–239, January 2013.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Chan:2012:CVM

[CCYW12] Raymond H. Chan, Tony H.Chan, Hau Man Yeung, andRoger Wei Wang. Compo-sition vector method basedon maximum entropy prin-

REFERENCES 103

ciple for sequence compar-ison. IEEE/ACM Trans-actions on ComputationalBiology and Bioinformatics,9(1):79–87, January 2012.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Cho:2008:CHC

[CD08] Hyuk Cho and Inderjit S.Dhillon. Coclustering ofhuman cancer microar-rays using minimum sum-squared residue cocluster-ing. IEEE/ACM Trans-actions on ComputationalBiology and Bioinformat-ics, 5(3):385–400, July 2008.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Chang:2016:RGR

[CDB+16] Young Hwan Chang, RoelDobbe, Palak Bhushan,Joe W. Gray, and Claire J.Tomlin. Reconstructionof gene regulatory net-works based on repairingsparse low-rank matrices.IEEE/ACM Transactionson Computational Biologyand Bioinformatics, 13(4):767–777, 2016. CODENITCBCY. ISSN 1545-5963(print), 1557-9964 (elec-tronic).

Chowriappa:2009:PSC

[CDKT09] Pradeep Chowriappa, SumeetDua, Jinko Kanno, and Hi-lary W. Thompson. Protein

structure classification basedon conserved hydrophobicresidues. IEEE/ACM Trans-actions on ComputationalBiology and Bioinformatics,6(4):639–651, October 2009.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Chen:2012:SID

[CDW12] Zhi-Zhong Chen, Fei Deng,and Lusheng Wang. Simul-taneous identification of du-plications, losses, and lateralgene transfers. IEEE/ACMTransactions on Computa-tional Biology and Bioin-formatics, 9(5):1515–1528,September 2012. CODENITCBCY. ISSN 1545-5963(print), 1557-9964 (elec-tronic).

Chen:2006:MFS

[CEFBS06] Duhong Chen, Oliver Eu-lenstein, David Fernandez-Baca, and Michael Sander-son. Minimum-flip su-pertrees: Complexity andalgorithms. IEEE/ACMTransactions on Computa-tional Biology and Bioinfor-matics, 3(2):165–173, April2006. CODEN ITCBCY.ISSN 1545-5963 (print),1557-9964 (electronic).

Cai:2014:GEI

[CEG14] Zhipeng Cai, Oliver Eulen-stein, and Cynthia Gibas.Guest editors introduction tothe special section on bioin-

REFERENCES 104

formatics research and appli-cations. IEEE/ACM Trans-actions on ComputationalBiology and Bioinformatics,11(3):453–454, May 2014.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Cickovski:2015:GPI

[CFIS+15] Trevor Cickovski, TiffanyFlor, Galen Irving-Sachs,Philip Novikov, James Parda,and Giri Narasimhan. GPUDe-PiCt: a parallel imple-mentation of a cluster-ing algorithm for comput-ing degenerate primers ongraphics processing units.IEEE/ACM Transactions onComputational Biology andBioinformatics, 12(2):445–454, March 2015. CODENITCBCY. ISSN 1545-5963(print), 1557-9964 (elec-tronic).

Carvalho:2006:EAI

[CFOS06] Alexandra M. Carvalho,Ana T. Freitas, Arlindo L.Oliveira, and Marie-FranceSagot. An efficient al-gorithm for the identifi-cation of structured mo-tifs in DNA promoter se-quences. IEEE/ACM Trans-actions on ComputationalBiology and Bioinformatics,3(2):126–140, April 2006.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Cheng:2012:MDT

[CGLF12] Yi-Ming Cheng, Srinivasa MurthyGopal, Sean M. Law, andMichael Feig. Molecular dy-namics trajectory compres-sion with a coarse-grainedmodel. IEEE/ACM Trans-actions on ComputationalBiology and Bioinformatics,9(2):476–486, March 2012.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Chu:2006:BSM

[CGPW06] Wei Chu, Zoubin Ghahra-mani, Alexei Podtelezh-nikov, and David L. Wild.Bayesian segmental mod-els with multiple sequencealignment profiles for pro-tein secondary structureand contact map predic-tion. IEEE/ACM Trans-actions on ComputationalBiology and Bioinformat-ics, 3(2):98–113, April 2006.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Cheng:2016:MDL

[CGW+16] Shuang Cheng, Maozu Guo,Chunyu Wang, Xiaoyan Liu,Yang Liu, and Xuejian Wu.MiRTDL: a deep learningapproach for miRNA tar-get prediction. IEEE/ACMTransactions on Computa-tional Biology and Bioin-formatics, 13(6):1161–1169,November 2016. CODENITCBCY. ISSN 1545-5963

REFERENCES 105


Chen:2015:DIN

[CGZ15] Huidong Chen, Jihong Guan,and Shuigeng Zhou. DPNuc:Identifying nucleosome posi-tions based on the Dirich-let process mixture model.IEEE/ACM Transactionson Computational Biologyand Bioinformatics, 12(6):1236–1247, November 2015.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Chen:2011:ARD

[CH11] Yang Chen and JingluHu. Accurate reconstruc-tion for DNA sequenc-ing by hybridization basedon a constructive heuris-tic. IEEE/ACM Transac-tions on Computational Bi-ology and Bioinformatics, 8(4):1134–1140, July 2011.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Cickovski:2005:FTD

[CHC+05] Trevor M. Cickovski, Cheng-bang Huang, Rajiv Chaturvedi,Tilmann Glimm, H. George E.Hentschel, Mark S. Al-ber, James A. Glazier, Stu-art A. Newman, and Je-sus A. Izaguirre. A frame-work for three-dimensionalsimulation of morphogene-sis. IEEE/ACM Transac-tions on Computational Bi-

ology and Bioinformatics, 2(4):273–288, October 2005.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Cheng:2010:SLM

[Che10] Qiang Cheng. A sparselearning machine for high-dimensional data with ap-plication to microarray geneanalysis. IEEE/ACM Trans-actions on ComputationalBiology and Bioinformatics,7(4):636–646, October 2010.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Chen:2012:GEA

[Che12] Yi-Ping Phoebe Chen. Guesteditorial: Application anddevelopment of bioinformat-ics. IEEE/ACM Transac-tions on Computational Bi-ology and Bioinformatics, 9(5):1265, September 2012.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Chen:2013:GEA

[Che13] Yi-Ping Phoebe Chen. Guesteditorial: Advanced al-gorithms of bioinformat-ics. IEEE/ACM Trans-actions on ComputationalBiology and Bioinformat-ics, 10(2):273, March 2013.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

REFERENCES 106

Cheng:2016:NTL

[Che16] Yu-Huei Cheng. A novelteaching-learning-based op-timization for improved mu-tagenic primer design inmismatch PCR-RFLP SNPgenotyping. IEEE/ACMTransactions on Computa-tional Biology and Bioinfor-matics, 13(1):86–98, January2016. CODEN ITCBCY.ISSN 1545-5963 (print),1557-9964 (electronic).

Czeizler:2017:GTA

[CHK17] Elena Czeizler, Tommi Hir-vola, and Kalle Karhu. Agraph-theoretical approachfor Motif discovery in pro-tein sequences. IEEE/ACMTransactions on Computa-tional Biology and Bioin-formatics, 14(1):121–130,January 2017. CODENITCBCY. ISSN 1545-5963(print), 1557-9964 (elec-tronic).

Chen:2012:EFT

[CHL+12] Xin Chen, Xiaohua Hu,Tze Yee Lim, Xiajiong Shen,E. K. Park, and Gail L.Rosen. Exploiting the func-tional and taxonomic struc-ture of genomic data byprobabilistic topic model-ing. IEEE/ACM Trans-actions on ComputationalBiology and Bioinformat-ics, 9(4):980–991, July 2012.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Cheng:2018:NPI

[CHN+18] Xiangfei Cheng, Yue Hou,Yumin Nie, Yiru Zhang,Huan Huang, Hongde Liu,and Xiao Sun. Nucleo-some positioning of intron-less genes in the humangenome. IEEE/ACM Trans-actions on ComputationalBiology and Bioinformatics,15(4):1111–1121, July 2018.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Chen:2020:FEC

[CHNW20] Zhi-Zhong Chen, YoutaHarada, Yuna Nakamura,and Lusheng Wang. Fasterexact computation of rSPRdistance via better approxi-mation. IEEE/ACM Trans-actions on ComputationalBiology and Bioinformatics,17(3):916–929, May 2020.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic). URL https://dl.acm.org/doi/10.1109/TCBB.2018.2878731.

Chiu:2018:ADR

[CHW+18] Yu-Chiao Chiu, Tzu-HungHsiao, Li-Ju Wang, YidongChen, and Eric Y. Chuang.Analyzing differential regu-latory networks modulatedby continuous-state genomicfeatures in glioblastoma mul-tiforme. IEEE/ACM Trans-actions on ComputationalBiology and Bioinformatics,15(6):1754–1764, November

REFERENCES 107

2018. CODEN ITCBCY.ISSN 1545-5963 (print),1557-9964 (electronic).

Chen:2019:SWC

[CHWY19] Xiaojun Chen, Joshua Z.Huang, Qingyao Wu, andMin Yang. Subspace weight-ing co-clustering of gene ex-pression data. IEEE/ACMTransactions on Computa-tional Biology and Bioin-formatics, 16(2):352–364,March 2019. CODENITCBCY. ISSN 1545-5963(print), 1557-9964 (elec-tronic). URL https://dl.acm.org/doi/abs/10.1109/TCBB.2017.2705686.

Chen:2016:SBD

[CHZ+16] Peng Chen, ShanShan Hu,Jun Zhang, Xin Gao, JinyanLi, Junfeng Xia, and BingWang. A sequence-baseddynamic ensemble learningsystem for protein ligand-binding site prediction.IEEE/ACM Transactionson Computational Biologyand Bioinformatics, 13(5):901–912, September 2016.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Ceri:2017:DMH

[CKM+17] Stefano Ceri, AbdulrahmanKaitoua, Marco Masseroli,Pietro Pinoli, and FrancescoVenco. Data managementfor heterogeneous genomicdatasets. IEEE/ACM Trans-

actions on ComputationalBiology and Bioinformatics,14(6):1251–1264, November2017. CODEN ITCBCY.ISSN 1545-5963 (print),1557-9964 (electronic).

Choi:2012:HAS

[CKWY12] Ickwon Choi, Michael W.Kattan, Brian J. Wells, andChanghong Yu. A hy-brid approach to survivalmodel building using integra-tion of clinical and molecu-lar information in censoreddata. IEEE/ACM Transac-tions on Computational Bi-ology and Bioinformatics, 9(4):1091–1105, July 2012.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Chin:2008:DMR

[CL08] Francis Chin and HenryC. M. Leung. DNA mo-tif representation with nu-cleotide dependency. IEEE/ACM Transactions on Com-putational Biology and Bioin-formatics, 5(1):110–119, Jan-uary 2008. CODEN ITCBCY.ISSN 1545-5963 (print),1557-9964 (electronic).

Chuang:2014:NSG

[CL14] Chia-Hua Chuang and Chun-Liang Lin. A novel syn-thesizing genetic logic cir-cuit: frequency multiplier.IEEE/ACM Transactions onComputational Biology andBioinformatics, 11(4):702–

REFERENCES 108

713, July 2014. CODENITCBCY. ISSN 1545-5963(print), 1557-9964 (elec-tronic).

Chen:2015:SGC

[CL15] Po-Kuei Chen and Chun-Liang Lin. Synthesis ofgenetic clock with combi-national biologic circuits.IEEE/ACM Transactionson Computational Biologyand Bioinformatics, 12(5):1206–1212, September 2015.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Chen:2017:ECR

[CLC+17] Qingfeng Chen, ChaowangLan, Baoshan Chen, LushengWang, Jinyan Li, andChengqi Zhang. Explor-ing consensus RNA substruc-tural patterns using sub-graph mining. IEEE/ACMTransactions on Computa-tional Biology and Bioin-formatics, 14(5):1134–1146,September 2017. CODENITCBCY. ISSN 1545-5963(print), 1557-9964 (elec-tronic).

Catanzaro:2013:IPF

[CLH13] Daniele Catanzaro, Mar-tine Labbe, and Bjarni V.Halldorsson. An integerprogramming formulationof the parsimonious lossof heterozygosity problem.IEEE/ACM Transactionson Computational Biology


Cheng:2015:USA

[CLH+15] Liang Cheng, Jie Li, YangHu, Yue Jiang, YongzhuangLiu, Yanshuo Chu, Zhenx-ing Wang, and YadongWang. Using semantic asso-ciation to extend and inferliterature-oriented relativitybetween terms. IEEE/ACMTransactions on Computa-tional Biology and Bioin-formatics, 12(6):1219–1226,November 2015. CODENITCBCY. ISSN 1545-5963(print), 1557-9964 (elec-tronic).

Chen:2010:BSI

[CLM10] Yifei Chen, Feng Liu, andBernard Manderick. Bi-oLMiner system: Inter-action normalization taskand interaction pair task inthe BioCreative II.5 chal-lenge. IEEE/ACM Trans-actions on ComputationalBiology and Bioinformat-ics, 7(3):428–441, July 2010.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Chowdhury:2010:COD

[CLR10] Rezaul Alan Chowdhury,Hai-Son Le, and VijayaRamachandran. Cache-oblivious dynamic program-

REFERENCES 109

ming for bioinformatics.IEEE/ACM Transactions onComputational Biology andBioinformatics, 7(3):495–510, July 2010. CODENITCBCY. ISSN 1545-5963(print), 1557-9964 (elec-tronic).

Cardona:2009:MPNa

[CLRV09a] Gabriel Cardona, MerceLlabres, Francesc Rossello,and Gabriel Valiente. Met-rics for phylogenetic net-works I: Generalizations ofthe Robinson–Foulds met-ric. IEEE/ACM Transac-tions on Computational Bi-ology and Bioinformatics,6(1):46–61, January 2009.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Cardona:2009:MPNb

[CLRV09b] Gabriel Cardona, MerceLlabres, Francesc Rossello,and Gabriel Valiente. Met-rics for phylogenetic net-works II: Nodal and tripletsmetrics. IEEE/ACM Trans-actions on ComputationalBiology and Bioinformat-ics, 6(3):454–469, July 2009.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Cardona:2009:NMR

[CLRV09c] Gabriel Cardona, MerceLlabres, Francesc Rossello,and Gabriel Valiente. OnNakhleh’s metric for re-

duced phylogenetic net-works. IEEE/ACM Transac-tions on Computational Bi-ology and Bioinformatics, 6(4):629–638, October 2009.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Cardona:2011:CGT

[CLRV11] Gabriel Cardona, MerceLlabres, Francesc Rossello,and Gabriel Valiente. Com-parison of galled trees.IEEE/ACM Transactions onComputational Biology andBioinformatics, 8(2):410–427, March 2011. CODENITCBCY. ISSN 1545-5963(print), 1557-9964 (elec-tronic).

Cheng:2019:CBC

[CLS19] Kin-On Cheng, Ngai-FongLaw, and Wan-Chi Siu.Clustering-based compres-sion for population DNA se-quences. IEEE/ACM Trans-actions on ComputationalBiology and Bioinformat-ics, 16(1):208–221, January2019. CODEN ITCBCY.ISSN 1545-5963 (print),1557-9964 (electronic).

Chan:2013:MAP

[CLST+13] Tak-Ming Chan, Leung-YauLo, Ho-Yin Sze-To, Kwong-Sak Leung, Xinshu Xiao, andMan-Hon Wong. Modelingassociated protein-DNA pat-tern discovery with unifiedscores. IEEE/ACM Trans-

REFERENCES 110

actions on ComputationalBiology and Bioinformatics,10(3):696–707, May 2013.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Carvajal-Lopez:2020:MBQ

[CLVT+20] Patricia Carvajal-Lopez, Fer-nando D. Von Borstel,Amada Torres, GabriellaRustici, Joaquın Gutierrez,and Eduardo Romero-Vivas.Microarray-based quality as-sessment as a supportingcriterion for de novo tran-scriptome assembly selec-tion. IEEE/ACM Transac-tions on Computational Bi-ology and Bioinformatics, 17(1):198–206, January 2020.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic). URL https://dl.acm.org/doi/abs/10.1109/TCBB.2018.2860997.

Chen:2013:MFP

[CLW13] Qingfeng Chen, Wei Lan,and Jianxin Wang. Miningfeatured patterns of MiRNAinteraction based on se-quence and structure simi-larity. IEEE/ACM Trans-actions on ComputationalBiology and Bioinformatics,10(2):415–422, March 2013.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Liang:2007:BBD

[cLWA07] Kuo ching Liang, Xiaodong

Wang, and Dimitris Anas-tassiou. Bayesian basecall-ing for DNA sequence anal-ysis using hidden Markovmodels. IEEE/ACM Trans-actions on ComputationalBiology and Bioinformat-ics, 4(3):430–440, July 2007.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Chen:2018:SCF

[CLZ+18] Shifu Chen, Ming Liu, Xi-aoni Zhang, Renwen Long,Yixing Wang, Yue Han, Shi-wei Zhang, Mingyan Xu, andJia Gu. A study of cell-freeDNA fragmentation patternand its application in DNAsample type classification.IEEE/ACM Transactionson Computational Biologyand Bioinformatics, 15(5):1718–1722, September 2018.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Christinat:2013:TPE

[CM13] Yann Christinat and BernardM. E. Moret. A transcriptperspective on evolution.IEEE/ACM Transactionson Computational Biologyand Bioinformatics, 10(6):1403–1411, November 2013.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Chicco:2015:SSG

[CM15] Davide Chicco and Marco

REFERENCES 111

Masseroli. Software suitefor gene and protein annota-tion prediction and similaritysearch. IEEE/ACM Trans-actions on ComputationalBiology and Bioinformatics,12(4):837–843, July 2015.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Chicco:2016:OBP

[CM16] Davide Chicco and MarcoMasseroli. Ontology-basedprediction and prioritizationof gene functional annota-tions. IEEE/ACM Trans-actions on ComputationalBiology and Bioinformatics,13(2):248–260, March 2016.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Czeizler:2012:QAS

[CMC+12] Eugen Czeizler, AndrzejMizera, Elena Czeizler,Ralph-Johan Back, John E.Eriksson, and Ion Pe-tre. Quantitative analysisof the self-assembly strate-gies of intermediate fila-ments from tetrameric Vi-mentin. IEEE/ACM Trans-actions on ComputationalBiology and Bioinformat-ics, 9(3):885–898, May 2012.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Chen:2020:BDF

[CMMZ20] Haifen Chen, D. A. K. Madu-

ranga, Piyushkumar A.Mundra, and Jie Zheng.Bayesian data fusion of geneexpression and histone mod-ification profiles for infer-ence of gene regulatory net-work. IEEE/ACM Trans-actions on ComputationalBiology and Bioinformatics,17(2):516–525, March 2020.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic). URL https://dl.acm.org/doi/abs/10.1109/TCBB.2018.2869590.

Cheng:2016:EIS

[CMQ+16] Xiaoqing Cheng, TomoyaMori, Yushan Qiu, Wai-KiChing, and Tatsuya Akutsu.Exact identification of thestructure of a probabilisticBoolean network from sam-ples. IEEE/ACM Trans-actions on ComputationalBiology and Bioinformatics,13(6):1107–1116, November2016. CODEN ITCBCY.ISSN 1545-5963 (print),1557-9964 (electronic).

Cai:2019:EAF

[CMR19] Xingyu Cai, Abdullah-AlMamun, and SanguthevarRajasekaran. Efficient algo-rithms for finding the closest`1-mers in biological data.IEEE/ACM Transactionson Computational Biologyand Bioinformatics, 16(6):1912–1921, November 2019.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964

REFERENCES 112

(electronic). URL https://dl.acm.org/doi/abs/10.1109/TCBB.2018.2843364.

Campello:2012:SMA

[CMS12] Ricardo J. G. B. Campello,Davoud Moulavi, and JoergSander. A simpler and moreaccurate AUTO–HDS frame-work for clustering and visu-alization of biological data.IEEE/ACM Transactionson Computational Biologyand Bioinformatics, 9(6):1850–1852, November 2012.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Chacon:2015:BFI

[CMSE+15] Alejandro Chacon, Santi-ago Marco-Sola, Antonio Es-pinosa, Paolo Ribeca, andJuan Carlos Moure. Boost-ing the FM-Index on theGPU: Effective techniquesto mitigate random mem-ory access. IEEE/ACMTransactions on Computa-tional Biology and Bioin-formatics, 12(5):1048–1059,September 2015. CODENITCBCY. ISSN 1545-5963(print), 1557-9964 (elec-tronic).

Chen:2012:GEB

[CN12] Luonan Chen and Michael K.Ng. Guest editorial: Bioin-formatics and computationalsystems biology. IEEE/ACMTransactions on Computa-tional Biology and Bioinfor-


Chalkidis:2011:HPH

[CNM11] Georgios Chalkidis, MasaoNagasaki, and Satoru Miyano.High performance hybridfunctional Petri net simu-lations of biological path-way models on CUDA.IEEE/ACM Transactionson Computational Biologyand Bioinformatics, 8(6):1545–1556, November 2011.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Carroll:2020:SSA

[COW20] Thomas C. Carroll, Jude-Thaddeus Ojiaku, and Pru-dence W. H. Wong. Semiglobalsequence alignment withgaps using GPU. IEEE/ACM Transactions on Com-putational Biology and Bioin-formatics, 17(6):2086–2097,November 2020. CODENITCBCY. ISSN 1545-5963(print), 1557-9964 (elec-tronic). URL https://dl.acm.org/doi/10.1109/TCBB.2019.2914105.

Caglar:2013:SMS

[CP13] Mehmet Umut Caglar andRanadip Pal. Stochas-tic model simulation usingKronecker product analysisand Zassenhaus formula ap-proximation. IEEE/ACM

REFERENCES 113

Transactions on Computa-tional Biology and Bioin-formatics, 10(5):1125–1136,September 2013. CODENITCBCY. ISSN 1545-5963(print), 1557-9964 (elec-tronic).

Chicco:2018:NIE

[CPM18] Davide Chicco, FernandoPalluzzi, and Marco Masseroli.Novelty indicator for en-hanced prioritization of pre-dicted gene ontology anno-tations. IEEE/ACM Trans-actions on ComputationalBiology and Bioinformatics,15(3):954–965, May 2018.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Ciocchetta:2008:ATS

[CPQ08] Federica Ciocchetta, Cor-rado Priami, and PaolaQuaglia. An automatictranslation of SBML intobeta-binders. IEEE/ACMTransactions on Computa-tional Biology and Bioinfor-matics, 5(1):80–90, January2008. CODEN ITCBCY.ISSN 1545-5963 (print),1557-9964 (electronic).

Charuvaka:2014:CPS

[CR14] Anveshi Charuvaka andHuzefa Rangwala. Classify-ing protein sequences usingregularized multi-task learn-ing. IEEE/ACM Transac-tions on Computational Bi-ology and Bioinformatics,

11(6):1087–1098, November2014. CODEN ITCBCY.ISSN 1545-5963 (print),1557-9964 (electronic).

Cleary:2019:EFR

[CRK+19] Alan Cleary, ThiruvaranganRamaraj, Indika Kahanda,Joann Mudge, and Bren-dan Mumey. Exploringfrequented regions in pan-genomic graphs. IEEE/ACMTransactions on Computa-tional Biology and Bioin-formatics, 16(5):1424–1435,September 2019. CODENITCBCY. ISSN 1545-5963(print), 1557-9964 (elec-tronic).

Czeizler:2012:PHS

[CRP12] Eugen Czeizler, VladimirRogojin, and Ion Petre. Thephosphorylation of the heatshock factor as a modulatorfor the heat shock response.IEEE/ACM Transactionson Computational Biologyand Bioinformatics, 9(5):1326–1337, September 2012.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Cardona:2009:CTC

[CRV09] Gabriel Cardona, FrancescRossello, and Gabriel Va-liente. Comparison oftree-child phylogenetic net-works. IEEE/ACM Transac-tions on Computational Bi-ology and Bioinformatics, 6(4):552–569, October 2009.

REFERENCES 114


Chu:2015:EPY

[CS15] Dominique Chu and An-ton Salykin. Evolution-ary pressures on the yeasttranscriptome. IEEE/ACMTransactions on Computa-tional Biology and Bioin-formatics, 12(5):1087–1093,September 2015. CODENITCBCY. ISSN 1545-5963(print), 1557-9964 (elec-tronic).

Chen:2011:MIS

[CSK+11] Carla C. M. Chen, Hol-ger Schwender, JonthanKeith, Robin Nunkesser,Kerrie Mengersen, and PaulaMacrossan. Methods foridentifying SNP interactions:a review on variations oflogic regression, randomforest and Bayesian logis-tic regression. IEEE/ACMTransactions on Computa-tional Biology and Bioin-formatics, 8(6):1580–1591,November 2011. CODENITCBCY. ISSN 1545-5963(print), 1557-9964 (elec-tronic).

Cobanoglu:2011:CGU

[CSS11] Murat Can Cobanoglu, Yu-cel Saygin, and Ugur Sez-erman. Classification ofGPCRs using family spe-cific motifs. IEEE/ACMTransactions on Computa-


Catanzaro:2016:CPD

[CSSS16] Daniele Catanzaro, Stan-ley E. Shackney, Alejan-dro A. Schaffer, and Rus-sell Schwartz. Classify-ing the progression of duc-tal carcinoma from single-cell sampled data via in-teger linear programming:a case study. IEEE/ACMTransactions on Computa-tional Biology and Bioinfor-matics, 13(4):643–655, 2016.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Csuros:2004:MSS

[Csu04] Miklos Csuros. Maximum-scoring segment sets. IEEE/ACM Transactions on Com-putational Biology and Bioin-formatics, 1(4):139–150, Oc-tober 2004. CODENITCBCY. ISSN 1545-5963(print), 1557-9964 (elec-tronic).

Chang:2011:NKD

[CSW11] Rui Chang, Robert Shoe-maker, and Wei Wang.A novel knowledge-drivensystems biology approachfor phenotype predictionupon genetic intervention.IEEE/ACM Transactions

REFERENCES 115


Caudai:2019:LSC

[CSZ+19] Claudia Caudai, EmanueleSalerno, Monica Zoppe, IvanMerelli, and Anna Tonazz-ini. ChromStruct 4: aPython code to estimatethe chromatin structure fromHi-C data. IEEE/ACMTransactions on Computa-tional Biology and Bioin-formatics, 16(6):1867–1878,November 2019. CODENITCBCY. ISSN 1545-5963(print), 1557-9964 (elec-tronic). URL https://dl.acm.org/doi/abs/10.1109/TCBB.2018.2838669.

Caudai:2019:ESC

[CSZT19] Claudia Caudai, EmanueleSalerno, Monica Zoppe, andAnna Tonazzini. Estima-tion of the spatial chro-matin structure based on amultiresolution bead-chainmodel. IEEE/ACM Trans-actions on ComputationalBiology and Bioinformatics,16(2):550–559, March 2019.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic). URL https://dl.acm.org/doi/abs/10.1109/TCBB.2018.2791439.

Comin:2014:BFR

[CV14] Matteo Comin and Da-

vide Verzotto. Beyondfixed-resolution alignment-free measures for mammalianenhancers sequence compar-ison. IEEE/ACM Trans-actions on ComputationalBiology and Bioinformatics,11(4):628–637, July 2014.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Cameron:2007:CCS

[CW07] Michael Cameron and HughWilliams. Comparing com-pressed sequences for fasternucleotide BLAST searches.IEEE/ACM Transactions onComputational Biology andBioinformatics, 4(3):349–364, July 2007. CODENITCBCY. ISSN 1545-5963(print), 1557-9964 (elec-tronic).

Chen:2009:SCP

[CW09a] Jie Chen and Yu-Ping Wang.A statistical change pointmodel approach for the de-tection of DNA copy num-ber variations in array CGHdata. IEEE/ACM Transac-tions on Computational Bi-ology and Bioinformatics, 6(4):529–541, October 2009.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Chen:2009:IAA

[CW09b] Zhi-Zhong Chen and LushengWang. Improved approxi-mation algorithms for recon-

REFERENCES 116

structing the history of tan-dem repeats. IEEE/ACMTransactions on Computa-tional Biology and Bioinfor-matics, 6(3):438–453, July2009. CODEN ITCBCY.ISSN 1545-5963 (print),1557-9964 (electronic).

Chen:2011:FEA

[CW11] Zhi-Zhong Chen and LushengWang. Fast exact algorithmsfor the closest string and sub-string problems with appli-cation to the planted (L, d)-motif model. IEEE/ACMTransactions on Computa-tional Biology and Bioin-formatics, 8(5):1400–1410,September 2011. CODENITCBCY. ISSN 1545-5963(print), 1557-9964 (elec-tronic).

Chen:2012:ARN

[CW12] Zhi-Zhong Chen and LushengWang. Algorithms forreticulate networks of mul-tiple phylogenetic trees.IEEE/ACM Transactions onComputational Biology andBioinformatics, 9(2):372–384, March 2012. CODENITCBCY. ISSN 1545-5963(print), 1557-9964 (elec-tronic).

Cameron:2004:IGA

[CWC04] Michael Cameron, Hugh E.Williams, and Adam Can-nane. Improved gappedalignment in BLAST. IEEE/ACM Transactions on Com-

putational Biology and Bioin-formatics, 1(3):116–129, July2004. CODEN ITCBCY.ISSN 1545-5963 (print),1557-9964 (electronic).

Carroll:2015:IRE

[CWDS15] Hyrum D. Carroll, Alex C.Williams, Anthony G. Davis,and John L. Spouge. Im-proving retrieval efficacyof homology searches us-ing the false discovery rate.IEEE/ACM Transactions onComputational Biology andBioinformatics, 12(3):531–537, May 2015. CODENITCBCY. ISSN 1545-5963(print), 1557-9964 (elec-tronic).

Czeizler:2018:STC

[CWG+18] Eugen Czeizler, Kai-ChiuWu, Cristian Gratie, Kr-ishna Kanhaiya, and IonPetre. Structural targetcontrollability of linear net-works. IEEE/ACM Transac-tions on Computational Bi-ology and Bioinformatics, 15(4):1217–1228, July 2018.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Chen:2012:DOR

[CWL12] Peng Chen, Limsoon Wong,and Jinyan Li. Detec-tion of outlier residues forimproving interface predic-tion in protein heterocom-plexes. IEEE/ACM Transac-tions on Computational Bi-

REFERENCES 117

ology and Bioinformatics, 9(4):1155–1165, July 2012.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Cheng:2015:CMD

[CWLS15] Kin-On Cheng, Paula Wu,Ngai-Fong Law, and Wan-Chi Siu. Compression ofmultiple DNA sequencesusing intra-sequence andinter-sequence similarities.IEEE/ACM Transactionson Computational Biologyand Bioinformatics, 12(6):1322–1332, November 2015.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Chen:2014:ANG

[CWLZ14] Peng Chen, Chao Wang,Xi Li, and Xuehai Zhou. Ac-celerating the next genera-tion long read mapping withthe FPGA-based system.IEEE/ACM Transactionson Computational Biologyand Bioinformatics, 11(5):840–852, September 2014.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Chaudhury:2019:MVS

[CWT+19] Ayan Chaudhury, Christo-pher Ward, Ali Talasaz,Alexander G. Ivanov, MarkBrophy, Bernard Grodzin-ski, Norman P. A. Huner,Rajnikant V. Patel, andJohn L. Barron. Machine

vision system for 3D plantphenotyping. IEEE/ACMTransactions on Computa-tional Biology and Bioin-formatics, 16(6):2009–2022,November 2019. CODENITCBCY. ISSN 1545-5963(print), 1557-9964 (elec-tronic). URL https://dl.acm.org/doi/abs/10.1109/TCBB.2018.2824814.

Christinat:2008:GED

[CWZ08] Yann Christinat, BerndWachmann, and Lei Zhang.Gene expression data analy-sis using a novel approach tobiclustering combining dis-crete and continuous data.IEEE/ACM Transactions onComputational Biology andBioinformatics, 5(4):583–593, October 2008. CODENITCBCY. ISSN 1545-5963(print), 1557-9964 (elec-tronic).

Cui:2008:AAU

[CWZL08] Yun Cui, Lusheng Wang,Daming Zhu, and Xi-aowen Liu. A (1.5 + ε)-approximation algorithm forunsigned translocation dis-tance. IEEE/ACM Trans-actions on ComputationalBiology and Bioinformatics,5(1):56–66, January 2008.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Cai:2015:IPC

[CWZW15] Bingjing Cai, Haiying Wang,

REFERENCES 118

Huiru Zheng, and Hui Wang.Identification of protein com-plexes from tandem affinitypurification/mass spectrom-etry data via biased randomwalk. IEEE/ACM Trans-actions on ComputationalBiology and Bioinformatics,12(2):455–466, March 2015.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Cho:2015:PFR

[CXS15] Young-Rae Cho, Yanan Xin,and Greg Speegle. P-Finder:reconstruction of signal-ing networks from protein–protein interactions and GOannotations. IEEE/ACMTransactions on Computa-tional Biology and Bioin-formatics, 12(2):309–321,March 2015. CODENITCBCY. ISSN 1545-5963(print), 1557-9964 (elec-tronic).

Chen:2013:RTR

[CXW+13] Xi Chen, Jianhua Xuan,Chen Wang, Ayesha N.Shajahan, Rebecca B. Rig-gins, and Robert Clarke.Reconstruction of tran-scriptional regulatory net-works by stability-based net-work component analysis.IEEE/ACM Transactionson Computational Biologyand Bioinformatics, 10(6):1347–1358, November 2013.CODEN ITCBCY. ISSN


Chai:2019:HWT

[CYJ+19] Guoshi Chai, Min Yu, LixuJiang, Yaocong Duan, andJian Huang. HMMCAS:a Web tool for the iden-tification and domain an-notations of CAS proteins.IEEE/ACM Transactions onComputational Biology andBioinformatics, 16(4):1313–1315, July 2019. CODENITCBCY. ISSN 1545-5963(print), 1557-9964 (elec-tronic).

Chuang:2013:OPU

[CYTY13] Li-Yeh Chuang, Cheng-HueiYang, Jui-Hung Tsai, andCheng-Hong Yang. Operonprediction using chaos em-bedded particle swarm op-timization. IEEE/ACMTransactions on Computa-tional Biology and Bioin-formatics, 10(5):1299–1309,September 2013. CODENITCBCY. ISSN 1545-5963(print), 1557-9964 (elec-tronic).

Chen:2012:GEI

[CZ12] Jianer Chen and Alexan-der Zelikovsky. Guest Ed-itors’ introduction to thespecial section on bioinfor-matics research and applica-tions. IEEE/ACM Transac-tions on Computational Bi-ology and Bioinformatics, 9(4):1002–1003, July 2012.

REFERENCES 119


Cao:2020:PEF

[CZ20] Zhen Cao and Shihua Zhang.Probe efficient feature rep-resentation of gapped K-mer frequency vectors fromsequences using deep neu-ral networks. IEEE/ACMTransactions on Computa-tional Biology and Bioin-formatics, 17(2):657–667,March 2020. CODENITCBCY. ISSN 1545-5963(print), 1557-9964 (elec-tronic). URL https://dl.acm.org/doi/abs/10.1109/TCBB.2018.2868071.

Czapla:2018:RSS

[Cza18] Roman Czapla. Random setsof stadiums in square andcollective behavior of bacte-ria. IEEE/ACM Transac-tions on Computational Bi-ology and Bioinformatics, 15(1):251–256, January 2018.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Chen:2016:AMU

[CZB+16] Cheng Chen, FengchaoZhang, Jamie Barras, Kas-par Althoefer, Swarup Bhu-nia, and Soumyajit Man-dal. Authentication ofmedicines using nuclearquadrupole resonance spec-troscopy. IEEE/ACM Trans-actions on Computational

Biology and Bioinformatics,13(3):417–430, May 2016.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Chen:2005:AOG

[CZF+05] Xin Chen, Jie Zheng, ZhengFu, Peng Nan, Yang Zhong,Stefano Lonardi, and TaoJiang. Assignment of orthol-ogous genes via genome re-arrangement. IEEE/ACMTransactions on Computa-tional Biology and Bioinfor-matics, 2(4):302–315, Octo-ber 2005. CODEN ITCBCY.ISSN 1545-5963 (print),1557-9964 (electronic).

Cheng:2017:EAB

[CZJ17] Shan Cheng, Long-LongZhao, and Xiao-Yu Jiang.An effective applicationof bacteria quorum sens-ing and circular eliminationin MOPSO. IEEE/ACMTransactions on Computa-tional Biology and Bioinfor-matics, 14(1):56–63, January2017. CODEN ITCBCY.ISSN 1545-5963 (print),1557-9964 (electronic).

Cui:2018:MND

[CZM+18] Xiaodong Cui, Lin Zhang,Jia Meng, Manjeet K. Rao,Yidong Chen, and YufeiHuang. MeTDiff: a noveldifferential RNA methyla-tion analysis for MeRIP-Seqdata. IEEE/ACM Trans-actions on Computational

REFERENCES 120

Biology and Bioinformatics,15(2):526–534, March 2018.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Cheng:2018:EIC

[CZW+18] Zhanzhan Cheng, ShuigengZhou, Yang Wang, HuiLiu, Jihong Guan, and Yi-Ping Phoebe Chen. Effec-tively identifying compound-protein interactions by learn-ing from positive and unla-beled examples. IEEE/ACMTransactions on Computa-tional Biology and Bioin-formatics, 15(6):1832–1843,November 2018. CODENITCBCY. ISSN 1545-5963(print), 1557-9964 (elec-tronic).

Chan:2015:MPP

[CZWT15] Shing-Chow Chan, Li Zhang,Ho-Chun Wu, and Kai-Man Tsui. A maxi-mum a posteriori proba-bility and time-varying ap-proach for inferring generegulatory networks fromtime course gene microarraydata. IEEE/ACM Transac-tions on Computational Bi-ology and Bioinformatics, 12(1):123–135, January 2015.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Cheng:2019:BGA

[CZX19] Haoyu Cheng, Yong Zhang,and Yun Xu. BitMapper2: a

GPU-accelerated all-mapperbased on the sparse q-gramindex. IEEE/ACM Trans-actions on ComputationalBiology and Bioinformatics,16(3):886–897, May 2019.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Dureau:2017:MIA

[DABV17] Maxime Dureau, AngeloAlessandri, Patrizia Bagner-ini, and Stephane Vincent.Modeling and identificationof amnioserosa cell mechani-cal behavior by using mass-spring lattices. IEEE/ACMTransactions on Computa-tional Biology and Bioin-formatics, 14(6):1476–1481,November 2017. CODENITCBCY. ISSN 1545-5963(print), 1557-9964 (elec-tronic).

dAcierno:2017:IID

[dAc17] Antonio dAcierno. IsAPro-teinDB: an indexed databaseof trypsinized proteins forfast peptide mass finger-printing. IEEE/ACM Trans-actions on ComputationalBiology and Bioinformatics,14(5):1195–1201, September2017. CODEN ITCBCY.ISSN 1545-5963 (print),1557-9964 (electronic).

Diaz:2010:ADL

[DADF+10] Ester Diaz, Guillermo Ay-ala, Maria Diaz-Fernandez,Liang Gong, and Derek

REFERENCES 121

Toomre. Automatic de-tection of large dense-corevesicles in secretory cellsand statistical analysis oftheir intracellular distribu-tion. IEEE/ACM Trans-actions on ComputationalBiology and Bioinformat-ics, 7(1):2–11, January 2010.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Dalton:2016:ORB

[Dal16] Lori A. Dalton. Opti-mal ROC-based classifica-tion and performance anal-ysis under Bayesian uncer-tainty models. IEEE/ACMTransactions on Computa-tional Biology and Bioinfor-matics, 13(4):719–729, 2016.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

David:2014:CEF

[DB14] Laszlo David and AlexanderBockmayr. Computing ele-mentary flux modes involv-ing a set of target reactions.IEEE/ACM Transactionson Computational Biologyand Bioinformatics, 11(6):1099–1107, November 2014.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Dutta:2018:ASS

[DBK18] Pritha Dutta, SubhadipBasu, and MahantapasKundu. Assessment of se-

mantic similarity betweenproteins using informationcontent and topologicalproperties of the gene on-tology graph. IEEE/ACMTransactions on Computa-tional Biology and Bioinfor-matics, 15(3):839–849, May2018. CODEN ITCBCY.ISSN 1545-5963 (print),1557-9964 (electronic).

Djeddi:2018:NCA

[DBN18] Warith Eddine Djeddi, SadokBen Yahia, and Engel-bert Mephu Nguifo. A novelcomputational approach forglobal alignment for mul-tiple biological networks.IEEE/ACM Transactionson Computational Biologyand Bioinformatics, 15(6):2060–2066, November 2018.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Davila:2007:FPA

[DBR07] Jaime Davila, Sudha Balla,and Sanguthevar Rajasekaran.Fast and practical algorithmsfor planted (l, d) motifsearch. IEEE/ACM Trans-actions on ComputationalBiology and Bioinformatics,4(4):544–552, October 2007.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Dougherty:2009:CBM

[DBTB09] Edward R. Dougherty, Mar-cel Brun, Jeffrey M. Trent,

REFERENCES 122

and Michael L. Bittner.Conditioning-based model-ing of contextual genomicregulation. IEEE/ACMTransactions on Computa-tional Biology and Bioinfor-matics, 6(2):310–320, April2009. CODEN ITCBCY.ISSN 1545-5963 (print),1557-9964 (electronic).

DeBlasio:2012:MEM

[DBZ12] Daniel DeBlasio, Joce-lyne Bruand, and ShaojieZhang. A memory effi-cient method for structure-based RNA multiple align-ment. IEEE/ACM Trans-actions on ComputationalBiology and Bioinformat-ics, 9(1):1–11, January 2012.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Deng:2015:IFF

[DC15] Lei Deng and Zhigang Chen.An integrated frameworkfor functional annotationof protein structural do-mains. IEEE/ACM Trans-actions on ComputationalBiology and Bioinformatics,12(4):902–913, July 2015.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

daCosta:2011:WPC

[dCAR11] Joaquim F. Pinto da Costa,Hugo Alonso, and LuisRoque. A weighted prin-cipal component analy-

sis and its applicationto gene expression data.IEEE/ACM Transactions onComputational Biology andBioinformatics, 8(1):246–252, January 2011. CODENITCBCY. ISSN 1545-5963(print), 1557-9964 (elec-tronic).

Deng:2017:ISK

[DCHW17] Su-Ping Deng, ShaolongCao, De-Shuang Huang, andYu-Ping Wang. Identify-ing stages of kidney re-nal cell carcinoma by com-bining gene expression andDNA methylation data.IEEE/ACM Transactionson Computational Biologyand Bioinformatics, 14(5):1147–1153, September 2017.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Delgado:2020:STR

[DCM20] Ramon A. Delgado, ZhiyongChen, and Richard H. Mid-dleton. Stepwise Tikhonovregularisation: Applicationto the prediction of HIV-1drug resistance. IEEE/ACMTransactions on Computa-tional Biology and Bioin-formatics, 17(1):292–301,January 2020. CODENITCBCY. ISSN 1545-5963(print), 1557-9964 (elec-tronic). URL https://dl.acm.org/doi/abs/10.1109/TCBB.2018.2849369.

REFERENCES 123

Dotu:2011:LPS

[DCVC11] Ivan Dotu, Manuel Cebrian,Pascal Van Hentenryck, andPeter Clote. On latticeprotein structure predic-tion revisited. IEEE/ACMTransactions on Computa-tional Biology and Bioin-formatics, 8(6):1620–1632,November 2011. CODENITCBCY. ISSN 1545-5963(print), 1557-9964 (elec-tronic).

daSilvaArruda:2018:GBH

[dDD18] Thiago da Silva Arruda,Ulisses Dias, and ZanoniDias. A GRASP-basedheuristic for the sorting bylength-weighted inversionsproblem. IEEE/ACM Trans-actions on ComputationalBiology and Bioinformatics,15(2):352–363, March 2018.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Dinc:2017:STS

[DDS+17] Imren Dinc, Semih Dinc,Madhav Sigdel, Madhu S.Sigdel, Marc L. Pusey, andRamazan S. Aygun. Super-thresholding: Supervisedthresholding of protein crys-tal images. IEEE/ACMTransactions on Computa-tional Biology and Bioinfor-matics, 14(4):986–998, July2017. CODEN ITCBCY.ISSN 1545-5963 (print),1557-9964 (electronic).

Dematte:2012:SGP

[Dem12] Lorenzo Dematte. Smol-dyn on graphics process-ing units: Massively paral-lel Brownian dynamics simu-lations. IEEE/ACM Trans-actions on ComputationalBiology and Bioinformat-ics, 9(3):655–667, May 2012.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

DiLena:2011:TOS

[DFM+11] Pietro Di Lena, PieroFariselli, Luciano Margara,Marco Vassura, and RitaCasadio. Is there anoptimal substitution ma-trix for contact predictionwith correlated mutations?IEEE/ACM Transactions onComputational Biology andBioinformatics, 8(4):1017–1028, July 2011. CODENITCBCY. ISSN 1545-5963(print), 1557-9964 (elec-tronic).

DiCamillo:2012:SSB

[DFTC12] Barbara Di Camillo, MarcoFalda, Gianna Toffolo, andClaudio Cobelli. Sim-BioNeT: a simulator of bi-ological network topology.IEEE/ACM Transactions onComputational Biology andBioinformatics, 9(2):592–600, March 2012. CODENITCBCY. ISSN 1545-5963(print), 1557-9964 (elec-tronic).

REFERENCES 124

Deng:2019:IKG

[DG19] Su-Ping Deng and Wei-LiGuo. Identifying key genesof liver cancer by network-ing of multiple data sets.IEEE/ACM Transactions onComputational Biology andBioinformatics, 16(3):792–800, May 2019. CODENITCBCY. ISSN 1545-5963(print), 1557-9964 (elec-tronic).

Dawy:2006:GMM

[DGH+06] Zaher Dawy, BernhardGoebel, Joachim Hage-nauer, Christophe Andreoli,Thomas Meitinger, andJakob C. Mueller. Genemapping and marker cluster-ing using Shannon’s mutualinformation. IEEE/ACMTransactions on Computa-tional Biology and Bioinfor-matics, 3(1):47–56, January2006. CODEN ITCBCY.ISSN 1545-5963 (print),1557-9964 (electronic).

Daniels:2015:MRH

[DGRC15] Noah M. Daniels, An-drew Gallant, Norman Ram-sey, and Lenore J. Cowen.MRFy: remote homology de-tection for beta-structuralproteins using Markov ran-dom fields and stochasticsearch. IEEE/ACM Trans-actions on ComputationalBiology and Bioinformatics,12(1):4–16, January 2015.CODEN ITCBCY. ISSN


Dias:2017:GWS

[DGV+17] Oscar Dias, Daniel Gomes,Paulo Vilaca, Joao Car-doso, Miguel Rocha, Eu-genio C. Ferreira, and Is-abel Rocha. Genome-wide semi-automated anno-tation of transporter sys-tems. IEEE/ACM Trans-actions on ComputationalBiology and Bioinformatics,14(2):443–456, March 2017.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Demir:2005:LTP

[DGY05] Cigdem Demir, S. Hu-mayun Gultekin, and BulentYener. Learning the topolog-ical properties of brain tu-mors. IEEE/ACM Trans-actions on ComputationalBiology and Bioinformat-ics, 2(3):262–270, July 2005.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Dress:2004:CSG

[DH04] Andreas W. M. Dressand Daniel H. Huson.Constructing splits graphs.IEEE/ACM Transactions onComputational Biology andBioinformatics, 1(3):109–115, July 2004. CODENITCBCY. ISSN 1545-5963(print), 1557-9964 (elec-tronic).

REFERENCES 125

Doyon:2012:EME

[DHC12] Jean-Philippe Doyon, SylvieHamel, and Cedric Chauve.An efficient method for ex-ploring the space of genetree/species tree reconcil-iations in a probabilisticframework. IEEE/ACMTransactions on Computa-tional Biology and Bioinfor-matics, 9(1):26–39, January2012. CODEN ITCBCY.ISSN 1545-5963 (print),1557-9964 (electronic).

Deng:2018:IIG

[DHCW18] Su-Ping Deng, Wenxing Hu,Vince D. Calhoun, andYu-Ping Wang. Integrat-ing imaging genomic datain the quest for biomark-ers of schizophrenia disease.IEEE/ACM Transactionson Computational Biologyand Bioinformatics, 15(5):1480–1491, September 2018.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

DeJesus:2015:CUM

[DI15] Michael A. DeJesus andThomas R. Ioerger. Cap-turing uncertainty by mod-eling local transposon in-sertion frequencies improvesdiscrimination of essentialgenes. IEEE/ACM Transac-tions on Computational Bi-ology and Bioinformatics, 12(1):92–102, January 2015.CODEN ITCBCY. ISSN


deJong:2008:SSS

[dJP08] Hidde de Jong and MichelPage. Search for steadystates of piecewise-linear dif-ferential equation modelsof genetic regulatory net-works. IEEE/ACM Trans-actions on ComputationalBiology and Bioinformatics,5(2):208–222, April 2008.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

DeRonne:2013:POP

[DK13] Kevin W. DeRonne andGeorge Karypis. Pareto opti-mal pairwise sequence align-ment. IEEE/ACM Trans-actions on ComputationalBiology and Bioinformatics,10(2):481–493, March 2013.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

DeBlasio:2017:LPA

[DK17] Dan DeBlasio and John Ke-cecioglu. Learning parameter-advising sets for multi-ple sequence alignment.IEEE/ACM Transactionson Computational Biologyand Bioinformatics, 14(5):1028–1041, September 2017.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

REFERENCES 126

Daniels:2012:TPS

[DKCM12] Noah Daniels, Anoop Ku-mar, Lenore Cowen, andMatt Menke. Touringprotein space with Matt.IEEE/ACM Transactions onComputational Biology andBioinformatics, 9(1):286–293, January 2012. CODENITCBCY. ISSN 1545-5963(print), 1557-9964 (elec-tronic).

Done:2010:PNH

[DKDD10] Bogdan Done, Purvesh Kha-tri, Arina Done, and SorinDraghici. Predicting novelhuman gene ontology anno-tations using semantic anal-ysis. IEEE/ACM Transac-tions on Computational Bi-ology and Bioinformatics,7(1):91–99, January 2010.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Du:2015:IAC

[DKS+15] Nan Du, Marc R. Knecht,Mark T. Swihart, ZhenghuaTang, Tiffany R. Walsh, andAidong Zhang. Identify-ing affinity classes of inor-ganic materials binding se-quences via a graph-basedmodel. IEEE/ACM Transac-tions on Computational Bi-ology and Bioinformatics, 12(1):193–204, January 2015.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

DeFrancesco:2012:EGE

[DLM12] Nicoletta De Francesco, Giu-seppe Lettieri, and LucaMartini. Efficient geno-type elimination via adap-tive allele consolidation.IEEE/ACM Transactions onComputational Biology andBioinformatics, 9(4):1180–1189, July 2012. CODENITCBCY. ISSN 1545-5963(print), 1557-9964 (elec-tronic).

Davidson:2018:EQR

[DLRW18] Ruth Davidson, MaLynLawhorn, Joseph Rusinko,and Noah Weber. Efficientquartet representations oftrees and applications to su-pertree and summary meth-ods. IEEE/ACM Transac-tions on Computational Bi-ology and Bioinformatics, 15(3):1010–1015, May 2018.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Dai:2010:MGN

[DLT10] Hong-Jie Dai, Po-Ting Lai,and Richard Tzong-HanTsai. Multistage gene nor-malization and SVM-basedranking for protein interac-tor extraction in full-text ar-ticles. IEEE/ACM Trans-actions on ComputationalBiology and Bioinformat-ics, 7(3):412–420, July 2010.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

REFERENCES 127

Diago:2009:EGC

[DM09] Luis A. Diago and ErnestoMoreno. Evaluation ofgeometric complementar-ity between molecular sur-faces using compactly sup-ported radial basis func-tions. IEEE/ACM Transac-tions on Computational Bi-ology and Bioinformatics, 6(4):689–694, October 2009.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Das:2013:ORS

[DMD13] Mouli Das, C. A. Murthy,and Rajat K. De. An op-timization rule for in sil-ico identification of targetedoverproduction in metabolicpathways. IEEE/ACMTransactions on Computa-tional Biology and Bioinfor-matics, 10(4):914–926, July2013. CODEN ITCBCY.ISSN 1545-5963 (print),1557-9964 (electronic).

Deznabi:2018:IAG

[DMJ+18] Iman Deznabi, MohammadMobayen, Nazanin Jafari,Oznur Tastan, and ErmanAyday. An inference at-tack on genomic data us-ing kinship, complex corre-lations, and phenotype infor-mation. IEEE/ACM Trans-actions on ComputationalBiology and Bioinformatics,15(4):1333–1343, July 2018.CODEN ITCBCY. ISSN


doNascimento:2017:CNV

[dNG17] Francisco do Nascimentoand Katia S. Guimaraes.Copy number variations de-tection: Unravelling theproblem in tangible aspects.IEEE/ACM Transactionson Computational Biologyand Bioinformatics, 14(6):1237–1250, November 2017.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Dasarathy:2015:DRP

[DNR15] Gautam Dasarathy, RobertNowak, and Sebastien Roch.Data requirement for phylo-genetic inference from mul-tiple loci: a new distancemethod. IEEE/ACM Trans-actions on ComputationalBiology and Bioinformatics,12(2):422–432, March 2015.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Dehghani:2019:EPA

[DNS19] Toktam Dehghani, Mah-moud Naghibzadeh, andJavad Sadri. Enhancementof protein β-sheet topologyprediction using maximumweight disjoint path cover.IEEE/ACM Transactionson Computational Biologyand Bioinformatics, 16(6):1936–1947, November 2019.CODEN ITCBCY. ISSN

REFERENCES 128

1545-5963 (print), 1557-9964(electronic). URL https://dl.acm.org/doi/abs/10.1109/TCBB.2018.2837753.

Ding:2017:NMM

[DPA+17] Yuchun Ding, Marie Chris-tine Pardon, AlessandraAgostini, Henryk Faas, Jin-ming Duan, Wil O. C. Ward,Felicity Easton, DorotheeAuer, and Li Bai. Novelmethods for microglia seg-mentation, feature extrac-tion, and classification.IEEE/ACM Transactionson Computational Biologyand Bioinformatics, 14(6):1366–1377, November 2017.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Dehzangi:2014:SBM

[DPL+14] Abdollah Dehzangi, KuldipPaliwal, James Lyons, AlokSharma, and Abdul Sat-tar. A segmentation-basedmethod to extract struc-tural and evolutionary fea-tures for protein fold recog-nition. IEEE/ACM Trans-actions on ComputationalBiology and Bioinformatics,11(3):510–519, May 2014.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Dehzangi:2013:CFE

[DPS+13] Abdollah Dehzangi, KuldipPaliwal, Alok Sharma, OmidDehzangi, and Abdul Sat-

tar. A combination offeature extraction methodswith an ensemble of differentclassifiers for protein struc-tural class prediction prob-lem. IEEE/ACM Transac-tions on Computational Bi-ology and Bioinformatics,10(3):564–575, May 2013.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Dwight:2012:UWB

[DPW12] Zachary L. Dwight, RobertPalais, and Carl T. Wit-twer. uAnalyze: Web-basedhigh-resolution DNA meltinganalysis with comparison tothermodynamic predictions.IEEE/ACM Transactionson Computational Biologyand Bioinformatics, 9(6):1805–1811, November 2012.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Disanto:2014:NRS

[DR14] Filippo Disanto and Noah A.Rosenberg. On the num-ber of ranked species treesproducing anomalous rankedgene trees. IEEE/ACMTransactions on Computa-tional Biology and Bioin-formatics, 11(6):1229–1238,November 2014. CODENITCBCY. ISSN 1545-5963(print), 1557-9964 (elec-tronic).

REFERENCES 129

Disanto:2016:APN

[DR16] Filippo Disanto and Noah A.Rosenberg. Asymptoticproperties of the number ofmatching coalescent historiesfor caterpillar-like families ofspecies trees. IEEE/ACMTransactions on Computa-tional Biology and Bioin-formatics, 13(5):913–925,September 2016. CODENITCBCY. ISSN 1545-5963(print), 1557-9964 (elec-tronic).

Degnan:2012:CSS

[DRS12] James H. Degnan, Noah A.Rosenberg, and Tanja Stadler.A characterization of the setof species trees that produceanomalous ranked gene trees.IEEE/ACM Transactionson Computational Biologyand Bioinformatics, 9(6):1558–1568, November 2012.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Davidson:2014:DBP

[DS14] Ruth Davidson and Seth Sul-livant. Distance-based phy-logenetic methods arounda polytomy. IEEE/ACMTransactions on Computa-tional Biology and Bioin-formatics, 11(2):325–335,March 2014. CODENITCBCY. ISSN 1545-5963(print), 1557-9964 (elec-tronic).

Ding:2019:CSN

[DS19] Dewu Ding and Xiao Sun.A comparative study of net-work motifs in the inte-grated transcriptional regu-lation and protein interac-tion networks of Shewanella.IEEE/ACM Transactions onComputational Biology andBioinformatics, 16(1):163–171, January 2019. CODENITCBCY. ISSN 1545-5963(print), 1557-9964 (elec-tronic).

Dutta:2020:EGC

[DSCM20] Pratik Dutta, SriparnaSaha, Saraansh Chopra, andVarnika Miglani. Ensem-bling of gene clusters uti-lizing deep learning andprotein-protein interactioninformation. IEEE/ACMTransactions on Computa-tional Biology and Bioin-formatics, 17(6):2005–2016,November 2020. CODENITCBCY. ISSN 1545-5963(print), 1557-9964 (elec-tronic). URL https://dl.acm.org/doi/10.1109/TCBB.2019.2918523.

Dawy:2008:FSG

[DSHM08] Zaher Dawy, Michel Sarkis,Joachim Hagenauer, andJakob C. Mueller. Fine-scale genetic mapping us-ing independent componentanalysis. IEEE/ACM Trans-actions on ComputationalBiology and Bioinformat-ics, 5(3):448–460, July 2008.

REFERENCES 130


deSouto:2013:GES

[dSK13] Marcilio C. P. de Souto andMaricel Kann. Guest ed-itorial for special sectionon BSB 2012. IEEE/ACMTransactions on Computa-tional Biology and Bioinfor-matics, 10(4):817–818, July2013. CODEN ITCBCY.ISSN 1545-5963 (print),1557-9964 (electronic).

daSilva:2017:GDH

[dSMDB17] Poly H. da Silva, RaphaelMachado, Simone Dantas,and Marilia D. V. Braga. Ge-nomic distance with high in-del costs. IEEE/ACM Trans-actions on ComputationalBiology and Bioinformatics,14(3):728–732, May 2017.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Rodrigues:2011:PCE

[dSRCT+11] Thiago de Souza Rodrigues,Fernanda Caldas Cardoso,Santuza Maria Ribeiro Tei-xeira, Sergio Costa Oliveira,and Antonio Padua Braga.Protein classification withextended-sequence coding bysliding window. IEEE/ACMTransactions on Computa-tional Biology and Bioin-formatics, 8(6):1721–1726,November 2011. CODENITCBCY. ISSN 1545-5963


Diekmann:2007:EUR

[DST07] Yoan Diekmann, Marie-France Sagot, and Eric Tan-nier. Evolution under re-versals: Parsimony and con-servation of common inter-vals. IEEE/ACM Trans-actions on ComputationalBiology and Bioinformatics,4(2):301–309, April 2007.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Dellen:2015:GSR

[DST15a] Babette Dellen, HannoScharr, and Carme Torras.Growth signatures of rosetteplants from time-lapse video.IEEE/ACM Transactionson Computational Biologyand Bioinformatics, 12(6):1470–1478, November 2015.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Dong:2015:ANA

[DST+15b] Liang Dong, Bing Shi,Guangdong Tian, YanBo Li,Bing Wang, and MengChuZhou. An accurate de novoalgorithm for glycan topol-ogy determination from massspectra. IEEE/ACM Trans-actions on ComputationalBiology and Bioinformatics,12(3):568–578, May 2015.CODEN ITCBCY. ISSN

REFERENCES 131


Duarte-Sanchez:2018:HAM

[DSVMM18] Jorge E. Duarte-Sanchez,Jaime Velasco-Medina, andPedro A. Moreno. Hard-ware accelerator for the mul-tifractal analysis of DNAsequences. IEEE/ACMTransactions on Computa-tional Biology and Bioin-formatics, 15(5):1611–1624,September 2018. CODENITCBCY. ISSN 1545-5963(print), 1557-9964 (elec-tronic).

Danziger:2006:FCM

[DSZ+06] Samuel A. Danziger, S. JoshuaSwamidass, Jue Zeng, Lawrence R.Dearth, Qiang Lu, Jonathan H.Chen, Jianlin Cheng, Vinh P.Hoang, Hiroto Saigo, RayLuo, Pierre Baldi, Rainer K.Brachmann, and Richard H.Lathrop. Functional cen-sus of mutation sequencespaces: The example ofp53 cancer rescue mutants.IEEE/ACM Transactions onComputational Biology andBioinformatics, 3(2):114–125, April 2006. CODENITCBCY. ISSN 1545-5963(print), 1557-9964 (elec-tronic).

Dubrova:2011:SBA

[DT11] Elena Dubrova and MaximTeslenko. A SAT-based algo-rithm for finding attractorsin synchronous Boolean net-

works. IEEE/ACM Trans-actions on ComputationalBiology and Bioinformatics,8(5):1393–1399, September2011. CODEN ITCBCY.ISSN 1545-5963 (print),1557-9964 (electronic).

Dost:2011:TFM

[DWSB11] Banu Dost, Chunlei Wu, An-drew Su, and Vineet Bafna.TCLUST: a fast method forclustering genome-scale ex-pression data. IEEE/ACMTransactions on Computa-tional Biology and Bioinfor-matics, 8(3):808–818, May/June 2011. CODENITCBCY. ISSN 1545-5963(print), 1557-9964 (elec-tronic).

Ding:2015:SHO

[DWZ+15] Xiaojun Ding, Jianxin Wang,Alex Zelikovsky, Xuan Guo,Minzhu Xie, and Yi Pan.Searching high-order SNPcombinations for complexdiseases based on energy dis-tribution difference. IEEE/ACM Transactions on Com-putational Biology and Bioin-formatics, 12(3):695–704,May 2015. CODEN ITCBCY.ISSN 1545-5963 (print),1557-9964 (electronic).

Dehghannasiri:2015:OED

[DYD15] Roozbeh Dehghannasiri, Byung-Jun Yoon, and Edward R.Dougherty. Optimal ex-perimental design for generegulatory networks in the

REFERENCES 132

presence of uncertainty.IEEE/ACM Transactions onComputational Biology andBioinformatics, 12(4):938–950, July 2015. CODENITCBCY. ISSN 1545-5963(print), 1557-9964 (elec-tronic).

Dong:2011:NNK

[DZ11] Qiwen Dong and ShuigengZhou. Novel nonlinearknowledge-based mean forcepotentials based on machinelearning. IEEE/ACM Trans-actions on ComputationalBiology and Bioinformatics,8(2):476–486, March 2011.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Daras:2006:TDS

[DZA+06] Petros Daras, DimitriosZarpalas, Apostolos Axenopou-los, Dimitrios Tzovaras,and Michael GerassimosStrintzis. Three-dimensionalshape-structure comparisonmethod for protein classifi-cation. IEEE/ACM Trans-actions on ComputationalBiology and Bioinformat-ics, 3(3):193–207, July 2006.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Deng:2016:PHG

[DZH16] Su-Ping Deng, Lin Zhu, andDe-Shuang Huang. Pre-dicting hub genes associatedwith cervical cancer through

gene co-expression networks.IEEE/ACM Transactions onComputational Biology andBioinformatics, 13(1):27–35,January 2016. CODENITCBCY. ISSN 1545-5963(print), 1557-9964 (elec-tronic).

ElBakry:2012:IDE

[EAS12] Ola ElBakry, M. Omair Ah-mad, and M. N. S. Swamy.Identification of differentiallyexpressed genes for time-course microarray data basedon modified RM ANOVA.IEEE/ACM Transactions onComputational Biology andBioinformatics, 9(2):451–466, March 2012. CODENITCBCY. ISSN 1545-5963(print), 1557-9964 (elec-tronic).

ElBakry:2013:IGR

[EAS13] Ola ElBakry, M. Omair Ah-mad, and M. N. S. Swamy.Inference of gene regulatorynetworks with variable timedelay from time-series mi-croarray data. IEEE/ACMTransactions on Computa-tional Biology and Bioinfor-matics, 10(3):671–687, May2013. CODEN ITCBCY.ISSN 1545-5963 (print),1557-9964 (electronic).

Elmsallati:2016:GAP

[ECK16] Ahed Elmsallati, ConnorClark, and Jugal Kalita.Global alignment of protein-protein interaction networks:

REFERENCES 133

a survey. IEEE/ACM Trans-actions on ComputationalBiology and Bioinformat-ics, 13(4):689–705, 2016.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Esfahani:2014:IBP

[ED14] Mohammad Shahrokh Esfa-hani and Edward R. Dough-erty. Incorporation of bio-logical pathway knowledge inthe construction of priors foroptimal Bayesian classifica-tion. IEEE/ACM Transac-tions on Computational Bi-ology and Bioinformatics, 11(1):202–218, January 2014.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Esfahani:2015:OBF

[ED15] Mohammad Shahrokh Esfa-hani and Edward R. Dough-erty. An optimization-basedframework for the transfor-mation of incomplete biolog-ical knowledge into a proba-bilistic structure and its ap-plication to the utilization ofgene/protein signaling path-ways in discrete phenotypeclassification. IEEE/ACMTransactions on Computa-tional Biology and Bioin-formatics, 12(6):1304–1321,November 2015. CODENITCBCY. ISSN 1545-5963(print), 1557-9964 (elec-tronic).

Eshra:2014:OPC

[EES14] Abeer Eshra and AymanEl-Sayed. An odd par-ity checker prototype usingDNAzyme finite state ma-chine. IEEE/ACM Trans-actions on ComputationalBiology and Bioinformatics,11(2):316–324, March 2014.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Elo:2008:ROT

[EFLA08] Laura L. Elo, Sanna Filen,Riitta Lahesmaa, and TeroAittokallio. Reproducibility-optimized test statistic forranking genes in microarraystudies. IEEE/ACM Trans-actions on ComputationalBiology and Bioinformat-ics, 5(3):423–431, July 2008.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Elias:2006:AAS

[EH06] Isaac Elias and Tzvika Hart-man. A 1.375-approximationalgorithm for sorting bytranspositions. IEEE/ACMTransactions on Computa-tional Biology and Bioinfor-matics, 3(4):369–379, Octo-ber 2006. CODEN ITCBCY.ISSN 1545-5963 (print),1557-9964 (electronic).

El-Manzalawy:2011:PMI

[EMDH11] Yasser El-Manzalawy, DrenaDobbs, and Vasant Honavar.

REFERENCES 134

Predicting MHC-II bind-ing affinity using mul-tiple instance regression.IEEE/ACM Transactions onComputational Biology andBioinformatics, 8(4):1067–1079, July 2011. CODENITCBCY. ISSN 1545-5963(print), 1557-9964 (elec-tronic).

Elmsallati:2018:IBN

[EMK18] Ahed Elmsallati, Abdul-ghani Msalati, and JugalKalita. Index-based net-work aligner of protein–protein interaction networks.IEEE/ACM Transactions onComputational Biology andBioinformatics, 15(1):330–336, January 2018. CODENITCBCY. ISSN 1545-5963(print), 1557-9964 (elec-tronic).

Eisenhaber:2014:GEI

[ESW14] Frank Eisenhaber, Wing-KinSung, and Limsoon Wong.Guest editorial for the in-ternational conference ongenome informatics (GIW2013). IEEE/ACM Trans-actions on ComputationalBiology and Bioinformat-ics, 11(1):5–6, January 2014.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Evans:2004:UDT

[EW04] Steven N. Evans and TandyWarnow. Unidentifiabledivergence times in rates-

across-sites models. IEEE/ACM Transactions on Com-putational Biology and Bioin-formatics, 1(3):130–134, July2004. CODEN ITCBCY.ISSN 1545-5963 (print),1557-9964 (electronic).

Ezzat:2017:DTI

[EZW+17] Ali Ezzat, Peilin Zhao, MinWu, Xiao-Li Li, and Chee-Keong Kwoh. Drug-targetinteraction prediction withgraph regularized matrixfactorization. IEEE/ACMTransactions on Computa-tional Biology and Bioinfor-matics, 14(3):646–656, May2017. CODEN ITCBCY.ISSN 1545-5963 (print),1557-9964 (electronic).

Frasca:2019:MPF

[FB19] Marco Frasca and Ni-colo Cesa Bianchi. Multitaskprotein function predictionthrough task dissimilarity.IEEE/ACM Transactionson Computational Biologyand Bioinformatics, 16(5):1550–1560, September 2019.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Fabris:2016:EEC

[FFT16] Fabio Fabris, Alex A. Fre-itas, and Jennifer M. A.Tullet. An extensive em-pirical comparison of prob-abilistic hierarchical classi-fiers in datasets of ageing-related genes. IEEE/ACM

REFERENCES 135

Transactions on Computa-tional Biology and Bioin-formatics, 13(6):1045–1058,November 2016. CODENITCBCY. ISSN 1545-5963(print), 1557-9964 (elec-tronic).

Fober:2011:SAL

[FGKH11] Thomas Fober, GergheiGlinca, Gerhard Klebe, andEyke Hullermeier. Su-perposition and alignmentof labeled point clouds.IEEE/ACM Transactionson Computational Biologyand Bioinformatics, 8(6):1653–1666, November 2011.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Fellows:2011:HIC

[FHH+11] Michael R. Fellows, TzvikaHartman, Danny Hermelin,Gad M. Landau, FrancesRosamond, and Liat Rozen-berg. Haplotype inferenceconstrained by plausible hap-lotype data. IEEE/ACMTransactions on Computa-tional Biology and Bioin-formatics, 8(6):1692–1699,November 2011. CODENITCBCY. ISSN 1545-5963(print), 1557-9964 (elec-tronic).

Fakhraei:2014:NBD

[FHRG14] Shobeir Fakhraei, BertHuang, Louiqa Raschid, andLise Getoor. Network-baseddrug-target interaction pre-

diction with probabilisticsoft logic. IEEE/ACMTransactions on Computa-tional Biology and Bioin-formatics, 11(5):775–787,September 2014. CODENITCBCY. ISSN 1545-5963(print), 1557-9964 (elec-tronic).

Feng:2011:MFB

[FJJ11] Jianxing Feng, Rui Jiang,and Tao Jiang. A max-flow-based approach to theidentification of protein com-plexes using protein inter-action and microarray data.IEEE/ACM Transactionson Computational Biologyand Bioinformatics, 8(3):621–634, May/June 2011.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Fan:2018:GES

[FJJ18] Xiaodan Fan, Xinglai Ji,and Rui Jiang. Guesteditorial for special sec-tion on the Sixth NationalConference on Bioinformat-ics and System Biology ofChina. IEEE/ACM Trans-actions on ComputationalBiology and Bioinformat-ics, 15(4):1092, July 2018.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Feret:2019:E

[FK19] Jerome Feret and HeinzKoeppl. Editorial. IEEE/

REFERENCES 136

ACM Transactions on Com-putational Biology and Bioin-formatics, 16(5):1561, Septem-ber 2019. CODEN ITCBCY.ISSN 1545-5963 (print),1557-9964 (electronic).

Foo:2019:MCG

[FKB19] Mathias Foo, Jongrae Kim,and Declan G. Bates. Mod-elling and control of gene reg-ulatory networks for pertur-bation mitigation. IEEE/ACM Transactions on Com-putational Biology and Bioin-formatics, 16(2):583–595,March 2019. CODENITCBCY. ISSN 1545-5963(print), 1557-9964 (elec-tronic). URL https://dl.acm.org/doi/abs/10.1109/TCBB.2017.2771775.

Fujarewicz:2007:ASM

[FKLS07] Krzysztof Fujarewicz, MarekKimmel, Tomasz Lipniacki,and Andrzej Swierniak. Ad-joint systems for models ofcell signaling pathways andtheir application to param-eter fitting. IEEE/ACMTransactions on Computa-tional Biology and Bioinfor-matics, 4(3):322–335, July2007. CODEN ITCBCY.ISSN 1545-5963 (print),1557-9964 (electronic).

Feret:2018:LTA

[FL18] Jerome Feret and Kim QuyenLy. Local traces: an over-approximation of the behav-ior of the proteins in rule-

based models. IEEE/ACMTransactions on Computa-tional Biology and Bioin-formatics, 15(4):1124–1137,July 2018. CODEN ITCBCY.ISSN 1545-5963 (print),1557-9964 (electronic).

Frost:2015:IFG

[FLAM15] H. Robert Frost, ZhigangLi, Folkert W. Asselbergs,and Jason H. Moore. Anindependent filter for geneset testing based on spec-tral enrichment. IEEE/ACMTransactions on Computa-tional Biology and Bioin-formatics, 12(5):1076–1086,September 2015. CODENITCBCY. ISSN 1545-5963(print), 1557-9964 (elec-tronic).

Fodeh:2020:CPC

[FLJS20] Samah J. Fodeh, TaihuaLi, Haya Jarad, and Bas-mah Safdar. Classifica-tion of patients with coro-nary microvascular dysfunc-tion. IEEE/ACM Trans-actions on ComputationalBiology and Bioinformatics,17(2):704–711, March 2020.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic). URL https://dl.acm.org/doi/abs/10.1109/TCBB.2019.2914442.

Fernandez:2016:OBS

[FLM+16] Javier D. Fernandez, Maur-izio Lenzerini, Marco Masseroli,Francesco Venco, and Ste-

REFERENCES 137

fano Ceri. Ontology-basedsearch of genomic meta-data. IEEE/ACM Trans-actions on ComputationalBiology and Bioinformatics,13(2):233–247, March 2016.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Fagundes-Lima:2012:CSS

[FLW12] Denise Fagundes-Lima andGerald Weber. Commenton “SCS: Signal, Con-text, and Structure Fea-tures for Genome-Wide Hu-man Promoter Recognition”.IEEE/ACM Transactions onComputational Biology andBioinformatics, 9(3):940–941, May 2012. CODENITCBCY. ISSN 1545-5963(print), 1557-9964 (elec-tronic).

Fan:2014:QSM

[FLW+14] Ying Fan, Ruoshui Lu,Lusheng Wang, MassimoAndreatta, and Shuai ChengLi. Quantifying signifi-cance of MHC II residues.IEEE/ACM Transactions onComputational Biology andBioinformatics, 11(1):17–25,January 2014. CODENITCBCY. ISSN 1545-5963(print), 1557-9964 (elec-tronic).

Feijao:2011:SBL

[FM11] Pedro Feijao and Joao Mei-danis. SCJ: a breakpoint-like distance that simplifies

several rearrangement prob-lems. IEEE/ACM Trans-actions on ComputationalBiology and Bioinformatics,8(5):1318–1329, September2011. CODEN ITCBCY.ISSN 1545-5963 (print),1557-9964 (electronic).

Felicioli:2012:BEA

[FM12] Claudio Felicioli and RobertoMarangoni. BpMatch: Anefficient algorithm for a seg-mental analysis of genomicsequences. IEEE/ACMTransactions on Computa-tional Biology and Bioinfor-matics, 9(4):1120–1127, July2012. CODEN ITCBCY.ISSN 1545-5963 (print),1557-9964 (electronic).

Feijao:2013:EAF

[FM13] Pedro Feijao and Joao Mei-danis. Extending thealgebraic formalism forgenome rearrangements toinclude linear chromosomes.IEEE/ACM Transactions onComputational Biology andBioinformatics, 10(4):819–831, July 2013. CODENITCBCY. ISSN 1545-5963(print), 1557-9964 (elec-tronic).

Fergus:2020:UDL

[FMA+20] Paul Fergus, Casimiro CurbeloMontanez, Basma Abdu-laimma, Paulo Lisboa, CarlChalmers, and Beth Pine-les. Utilizing deep learn-ing and genome wide asso-

REFERENCES 138

ciation studies for epistatic-driven preterm birth classifi-cation in African–Americanwomen. IEEE/ACM Trans-actions on ComputationalBiology and Bioinformatics,17(2):668–678, March 2020.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic). URL https://dl.acm.org/doi/abs/10.1109/TCBB.2018.2868667.

Fotoohifiroozabadi:2018:NFN

[FMD18] Samira Fotoohifiroozabadi,Mohd Saberi Mohamad, andSafaai Deris. NAHAL-Flex: a numerical and al-phabetical hinge detectionalgorithm for flexible pro-tein structure alignment.IEEE/ACM Transactions onComputational Biology andBioinformatics, 15(3):934–943, May 2018. CODENITCBCY. ISSN 1545-5963(print), 1557-9964 (elec-tronic).

Fages:2018:INC

[FMRS18] Francois Fages, Thierry Mar-tinez, David A. Rosenblueth,and Sylvain Soliman. In-fluence networks comparedwith reaction networks: Se-mantics, expressivity and at-tractors. IEEE/ACM Trans-actions on ComputationalBiology and Bioinformatics,15(4):1138–1151, July 2018.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Fa:2014:NRG

[FN14] Rui Fa and Asoke K. Nandi.Noise resistant generalizedparametric validity index ofclustering for gene expressiondata. IEEE/ACM Trans-actions on ComputationalBiology and Bioinformatics,11(4):741–752, July 2014.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Fu:2020:PDM

[FPC20] Laiyi Fu, Qinke Peng, andLing Chai. Predicting DNAmethylation states with hy-brid information based deep-learning model. IEEE/ACMTransactions on Computa-tional Biology and Bioin-formatics, 17(5):1721–1728,September 2020. CODENITCBCY. ISSN 1545-5963(print), 1557-9964 (elec-tronic). URL https://dl.acm.org/doi/10.1109/TCBB.2019.2909237.

Ferraro:2011:ACQ

[FPPR11] Nicola Ferraro, Luigi Palopoli,Simona Panni, and Si-mona E. Rombo. Asymmet-ric comparison and query-ing of biological networks.IEEE/ACM Transactions onComputational Biology andBioinformatics, 8(4):876–889, July 2011. CODENITCBCY. ISSN 1545-5963(print), 1557-9964 (elec-tronic).

REFERENCES 139

Fages:2012:GEI

[FS12] Francois Fages and SylvainSoliman. Guest Editors’introduction to the specialsection on computationalmethods in systems biology.IEEE/ACM Transactionson Computational Biologyand Bioinformatics, 9(5):1314–1315, September 2012.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Fages:2013:GEI

[FS13a] Francois Fages and SylvainSoliman. Guest Editors’introduction to the specialsection on computationalmethods in systems biol-ogy. IEEE/ACM Transac-tions on Computational Bi-ology and Bioinformatics,10(2):308–309, March 2013.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Florea:2013:GGT

[FS13b] Liliana D. Florea andSteven L. Salzberg. Genome-guided transcriptome as-sembly in the age ofnext-generation sequencing.IEEE/ACM Transactionson Computational Biologyand Bioinformatics, 10(5):1234–1240, September 2013.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Frith:2018:SDC

[FS18] Martin C. Frith and AnishM. S. Shrestha. A simplifieddescription of child tables forsequence similarity search.IEEE/ACM Transactionson Computational Biologyand Bioinformatics, 15(6):2067–2073, November 2018.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Flores:2011:FFM

[FSB+11] Samuel Coulbourn Flores,Michael Sherman, Christo-pher M. Bruns, Peter East-man, and Russ B. Altman.Fast flexible modeling ofRNA structure using inter-nal coordinates. IEEE/ACMTransactions on Computa-tional Biology and Bioin-formatics, 8(5):1247–1257,September 2011. CODENITCBCY. ISSN 1545-5963(print), 1557-9964 (elec-tronic).

Fujita:2011:ICR

[FSD+11] Andre Fujita, Joao Ri-cardo Sato, Marcos AlmeidaDemasi, Rui Yamaguchi,Teppei Shimamura, Car-los Eduardo Ferreira, Mari CleideSogayar, and Satoru Miyano.Inferring contagion in regula-tory networks. IEEE/ACMTransactions on Computa-tional Biology and Bioinfor-matics, 8(2):570–576, March2011. CODEN ITCBCY.

REFERENCES 140


Fang:2016:IGS

[FSDR16] Yi Fang, Mengtian Sun,Guoxian Dai, and KarthikRamain. The intrinsic geo-metric structure of protein-protein interaction networksfor protein interaction pre-diction. IEEE/ACM Trans-actions on ComputationalBiology and Bioinformatics,13(1):76–85, January 2016.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Feng:2015:RES

[FSL+15] Weixing Feng, Peichao Sang,Deyuan Lian, YanshengDong, Fengfei Song, MengLi, Bo He, Fenglin Cao, andYunlong Liu. ResSeq: en-hancing short-read sequenc-ing alignment by rescu-ing error-containing reads.IEEE/ACM Transactions onComputational Biology andBioinformatics, 12(4):795–798, July 2015. CODENITCBCY. ISSN 1545-5963(print), 1557-9964 (elec-tronic).

Furlanello:2005:SLM

[FSMJ05] Cesare Furlanello, Maria Ser-afini, Stefano Merler, andGiuseppe Jurman. Semisu-pervised learning for molec-ular profiling. IEEE/ACMTransactions on Computa-tional Biology and Bioinfor-

matics, 2(2):110–118, April2005. CODEN ITCBCY.ISSN 1545-5963 (print),1557-9964 (electronic).

Fang:2019:PPB

[FSX19] Chao Fang, Yi Shang, andDong Xu. Prediction ofprotein backbone torsionangles using deep resid-ual inception neural net-works. IEEE/ACM Transac-tions on Computational Bi-ology and Bioinformatics, 16(3):1020–1028, May 2019.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Fernandez:2015:FFB

[FVLN15] Edward B. Fernandez, JasonVillarreal, Stefano Lonardi,and Walid A. Najjar. FHAST:FPGA-based accelerationof bowtie in hardware.IEEE/ACM Transactionson Computational Biologyand Bioinformatics, 12(5):973–981, September 2015.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Filipovic:2020:CNM

[FVP+20] Jirı Filipovic, Ondrej Vavra,Jan Plhak, David Bednar,Sergio M. Marques, Jan Bre-zovsky, Ludek Matyska, andJirı Damborsky. CaverDock:a novel method for the fastanalysis of ligand transport.IEEE/ACM Transactionson Computational Biology

REFERENCES 141

and Bioinformatics, 17(5):1625–1638, September 2020.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic). URL https://dl.acm.org/doi/10.1109/TCBB.2019.2907492.

Feng:2020:EEL

[FW20] Zhan-Ying Feng and YongWang. ELF: Extract land-mark features by optimiz-ing topology maintenance,redundancy, and specificity.IEEE/ACM Transactions onComputational Biology andBioinformatics, 17(2):411–421, March 2020. CODENITCBCY. ISSN 1545-5963(print), 1557-9964 (elec-tronic). URL https://dl.acm.org/doi/abs/10.1109/TCBB.2018.2846225.

Freitas:2010:ICC

[FWA10] Alex A. Freitas, Daniela C.Wieser, and Rolf Ap-weiler. On the impor-tance of comprehensible clas-sification models for pro-tein function prediction.IEEE/ACM Transactions onComputational Biology andBioinformatics, 7(1):172–182, January 2010. CODENITCBCY. ISSN 1545-5963(print), 1557-9964 (elec-tronic).

Fan:2019:ILS

[FWXZ19] Anjing Fan, Haitao Wang,Hua Xiang, and XiufenZou. Inferring large-scale

gene regulatory networks us-ing a randomized algorithmbased on singular value de-composition. IEEE/ACMTransactions on Computa-tional Biology and Bioin-formatics, 16(6):1997–2008,November 2019. CODENITCBCY. ISSN 1545-5963(print), 1557-9964 (elec-tronic). URL https://dl.acm.org/doi/abs/10.1109/TCBB.2018.2825446.

Fan:2015:AMD

[FWY+15] Yetian Fan, Wei Wu, JieYang, Wenyu Yang, andRongrong Liu. An algorithmfor motif discovery with it-eration on lengths of mo-tifs. IEEE/ACM Transac-tions on Computational Bi-ology and Bioinformatics, 12(1):136–141, January 2015.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Feng:2019:PAP

[FWY19] Pengmian Feng, ZhenyiWang, and Xiaoyu Yu. Pre-dicting antimicrobial pep-tides by using increment ofdiversity with quadratic dis-criminant analysis method.IEEE/ACM Transactions onComputational Biology andBioinformatics, 16(4):1309–1312, July 2019. CODENITCBCY. ISSN 1545-5963(print), 1557-9964 (elec-tronic).

REFERENCES 142

Feng:2012:LSL

[FYSM12] Zeny Z. Feng, XiaojianYang, Sanjeena Subedi, andPaul D. McNicholas. TheLASSO and sparse leastsquares regression methodsfor SNP selection in pre-dicting quantitative traits.IEEE/ACM Transactions onComputational Biology andBioinformatics, 9(2):629–636, March 2012. CODENITCBCY. ISSN 1545-5963(print), 1557-9964 (elec-tronic).

Feng:2019:DLA

[FYZ+19] Yujie Feng, Fan Yang, Xi-chuan Zhou, Yanli Guo,Fang Tang, Fengbo Ren,Jishun Guo, and ShuiwangJi. A deep learning ap-proach for targeted contrast-enhanced ultrasound basedprostate cancer detection.IEEE/ACM Transactionson Computational Biologyand Bioinformatics, 16(6):1794–1801, November 2019.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic). URL https://dl.acm.org/doi/abs/10.1109/TCBB.2018.2835444.

Faisal:2015:GNA

[FZM15] Fazle Elahi Faisal, Han Zhao,and Tijana Milenkovic.Global network alignmentin the context of aging.IEEE/ACM Transactions onComputational Biology andBioinformatics, 12(1):40–52,

January 2015. CODENITCBCY. ISSN 1545-5963(print), 1557-9964 (elec-tronic).

Feng:2020:DMP

[FZM20] Yangqin Feng, Lei Zhang,and Juan Mo. Deep mani-fold preserving autoencoderfor classifying breast can-cer histopathological im-ages. IEEE/ACM Transac-tions on Computational Bi-ology and Bioinformatics, 17(1):91–101, January 2020.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic). URL https://dl.acm.org/doi/abs/10.1109/TCBB.2018.2858763.

Fan:2017:FTS

[FZWS17] Xiaofei Fan, Xian Zhang,Ligang Wu, and MichaelShi. Finite-time stabilityanalysis of reaction-diffusiongenetic regulatory networkswith time-varying delays.IEEE/ACM Transactions onComputational Biology andBioinformatics, 14(4):868–879, July 2017. CODENITCBCY. ISSN 1545-5963(print), 1557-9964 (elec-tronic).

Giard:2011:FSB

[GAGM11] Joachim Giard, Patrice Ron-dao Alface, Jean-Luc Gala,and Benoit Macq. Fastsurface-based travel depthestimation algorithm formacromolecule surface shape

REFERENCES 143

description. IEEE/ACMTransactions on Computa-tional Biology and Bioinfor-matics, 8(1):59–68, January2011. CODEN ITCBCY.ISSN 1545-5963 (print),1557-9964 (electronic).

Ghaffari:2018:ENT

[GAJ+18] Noushin Ghaffari, Osama A.Arshad, Hyundoo Jeong,John Thiltges, Michael F.Criscitiello, Byung-Jun Yoon,Aniruddha Datta, and Charles D.Johnson. Examining DeNovo transcriptome assem-blies via a quality assessmentpipeline. IEEE/ACM Trans-actions on ComputationalBiology and Bioinformatics,15(2):494–505, March 2018.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Gonzalez:2009:MLT

[GAR+09] Ana M. Gonzalez, Fran-cisco J. Azuaje, Jose L.Ramirez, Jose F. da Sil-veira, and Jose R. Dor-ronsoro. Machine learningtechniques for the automatedclassification of adhesin-likeproteins in the human proto-zoan parasite Trypanosomacruzi . IEEE/ACM Transac-tions on Computational Bi-ology and Bioinformatics, 6(4):695–702, October 2009.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Gonzalez-Alvarez:2015:FPP

[GAVRRL15] David L. Gonzalez-Alvarez,Miguel A. Vega-Rodrıguez,and Alvaro Rubio-Largo.Finding patterns in proteinsequences by using a hy-brid multiobjective teach-ing learning based optimiza-tion algorithm. IEEE/ACMTransactions on Computa-tional Biology and Bioinfor-matics, 12(3):656–666, May2015. CODEN ITCBCY.ISSN 1545-5963 (print),1557-9964 (electronic).

Guillemot:2010:FPT

[GB10] Sylvain Guillemot and Vin-cent Berry. Fixed-parametertractability of the maximumagreement supertree prob-lem. IEEE/ACM Transac-tions on Computational Bi-ology and Bioinformatics,7(2):342–353, April 2010.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Guziolowski:2011:DLR

[GBB+11] Carito Guziolowski, Syl-vain Blachon, Tatiana Bau-muratova, Gautier Stoll,Ovidiu Radulescu, and AnneSiegel. Designing logi-cal rules to model the re-sponse of biomolecular net-works with complex interac-tions: An application to can-cer modeling. IEEE/ACMTransactions on Computa-tional Biology and Bioin-

REFERENCES 144

formatics, 8(5):1223–1234,September 2011. CODENITCBCY. ISSN 1545-5963(print), 1557-9964 (elec-tronic).

Galvao:2017:SCP

[GBD17] Gustavo Rodrigues Gal-vao, Christian Baudet, andZanoni Dias. Sorting cir-cular permutations by supershort reversals. IEEE/ACMTransactions on Computa-tional Biology and Bioinfor-matics, 14(3):620–633, May2017. CODEN ITCBCY.ISSN 1545-5963 (print),1557-9964 (electronic).

Gupta:2008:EDS

[GBJ08] Anupam Gupta and Ziv Bar-Joseph. Extracting dynamicsfrom static cancer expressiondata. IEEE/ACM Trans-actions on ComputationalBiology and Bioinformatics,5(2):172–182, April 2008.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Ghoraie:2014:RSS

[GBLZ14] Laleh Soltan Ghoraie, ForbesBurkowski, Shuai Cheng Li,and Mu Zhu. Residue-specific side-chain polymor-phisms via particle beliefpropagation. IEEE/ACMTransactions on Computa-tional Biology and Bioinfor-matics, 11(1):33–41, January2014. CODEN ITCBCY.


Gong:2011:ITM

[GBS11] Liuling Gong, Nidhal Bouay-naya, and Dan Schon-feld. Information-theoreticmodel of evolution over pro-tein communication chan-nel. IEEE/ACM Transac-tions on Computational Bi-ology and Bioinformatics, 8(1):143–151, January 2011.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Guan:2014:BDC

[GBTL14] Benjamin X. Guan, BirBhanu, Prue Talbot, andSabrina Lin. Bio-drivencell region detection in hu-man embryonic stem cell as-say. IEEE/ACM Transac-tions on Computational Bi-ology and Bioinformatics,11(3):604–611, May 2014.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Guan:2016:EBH

[GBTW16] Benjamin X. Guan, BirBhanu, Prue Talbot, andNikki Jo-Hao Weng. Ex-traction of blebs in hu-man embryonic stem cellvideos. IEEE/ACM Trans-actions on ComputationalBiology and Bioinformat-ics, 13(4):678–688, 2016.CODEN ITCBCY. ISSN

REFERENCES 145


Gossmann:2018:SRM

[GCB+18] Alexej Gossmann, ShaolongCao, Damian Brzyski, Lan-Juan Zhao, Hong-Wen Deng,and Yu-Ping Wang. Asparse regression method forgroup-wise feature selectionwith false discovery rate con-trol. IEEE/ACM Transac-tions on Computational Bi-ology and Bioinformatics, 15(4):1066–1078, July 2018.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Gao:2014:HTZ

[GCC+14] Yuan Gao, Rosa H. M. Chan,Tommy W. S. Chow, LiyunZhang, Sylvia Bonilla, Chi-Pui Pang, Mingzhi Zhang,and Yuk Fai Leung. A high-throughput zebrafish screen-ing method for visual mu-tants by light-induced loco-motor response. IEEE/ACMTransactions on Computa-tional Biology and Bioinfor-matics, 11(4):693–701, July2014. CODEN ITCBCY.ISSN 1545-5963 (print),1557-9964 (electronic).

Guo:2018:RDM

[GCL+18] Yi-Nan Guo, Jian Cheng,Sha Luo, Dunwei Gong, andYu Xue. Robust dynamicmulti-objective vehicle rout-ing optimization method.IEEE/ACM Transactions

on Computational Biologyand Bioinformatics, 15(6):1891–1903, November 2018.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Cao:2010:IAM

[gCLL+10] Yong gang Cao, ZuofengLi, Feifan Liu, ShashankAgarwal, Qing Zhang, andHong Yu. An IR-aided ma-chine learning framework forthe BioCreative II.5 chal-lenge. IEEE/ACM Trans-actions on ComputationalBiology and Bioinformat-ics, 7(3):454–461, July 2010.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Gao:2018:MMA

[GCZ18] Xin Gao, Jake Y. Chen, andMohammed J. Zaki. Multi-scale and multimodal anal-ysis for computational bi-ology. IEEE/ACM Trans-actions on ComputationalBiology and Bioinformatics,15(6):1951–1952, November2018. CODEN ITCBCY.ISSN 1545-5963 (print),1557-9964 (electronic).

Grassi:2012:KSP

[GDM12] Elena Grassi, Federico DiGregorio, and Ivan Mo-lineris. KungFQ: a sim-ple and powerful approachto compress fastq files.IEEE/ACM Transactionson Computational Biology

REFERENCES 146


Gonzalez-Dominguez:2018:MPC

[GDM18] Jorge Gonzalez-Dominguezand Maria J. Martin. MPI-GeneNet: Parallel calcula-tion of gene co-expressionnetworks on multicore clus-ters. IEEE/ACM Transac-tions on Computational Bi-ology and Bioinformatics,15(5):1732–1737, September2018. CODEN ITCBCY.ISSN 1545-5963 (print),1557-9964 (electronic).

Gonzalez-Dominguez:2015:PED

[GDWK+15] Jorge Gonzalez-Dominguez,Lars Wienbrandt, Jan Chris-tian Kassens, David Elling-haus, Manfred Schimmler,and Bertil Schmidt. Paral-lelizing epistasis detection inGWAS on FPGA and GPU-accelerated computing sys-tems. IEEE/ACM Trans-actions on ComputationalBiology and Bioinformat-ics, 12(5):982–994, Septem-ber 2015. CODEN ITCBCY.ISSN 1545-5963 (print),1557-9964 (electronic).

Gorecki:2014:MDC

[GE14] Pawel Gorecki and OliverEulenstein. Maximizing deepcoalescence cost. IEEE/ACM Transactions on Com-putational Biology and Bioin-

formatics, 11(1):231–242,January 2014. CODENITCBCY. ISSN 1545-5963(print), 1557-9964 (elec-tronic).

Gorecki:2015:GTD

[GE15] Pawe Gorecki and Oliver Eu-lenstein. Gene tree diam-eter for deep coalescence.IEEE/ACM Transactions onComputational Biology andBioinformatics, 12(1):155–165, January 2015. CODENITCBCY. ISSN 1545-5963(print), 1557-9964 (elec-tronic).

Gorecki:2018:BDG

[GE18] Pawel Gorecki and OliverEulenstein. Bijective di-ameters of gene tree par-simony costs. IEEE/ACMTransactions on Computa-tional Biology and Bioin-formatics, 15(5):1723–1727,September 2018. CODENITCBCY. ISSN 1545-5963(print), 1557-9964 (elec-tronic).

Goodacre:2017:PND

[GED+17] Norman Goodacre, NathanEdwards, Mark Danielsen,Peter Uetz, and CathyWu. Predicting nsSNPsthat disrupt protein-proteininteractions using docking.IEEE/ACM Transactionson Computational Biologyand Bioinformatics, 14(5):1082–1093, September 2017.CODEN ITCBCY. ISSN

REFERENCES 147


Gorecki:2013:UTR

[GET13] Pawel Gorecki, Oliver Eu-lenstein, and Jerzy Tiuryn.Unrooted tree reconcilia-tion: a unified approach.IEEE/ACM Transactions onComputational Biology andBioinformatics, 10(2):522–536, March 2013. CODENITCBCY. ISSN 1545-5963(print), 1557-9964 (elec-tronic).

Godin:2010:QDS

[GF10] Christophe Godin and Pas-cal Ferraro. Quantifyingthe degree of self-nestednessof trees: Application tothe structural analysis ofplants. IEEE/ACM Transac-tions on Computational Bi-ology and Bioinformatics, 7(4):688–703, October 2010.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Gong:2016:PDA

[GFG16] Yanmin Gong, YuguangFang, and Yuanxiong Guo.Private data analytics onbiomedical sensing datavia distributed computa-tion. IEEE/ACM Trans-actions on ComputationalBiology and Bioinformatics,13(3):431–444, May 2016.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Gordon:2013:HWP

[GFS13] Kevaughn Gordon, EricFord, and Katherine St.John. Hamiltonian walksof phylogenetic treespaces.IEEE/ACM Transactions onComputational Biology andBioinformatics, 10(4):1076–1079, July 2013. CODENITCBCY. ISSN 1545-5963(print), 1557-9964 (elec-tronic).

Gysel:2011:EIC

[GG11] Rob Gysel and Daniel Gus-field. Extensions and im-provements to the chordalgraph approach to the multi-state perfect phylogeny prob-lem. IEEE/ACM Trans-actions on ComputationalBiology and Bioinformat-ics, 8(4):912–917, July 2011.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Gao:2013:MMA

[GGH+13] Qian Gao, David Gilbert,Monika Heiner, Fei Liu,Daniele Maccagnola, andDavid Tree. Multiscalemodeling and analysis ofplanar cell polarity in theDrosophila wing. IEEE/ACM Transactions on Com-putational Biology and Bioin-formatics, 10(2):337–351,March 2013. CODENITCBCY. ISSN 1545-5963(print), 1557-9964 (elec-tronic).

REFERENCES 148

Ganapathy:2006:PIB

[GGJ+06] Ganeshkumar Ganapathy,Barbara Goodson, RobertJansen, Hai son Le, Vi-jaya Ramachandran, andTandy Warnow. Patternidentification in biogeogra-phy. IEEE/ACM Transac-tions on Computational Bi-ology and Bioinformatics, 3(4):334–346, October 2006.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Genovese:2008:SAH

[GGP08] Loredana M. Genovese, Fil-ippo Geraci, and Marco Pel-legrini. SpeedHap: An ac-curate heuristic for the sin-gle individual SNP haplotyp-ing problem with many gaps,high reading error rate andlow coverage. IEEE/ACMTransactions on Computa-tional Biology and Bioinfor-matics, 5(4):492–502, Octo-ber 2008. CODEN ITCBCY.ISSN 1545-5963 (print),1557-9964 (electronic).

Gan:2014:ICR

[GGZZ14] Yanglan Gan, Jihong Guan,Shuigeng Zhou, and Weix-iong Zhang. Identifyingcis-regulatory elements andmodules using conditionalrandom fields. IEEE/ACMTransactions on Computa-tional Biology and Bioinfor-matics, 11(1):73–82, January2014. CODEN ITCBCY.


Gambette:2008:ILP

[GH08a] Philippe Gambette andDaniel H. Huson. Improvedlayout of phylogenetic net-works. IEEE/ACM Trans-actions on ComputationalBiology and Bioinformat-ics, 5(3):472–479, July 2008.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Giancarlo:2008:GEI

[GH08b] Raffaele Giancarlo and Srid-har Hannenhalli. Guest Edi-tors’ introduction to the spe-cial section on algorithms inbioinformatics. IEEE/ACMTransactions on Computa-tional Biology and Bioinfor-matics, 5(4):482–483, Octo-ber 2008. CODEN ITCBCY.ISSN 1545-5963 (print),1557-9964 (electronic).

Golshan:2015:OLB

[GH15] Hosein M. Golshan and RezaP. R. Hasanzadeh. Anoptimized LMMSE basedmethod for 3D MRI denois-ing. IEEE/ACM Transac-tions on Computational Bi-ology and Bioinformatics,12(4):861–870, July 2015.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

REFERENCES 149

Gustafsson:2005:CAL

[GHL05] Mika Gustafsson, MichaelHornquist, and Anna Lom-bardi. Constructing and an-alyzing a large-scale gene-to-gene regulatory network-lasso-constrained inferenceand biological validation.IEEE/ACM Transactions onComputational Biology andBioinformatics, 2(3):254–261, July 2005. CODENITCBCY. ISSN 1545-5963(print), 1557-9964 (elec-tronic).

Guo:2019:GES

[GJH19] Feng-Biao Guo, Xinglai Ji,and Jian Huang. Guesteditorial for special sec-tion on the 7th NationalConference on Bioinformat-ics and Systems Biology ofChina. IEEE/ACM Trans-actions on ComputationalBiology and Bioinformatics,16(4):1262–1263, July 2019.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Gopinath:2015:DKD

[GJK15] Krishnasamy Gopinath, Ra-maraj Jayakumararaj, andMuthusamy Karthikeyan.DAPD: a knowledgebasefor diabetes associated pro-teins. IEEE/ACM Trans-actions on ComputationalBiology and Bioinformatics,12(3):604–610, May 2015.CODEN ITCBCY. ISSN


Garcia-Jimenez:2014:PPR

[GJPSV14] Beatriz Garcıa-Jimenez, TirsoPons, Araceli Sanchis, andAlfonso Valencia. Predict-ing protein relationships tohuman pathways through arelational learning approachbased on simple sequencefeatures. IEEE/ACM Trans-actions on ComputationalBiology and Bioinformatics,11(4):753–765, July 2014.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Guillemot:2011:CSM

[GJS11] Sylvain Guillemot, JesperJansson, and Wing-KinSung. Computing a small-est multilabeled phylogenetictree from rooted triplets.IEEE/ACM Transactions onComputational Biology andBioinformatics, 8(4):1141–1147, July 2011. CODENITCBCY. ISSN 1545-5963(print), 1557-9964 (elec-tronic).

Guo:2014:RFE

[GJY+14] Jing Guo, Ritika Jain, PengYang, Rui Fan, Chee KeongKwoh, and Jie Zheng. Re-liable and fast estimation ofrecombination rates by con-vergence diagnosis and par-allel Markov Chain MonteCarlo. IEEE/ACM Trans-actions on Computational

REFERENCES 150

Biology and Bioinformatics,11(1):63–72, January 2014.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Gu:2017:RGS

[GJZH17] Deqing Gu, Xingxing Jian,Cheng Zhang, and QiangHua. Reframed genome-scalemetabolic model to facilitategenetic design and integra-tion with expression data.IEEE/ACM Transactionson Computational Biologyand Bioinformatics, 14(6):1410–1418, November 2017.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Gondro:2008:OCM

[GK08] Cedric Gondro and Brian P.Kinghorn. Optimizationof cDNA microarray ex-perimental designs usingan evolutionary algorithm.IEEE/ACM Transactions onComputational Biology andBioinformatics, 5(4):630–638, October 2008. CODENITCBCY. ISSN 1545-5963(print), 1557-9964 (elec-tronic).

Ghosh:2019:FFS

[GK19] Priyanka Ghosh and AnanthKalyanaraman. FastEtch: afast sketch-based assemblerfor genomes. IEEE/ACMTransactions on Computa-tional Biology and Bioin-formatics, 16(4):1091–1106,


Gasbarra:2011:EHF

[GKPS11] Dario Gasbarra, Sangita Ku-lathinal, Matti Pirinen, andMikko J. Sillanpaa. Estimat-ing haplotype frequencies bycombining data from largeDNA pools with databaseinformation. IEEE/ACMTransactions on Computa-tional Biology and Bioinfor-matics, 8(1):36–44, January2011. CODEN ITCBCY.ISSN 1545-5963 (print),1557-9964 (electronic).

Gupta:2010:AHD

[GLG10] Gunjan Gupta, AlexanderLiu, and Joydeep Ghosh.Automated hierarchical den-sity shaving: a robust au-tomated clustering and vi-sualization framework forlarge biological data sets.IEEE/ACM Transactions onComputational Biology andBioinformatics, 7(2):223–237, April 2010. CODENITCBCY. ISSN 1545-5963(print), 1557-9964 (elec-tronic).

Gao:2018:NCD

[GLL+18] Chao Gao, Mingxin Liang,Xianghua Li, Zili Zhang,Zhen Wang, and ZhiliZhou. Network com-munity detection basedon the Physarum-inspiredcomputational framework.

REFERENCES 151

IEEE/ACM Transactionson Computational Biologyand Bioinformatics, 15(6):1916–1928, November 2018.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Ganesan:2016:PSC

[GLS+16] Narayan Ganesan, Jie Li,Vishakha Sharma, HanyuJiang, and Adriana Com-pagnoni. Process simu-lation of complex biolog-ical pathways in physicalreactive space and refor-mulated for massively par-allel computing platforms.IEEE/ACM Transactions onComputational Biology andBioinformatics, 13(2):365–379, March 2016. CODENITCBCY. ISSN 1545-5963(print), 1557-9964 (elec-tronic).

Gonzalez:2012:PLB

[GLW12] Alvaro J. Gonzalez, Li Liao,and Cathy H. Wu. Predict-ing ligand binding residuesand functional sites us-ing multipositional corre-lations with graph theo-retic clustering and kernelCCA. IEEE/ACM Trans-actions on ComputationalBiology and Bioinformatics,9(4):992–1001, July 2012.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Grunewald:2009:MPT

[GM09] Stefan Grunewald and Vin-cent Moulton. Maximumparsimony for tree mix-tures. IEEE/ACM Transac-tions on Computational Bi-ology and Bioinformatics, 6(1):97–102, January 2009.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Goncalves:2014:LEH

[GM14] Joana P. Goncalves andSara C. Madeira. LateBi-clustering: efficient heuris-tic algorithm for time-lagged bicluster identifica-tion. IEEE/ACM Trans-actions on ComputationalBiology and Bioinformat-ics, 11(5):801–813, Septem-ber 2014. CODEN ITCBCY.ISSN 1545-5963 (print),1557-9964 (electronic).

Guzzi:2016:GES

[GM16] Pietro H. Guzzi and MarcoMina. Guest editorial forspecial section on semantic-based approaches for anal-ysis of biological data.IEEE/ACM Transactionson Computational Biologyand Bioinformatics, 13(2):196, March 2016. CODENITCBCY. ISSN 1545-5963(print), 1557-9964 (elec-tronic).

Gregory:2014:LFD

[GMCB14] Karl B. Gregory, Amin A.Momin, Kevin R. Coombes,

REFERENCES 152

and Veerabhadran Baladan-dayuthapani. Latent fea-ture decompositions for in-tegrative analysis of multi-platform genomic data.IEEE/ACM Transactionson Computational Biologyand Bioinformatics, 11(6):984–994, November 2014.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Gusev:2008:HSG

[GMP08] Alexander Gusev, Ion I.Mandoiu, and Bogdan Pasaniuc.Highly scalable genotypephasing by entropy min-imization. IEEE/ACMTransactions on Computa-tional Biology and Bioinfor-matics, 5(2):252–261, April2008. CODEN ITCBCY.ISSN 1545-5963 (print),1557-9964 (electronic).

Ghorai:2011:CCG

[GMSD11] Santanu Ghorai, AnirbanMukherjee, SanghamitraSengupta, and Pranab K.Dutta. Cancer classifica-tion from gene expressiondata by NPPC ensemble.IEEE/ACM Transactionson Computational Biologyand Bioinformatics, 8(3):659–671, May/June 2011.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Goni:2013:NAI

[Gon13] Osman Goni. A new ap-

proach to implement ab-sorbing boundary conditionin biomolecular electrostat-ics. IEEE/ACM Transac-tions on Computational Bi-ology and Bioinformatics,10(3):799–804, May 2013.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Gossler:2011:CBM

[Gos11] Gregor Gossler. Component-based modeling and reacha-bility analysis of genetic net-works. IEEE/ACM Trans-actions on ComputationalBiology and Bioinformat-ics, 8(3):672–682, May/June2011. CODEN ITCBCY.ISSN 1545-5963 (print),1557-9964 (electronic).

Goutsias:2006:HMM

[Gou06] John Goutsias. A hiddenMarkov model for transcrip-tional regulation in singlecells. IEEE/ACM Trans-actions on ComputationalBiology and Bioinformatics,3(1):57–71, January 2006.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Guo:2020:NEE

[GPC+20] Qian Guo, Tianhong Pan,Shan Chen, Xiaobo Zou, andDorothy Yu Huang. A noveledge effect detection methodfor real-time cellular ana-lyzer using functional prin-cipal component analysis.

REFERENCES 153

IEEE/ACM Transactionson Computational Biologyand Bioinformatics, 17(5):1563–1572, September 2020.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic). URL https://dl.acm.org/doi/10.1109/TCBB.2019.2903094.

Gorecki:2017:UDD

[GPE17] Pawel Pawel Gorecki, JaroslawPaszek, and Oliver Eulen-stein. Unconstrained diam-eters for deep coalescence.IEEE/ACM Transactionson Computational Biologyand Bioinformatics, 14(5):1002–1012, September 2017.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Gibbs:2020:AVS

[GPF+20] Jonathon A. Gibbs, Michael P.Pound, Andrew P. French,Darren M. Wells, Erik H.Murchie, and Tony P. Prid-more. Active vision andsurface reconstruction for3D plant shoot modelling.IEEE/ACM Transactionson Computational Biologyand Bioinformatics, 17(6):1907–1917, November 2020.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic). URL https://dl.acm.org/doi/10.1109/TCBB.2019.2896908.

Gong:2016:GBN

[GPMH16] Maoguo Gong, ZhenglinPeng, Lijia Ma, and Jiaxi-

ang Huang. Global biologicalnetwork alignment by usingefficient memetic algorithm.IEEE/ACM Transactionson Computational Biologyand Bioinformatics, 13(6):1117–1129, November 2016.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Gomez-Pulido:2015:ABA

[GPScF15] Juan A. Gomez-Pulido,Bertil Schmidt, and Wu chunFeng. Accelerating bioin-formatics applications viaemerging parallel comput-ing systems. IEEE/ACMTransactions on Computa-tional Biology and Bioin-formatics, 12(5):971–972,September 2015. CODENITCBCY. ISSN 1545-5963(print), 1557-9964 (elec-tronic).

Ganor:2020:NGT

[GPZ20] Dor Ganor, Ron Y. Pin-ter, and Meirav Zehavi. Anote on GRegNetSim: atool for the discrete simu-lation and analysis of ge-netic regulatory networks.IEEE/ACM Transactions onComputational Biology andBioinformatics, 17(1):316–320, January 2020. CO-DEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic). URL https://dl.acm.org/doi/abs/10.1109/TCBB.2018.2878749.

REFERENCES 154

Gramm:2004:PTA

[Gra04] Jens Gramm. A polynomial-time algorithm for thematching of crossing contact-map patterns. IEEE/ACMTransactions on Computa-tional Biology and Bioinfor-matics, 1(4):171–180, Octo-ber 2004. CODEN ITCBCY.ISSN 1545-5963 (print),1557-9964 (electronic).

GaneshKumar:2014:HAB

[GRDV14] Pugalendhi GaneshKumar,Chellasamy Rani, DurairajDevaraj, and T. Aruldoss Al-bert Victoire. Hybrid ant beealgorithm for fuzzy expertsystem based sample classi-fication. IEEE/ACM Trans-actions on ComputationalBiology and Bioinformatics,11(2):347–360, March 2014.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Goeffon:2008:PTN

[GRH08] Adrien Goeffon, Jean-MichelRicher, and Jin-Kao Hao.Progressive tree neighbor-hood applied to the max-imum parsimony problem.IEEE/ACM Transactions onComputational Biology andBioinformatics, 5(1):136–145, January 2008. CODENITCBCY. ISSN 1545-5963(print), 1557-9964 (elec-tronic).

Garcia:2013:GDA

[GRS+13] Sara P. Garcia, Joao M. O. S.Rodrigues, Sergio Santos,Diogo Pratas, Vera Afreixo,Carlos Bastos, Paulo J.S. G. Ferreira, and Ar-mando J. Pinho. A ge-nomic distance for assem-bly comparison based oncompressed maximal exactmatches. IEEE/ACM Trans-actions on ComputationalBiology and Bioinformatics,10(3):793–798, May 2013.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Grusea:2011:DNC

[Gru11] Simona Grusea. On thedistribution of the numberof cycles in the breakpointgraph of a random signedpermutation. IEEE/ACMTransactions on Computa-tional Biology and Bioin-formatics, 8(5):1411–1416,September 2011. CODENITCBCY. ISSN 1545-5963(print), 1557-9964 (elec-tronic).

Grunewald:2013:SCS

[GSB+13] Stefan Grunewald, AndreasSpillner, Sarah Bastkowski,Anja Bogershausen, andVincent Moulton. SuperQ:Computing supernetworksfrom quartets. IEEE/ACMTransactions on Computa-tional Biology and Bioin-formatics, 10(1):151–160,January 2013. CODEN

REFERENCES 155


Grewal:2017:EAO

[GSC17] Nivit Grewal, ShailendraSingh, and Trilok Chand. Ef-fect of aggregation operatorson network-based diseasegene prioritization: a casestudy on blood disorders.IEEE/ACM Transactionson Computational Biologyand Bioinformatics, 14(6):1276–1287, November 2017.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Gao:2018:ISE

[GSC+18] Shangce Gao, ShuangbaoSong, Jiujun Cheng, YukiTodo, and MengChu Zhou.Incorporation of solvent ef-fect into multi-objective evo-lutionary algorithm for im-proved protein structure pre-diction. IEEE/ACM Trans-actions on ComputationalBiology and Bioinformatics,15(4):1365–1378, July 2018.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Gremme:2013:GCS

[GSK13] Gordon Gremme, SaschaSteinbiss, and Stefan Kurtz.GenomeTools: a comprehen-sive software library for ef-ficient processing of struc-tured genome annotations.IEEE/ACM Transactions on

Computational Biology andBioinformatics, 10(3):645–656, May 2013. CODENITCBCY. ISSN 1545-5963(print), 1557-9964 (elec-tronic).

Guo:2018:GPS

[GSX+18] Weian Guo, Chengyong Si,Yu Xue, Yanfen Mao, LeiWang, and Qidi Wu. Agrouping particle swarmoptimizer with personal-best-position guidance forlarge scale optimization.IEEE/ACM Transactionson Computational Biologyand Bioinformatics, 15(6):1904–1915, November 2018.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Gabr:2015:RAP

[GTDK15] Haitham Gabr, AndreiTodor, Alin Dobra, andTamer Kahveci. Reach-ability analysis in proba-bilistic biological networks.IEEE/ACM Transactions onComputational Biology andBioinformatics, 12(1):53–66,January 2015. CODENITCBCY. ISSN 1545-5963(print), 1557-9964 (elec-tronic).

Goldweber:2017:PGB

[GTTR+17] Scott Goldweber, JamalTheodore, John Torcivia-Rodriguez, Vahan Simonyan,and Raja Mazumder. Pub-cast and Genecast: Brows-

REFERENCES 156

ing and exploring publica-tions and associated curatedcontent in biology throughmobile devices. IEEE/ACMTransactions on Computa-tional Biology and Bioin-formatics, 14(2):498–500,March 2017. CODENITCBCY. ISSN 1545-5963(print), 1557-9964 (elec-tronic).

Gu:2016:MSO

[Gu16] Xu Gu. A multi-state opti-mization framework for pa-rameter estimation in bio-logical systems. IEEE/ACMTransactions on Computa-tional Biology and Bioinfor-matics, 13(3):472–482, May2016. CODEN ITCBCY.ISSN 1545-5963 (print),1557-9964 (electronic).

Gusfield:2004:INA

[Gus04a] Dan Gusfield. Introduc-tion of new Associate Edi-tors. IEEE/ACM Transac-tions on Computational Bi-ology and Bioinformatics, 1(3):97, July 2004. CODENITCBCY. ISSN 1545-5963(print), 1557-9964 (elec-tronic).

Gusfield:2004:IIA

[Gus04b] Dan Gusfield. Introductionto the IEEE/ACM Trans-actions on ComputationalBiology and Bioinformat-ics. IEEE/ACM Trans-actions on ComputationalBiology and Bioinformat-

ics, 1(1):2–3, January 2004.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Gusfield:2005:EST

[Gus05] Dan Gusfield. Editorial-state of the transaction.IEEE/ACM Transactionson Computational Biologyand Bioinformatics, 2(1):39, January 2005. CODENITCBCY. ISSN 1545-5963(print), 1557-9964 (elec-tronic).

Gusfield:2006:INA

[Gus06a] Dan Gusfield. Introduc-tion of new Associate Ed-itors. IEEE/ACM Trans-actions on ComputationalBiology and Bioinformat-ics, 3(2):97, April 2006.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Gusfield:2006:SJ

[Gus06b] Dan Gusfield. State ofthe journal. IEEE/ACMTransactions on Computa-tional Biology and Bioinfor-matics, 3(1):1, January 2006.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Gusfield:2007:AEAa

[Gus07a] Dan Gusfield. Associate Ed-itor appreciation and wel-come. IEEE/ACM Trans-actions on Computational

REFERENCES 157

Biology and Bioinformat-ics, 4(1):2, January 2007.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Gusfield:2007:AEAb

[Gus07b] Dan Gusfield. Associate Ed-itor appreciation and wel-come. IEEE/ACM Trans-actions on ComputationalBiology and Bioinformat-ics, 4(3):321, July 2007.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Gusfield:2007:SJ

[Gus07c] Dan Gusfield. State ofthe Journal. IEEE/ACMTransactions on Computa-tional Biology and Bioinfor-matics, 4(1):1, January 2007.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Gusfield:2008:EE

[Gus08] Dan Gusfield. EIC edito-rial. IEEE/ACM Trans-actions on ComputationalBiology and Bioinformat-ics, 5(4):481, October 2008.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Gusfield:2009:FFY

[Gus09a] Dan Gusfield. Final,five-year end, editorial.IEEE/ACM Transactionson Computational Biology

and Bioinformatics, 6(1):1–2, January 2009. CODENITCBCY. ISSN 1545-5963(print), 1557-9964 (elec-tronic).

Gusfield:2009:OEE

[Gus09b] Dan Gusfield. OutgoingEIC editorial for this spe-cial section of TCBB withthe theme of phylogenet-ics. IEEE/ACM Trans-actions on ComputationalBiology and Bioinformat-ics, 6(1):96, January 2009.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Ge:2017:CSD

[GXSZ17] Shu-Guang Ge, Junfeng Xia,Wen Sha, and Chun-HouZheng. Cancer subtype dis-covery based on integrativemodel of multigenomic data.IEEE/ACM Transactionson Computational Biologyand Bioinformatics, 14(5):1115–1121, September 2017.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Guo:2017:SGW

[GZC+17] Xuan Guo, Jing Zhang,Zhipeng Cai, Ding-Zhu Du,and Yi Pan. Searchinggenome-wide multi-locus as-sociations for multiple dis-eases based on Bayesian in-ference. IEEE/ACM Trans-actions on ComputationalBiology and Bioinformatics,

REFERENCES 158

14(3):600–610, May 2017.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Gao:2015:CCE

[GZFT15] Nan Gao, Yan Zhang, BingFeng, and Jijun Tang. A co-operative co-evolutionary ge-netic algorithm for tree scor-ing and ancestral genome in-ference. IEEE/ACM Trans-actions on ComputationalBiology and Bioinformatics,12(6):1248–1254, November2015. CODEN ITCBCY.ISSN 1545-5963 (print),1557-9964 (electronic).

Gangeh:2017:FSF

[GZG17] Mehrdad J. Gangeh, HadiZarkoob, and Ali Ghodsi.Fast and scalable featureselection for gene expres-sion data using Hilbert–Schmidt independence crite-rion. IEEE/ACM Transac-tions on Computational Bi-ology and Bioinformatics, 14(1):167–181, January 2017.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Gan:2014:NWB

[GZGX14] Yanglan Gan, Guobing Zou,Jihong Guan, and Guang-wei Xu. A novel wavelet-based approach for predict-ing nucleosome positions us-ing DNA structural infor-mation. IEEE/ACM Trans-actions on Computational

Biology and Bioinformatics,11(4):638–647, July 2014.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Ghoshal:2018:DCM

[GZR+18] Asish Ghoshal, Jinyi Zhang,Michael A. Roth, Kevin MuyuanXia, Ananth Y. Grama, andSomali Chaterji. A dis-tributed classifier for Mi-croRNA target predictionwith validation throughTCGA expression data.IEEE/ACM Transactions onComputational Biology andBioinformatics, 15(4):1037–1051, July 2018. CODENITCBCY. ISSN 1545-5963(print), 1557-9964 (elec-tronic).

Giegerich:2011:SAS

[GzS11] Robert Giegerich and Chris-tian Hoener zu Siederdissen.Semantics and ambiguity ofstochastic RNA family mod-els. IEEE/ACM Transac-tions on Computational Bi-ology and Bioinformatics, 8(2):499–516, March 2011.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Gyorffy:2012:PMR

[GZS12] Daniel Gyorffy, Peter Za-vodszky, and Andras Szi-lagyi. “pull moves” for rect-angular lattice polymer mod-els are not fully reversible.IEEE/ACM Transactions

REFERENCES 159


Higa:2013:GSG

[HAH13] Carlos H. A. Higa, Tales P.Andrade, and Ronaldo Fu-mio Hashimoto. Growingseed genes from time se-ries data and thresholdedBoolean networks with per-turbation. IEEE/ACMTransactions on Computa-tional Biology and Bioinfor-matics, 10(1):37–49, January2013. CODEN ITCBCY.ISSN 1545-5963 (print),1557-9964 (electronic).

Hashemikhabir:2012:LSS

[HAK+12] Seyedsasan Hashemikhabir,Eyup Serdar Ayaz, YusufKavurucu, Tolga Can, andTamer Kahveci. Large-scale signaling network re-construction. IEEE/ACMTransactions on Computa-tional Biology and Bioin-formatics, 9(6):1696–1708,November 2012. CODENITCBCY. ISSN 1545-5963(print), 1557-9964 (elec-tronic).

Han:2010:NPC

[Han10] Xiaoxu Han. Nonnegativeprincipal component analy-sis for cancer molecular pat-tern discovery. IEEE/ACMTransactions on Computa-

tional Biology and Bioinfor-matics, 7(3):537–549, July2010. CODEN ITCBCY.ISSN 1545-5963 (print),1557-9964 (electronic).

Hawkins:2005:ARN

[HB05] John Hawkins and MikaelBoden. The applicabilityof recurrent neural networksfor biological sequence anal-ysis. IEEE/ACM Trans-actions on ComputationalBiology and Bioinformat-ics, 2(3):243–253, July 2005.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Hudek:2011:FSL

[HB11] Alexander K. Hudek andDaniel G. Brown. FEAST:Sensitive local alignmentwith multiple rates of evo-lution. IEEE/ACM Trans-actions on ComputationalBiology and Bioinformat-ics, 8(3):698–709, May/June2011. CODEN ITCBCY.ISSN 1545-5963 (print),1557-9964 (electronic).

Hickey:2011:AAN

[HBC+11] Glenn Hickey, MathieuBlanchette, Paz Carmi, AnilMaheshwari, and NorbertZeh. An approximation al-gorithm for the Noah’s ArkProblem with random fea-ture loss. IEEE/ACM Trans-actions on ComputationalBiology and Bioinformatics,8(2):551–556, March 2011.

REFERENCES 160


Huang:2016:GES

[HBG16] De-Shuang Huang, Vi-toantonio Bevilacqua, andM. Michael Gromiha. Guesteditorial for special sec-tion on the 10th Interna-tional Conference on Intel-ligent Computing (ICIC).IEEE/ACM Transactions onComputational Biology andBioinformatics, 13(1):1–3,January 2016. CODENITCBCY. ISSN 1545-5963(print), 1557-9964 (elec-tronic).

Huang:2017:GES

[HBG17] De-Shuang Huang, Vi-toantonio Bevilacqua, andM. Michael Gromiha. Guesteditorial for special sec-tion on the 11th Interna-tional Conference on In-telligent Computing ICIC.IEEE/ACM Transactionson Computational Biologyand Bioinformatics, 14(5):1104–1105, September 2017.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Huang:2018:GES

[HBG18] De-Shuang Huang, Vi-toantonio Bevilacqua, andM. Michael Gromiha. Guesteditorial for special sec-tion on the 12th Interna-tional Conference on In-

telligent Computing ICIC.IEEE/ACM Transactionson Computational Biologyand Bioinformatics, 15(5):1433–1435, September 2018.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Huang:2019:GES

[HBG19] De-Shuang Huang, Vi-toantonio Bevilacqua, andM. Michael Gromiha. Guesteditorial for special sec-tion on the 13th Interna-tional Conference on In-telligent Computing ICIC.IEEE/ACM Transactions onComputational Biology andBioinformatics, 16(3):749–750, May 2019. CODENITCBCY. ISSN 1545-5963(print), 1557-9964 (elec-tronic).

Huang:2020:GES

[HBG20] De-Shuang Huang, Vitoanto-nio Bevilacqua, and MichaelGromiha. Guest editorialfor special section on the14th International Confer-ence on Intelligent Comput-ing (ICIC). IEEE/ACMTransactions on Computa-tional Biology and Bioin-formatics, 17(5):1474–1475,September 2020. CODENITCBCY. ISSN 1545-5963(print), 1557-9964 (elec-tronic). URL https://dl.acm.org/doi/10.1109/TCBB.2020.2989800.

REFERENCES 161

Hanczar:2012:NMC

[HBH12] Blaise Hanczar and AvnerBar-Hen. A new mea-sure of classifier performancefor gene expression data.IEEE/ACM Transactionson Computational Biologyand Bioinformatics, 9(5):1379–1386, September 2012.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Hartmann:2019:EAS

[HBM19] Tom Hartmann, MatthiasBernt, and Martin Midden-dorf. An exact algorithmfor sorting by weighted pre-serving genome rearrange-ments. IEEE/ACM Trans-actions on ComputationalBiology and Bioinformatics,16(1):52–62, January 2019.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Haack:2013:SRL

[HBRU13] Fiete Haack, Kevin Bur-rage, Ronald Redmer, andAdelinde M. Uhrmacher.Studying the role of lipidrafts on protein receptorbindings with cellular au-tomata. IEEE/ACM Trans-actions on ComputationalBiology and Bioinformatics,10(3):760–770, May 2013.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Huang:2007:EGS

[HC07] D. Huang and TommyChow. Effective gene selec-tion method with small sam-ple sets using gradient-basedand point injection tech-niques. IEEE/ACM Trans-actions on ComputationalBiology and Bioinformat-ics, 4(3):467–475, July 2007.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Hu:2013:UBT

[HC13] Allen L. Hu and Keith C. C.Chan. Utilizing both topo-logical and attribute infor-mation for protein complexidentification in PPI net-works. IEEE/ACM Trans-actions on ComputationalBiology and Bioinformatics,10(3):780–792, May 2013.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Healy:2014:AKM

[HC14a] John Healy and DesmondChambers. Approximate k-mer matching using fuzzyhash maps. IEEE/ACMTransactions on Computa-tional Biology and Bioin-formatics, 11(1):258–264,January 2014. CODENITCBCY. ISSN 1545-5963(print), 1557-9964 (elec-tronic).

REFERENCES 162

Horta:2014:SMC

[HC14b] Danilo Horta and Ricardo J.G. B. Campello. Similar-ity measures for comparingbiclusterings. IEEE/ACMTransactions on Computa-tional Biology and Bioin-formatics, 11(5):942–954,September 2014. CODENITCBCY. ISSN 1545-5963(print), 1557-9964 (elec-tronic).

Huang:2015:GEA

[HC15] Hsien-Da Huang and Yi-Ping Phoebe Chen. Guesteditorial for the 13th AsiaPacific Bioinformatics Con-ference. IEEE/ACM Trans-actions on ComputationalBiology and Bioinformatics,12(6):1217–1218, November2015. CODEN ITCBCY.ISSN 1545-5963 (print),1557-9964 (electronic).

Hsieh:2016:FCM

[HC16] Sun-Yuan Hsieh and Yu-Chun Chou. A faster cDNAmicroarray gene expressiondata classifier for diagnosingdiseases. IEEE/ACM Trans-actions on ComputationalBiology and Bioinformatics,13(1):43–54, January 2016.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Hu:2017:ECF

[HC17] Lun Hu and Keith C. C.Chan. Extracting coevolu-

tionary features from pro-tein sequences for predict-ing protein–protein interac-tions. IEEE/ACM Transac-tions on Computational Bi-ology and Bioinformatics, 14(1):155–166, January 2017.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

He:2018:EGC

[HC18] Tiantian He and KeithC. C. Chan. Evolution-ary graph clustering forprotein complex identifica-tion. IEEE/ACM Trans-actions on ComputationalBiology and Bioinformatics,15(3):892–904, May 2018.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

He:2019:MBP

[HC19] Tiantian He and Keith C. C.Chan. Measuring bound-edness for protein complexidentification in PPI net-works. IEEE/ACM Trans-actions on ComputationalBiology and Bioinformatics,16(3):967–979, May 2019.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Han:2010:MPC

[HCA+10] Ju Han, Hang Chang, Ku-mari Andarawewa, PaulYaswen, Mary Helen Barcellos-Hoff, and Bahram Parvin.Multidimensional profiling of

REFERENCES 163

cell surface proteins and nu-clear markers. IEEE/ACMTransactions on Computa-tional Biology and Bioinfor-matics, 7(1):80–90, January2010. CODEN ITCBCY.ISSN 1545-5963 (print),1557-9964 (electronic).

Hoque:2011:TRG

[HCLS11] Md Tamjidul Hoque, MadhuChetty, Andrew Lewis, andAbdul Sattar. Twin re-moval in genetic algorithmsfor protein structure pre-diction using low-resolutionmodel. IEEE/ACM Transac-tions on Computational Bi-ology and Bioinformatics, 8(1):234–245, January 2011.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Hartmann:2018:CTD

[HCMB18] Tom Hartmann, An-ChiangChu, Martin Middendorf,and Matthias Bernt. Com-binatorics of tandem dupli-cation random loss muta-tions on circular genomes.IEEE/ACM Transactions onComputational Biology andBioinformatics, 15(1):83–95,January 2018. CODENITCBCY. ISSN 1545-5963(print), 1557-9964 (elec-tronic).

Halder:2019:LII

[HCN+19] Anup Kumar Halder, PiyaliChatterjee, Mita Nasipuri,Dariusz Plewczynski, and

Subhadip Basu. 3gClust:Human protein cluster anal-ysis. IEEE/ACM Transac-tions on Computational Bi-ology and Bioinformatics,16(6):1773–1784, November2019. CODEN ITCBCY.ISSN 1545-5963 (print),1557-9964 (electronic). URLhttps://dl.acm.org/doi/abs/10.1109/TCBB.2018.2840996.

Huang:2014:SAI

[HCQ14] Yufei Huang, Yidong Chen,and Xiaoning Qian. Selectedarticles from the 2012 IEEEInternational Workshop onGenomic Signal Processingand Statistics (GENSIPS2012). IEEE/ACM Transac-tions on Computational Bi-ology and Bioinformatics, 11(6):981–983, November 2014.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Huson:2004:PSN

[HDKS04] Daniel H. Huson, TobiasDezulian, Tobias Klopper,and Mike A. Steel. Phylo-genetic super-networks frompartial trees. IEEE/ACMTransactions on Computa-tional Biology and Bioinfor-matics, 1(4):151–158, Octo-ber 2004. CODEN ITCBCY.ISSN 1545-5963 (print),1557-9964 (electronic).

Hu:2018:FSO

[HDS+18] Bin Hu, Yongqiang Dai,Yun Su, Philip Moore, Xi-

REFERENCES 164

aowei Zhang, ChengshengMao, Jing Chen, and LixinXu. Feature selection foroptimized high-dimensionalbiomedical data using an im-proved shuffled frog leap-ing algorithm. IEEE/ACMTransactions on Computa-tional Biology and Bioin-formatics, 15(6):1765–1773,November 2018. CODENITCBCY. ISSN 1545-5963(print), 1557-9964 (elec-tronic).

Hashem:2018:CML

[HEE+18] Somaya Hashem, Gamal Es-mat, Wafaa Elakel, ShahiraHabashy, Safaa Abdel Raouf,Mohamed Elhefnawi, Mo-hamed Eladawy, and Mah-moud ElHefnawi. Com-parison of machine learn-ing approaches for predic-tion of advanced liver fibro-sis in chronic hepatitis C pa-tients. IEEE/ACM Trans-actions on ComputationalBiology and Bioinformatics,15(3):861–868, May 2018.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Hayamizu:2017:CMS

[HEF17] Momoko Hayamizu, HiroshiEndo, and Kenji Fukumizu.A characterization of mini-mum spanning tree-like met-ric spaces. IEEE/ACMTransactions on Computa-tional Biology and Bioin-formatics, 14(2):468–471,

March 2017. CODENITCBCY. ISSN 1545-5963(print), 1557-9964 (elec-tronic).

Hamad:2018:DWU

[HEK18] Safwat Hamad, Ahmed El-hadad, and Amal Khal-ifa. DNA watermarking us-ing codon postfix technique.IEEE/ACM Transactionson Computational Biologyand Bioinformatics, 15(5):1605–1610, September 2018.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Hecht:2007:HTL

[HF07] David Hecht and Gary Fo-gel. High-throughput lig-and screening via precluster-ing and evolved neural net-works. IEEE/ACM Trans-actions on ComputationalBiology and Bioinformat-ics, 4(3):476–484, July 2007.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Huang:2012:GCU

[HF12] Hong Huang and HailiangFeng. Gene classificationusing parameter-free semi-supervised manifold learn-ing. IEEE/ACM Trans-actions on ComputationalBiology and Bioinformat-ics, 9(3):818–827, May 2012.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

REFERENCES 165

Hu:2016:RTN

[HG16] Yuanqi Hu and PantelisGeorgiou. A real-time denovo DNA sequencing as-sembly platform based onan FPGA implementation.IEEE/ACM Transactions onComputational Biology andBioinformatics, 13(2):291–300, March 2016. CODENITCBCY. ISSN 1545-5963(print), 1557-9964 (elec-tronic).

Hu:2020:DRL

[HGC+20] Haigen Hu, Qiu Guan,Shengyong Chen, ZhiweiJi, and Yao Lin. Detec-tion and recognition for lifestate of cell cancer usingtwo-stage cascade CNNs.IEEE/ACM Transactions onComputational Biology andBioinformatics, 17(3):887–898, May 2020. CODENITCBCY. ISSN 1545-5963(print), 1557-9964 (elec-tronic). URL https://dl.acm.org/doi/10.1109/TCBB.2017.2780842.

Huang:2018:GNA

[HGM18] Jiaxiang Huang, MaoguoGong, and Lijia Ma. Aglobal network alignmentmethod using discrete par-ticle swarm optimization.IEEE/ACM Transactions onComputational Biology andBioinformatics, 15(3):705–718, May 2018. CODENITCBCY. ISSN 1545-5963


Hu:2020:LMN

[HHCY20] Pengwei Hu, Yu-An Huang,Keith C. C. Chan, and Zhu-Hong You. Learning mul-timodal networks from het-erogeneous data for pre-diction of lncRNA–miRNAinteractions. IEEE/ACMTransactions on Computa-tional Biology and Bioin-formatics, 17(5):1516–1524,September 2020. CODENITCBCY. ISSN 1545-5963(print), 1557-9964 (elec-tronic). URL https://dl.acm.org/doi/10.1109/TCBB.2019.2957094.

Hu:2020:ICI

[HHL+20] Lun Hu, Pengwei Hu, XinLuo, Xiaohui Yuan, and Zhu-Hong You. Incorporatingthe coevolving information ofsubstrates in predicting HIV-1 protease cleavage sites.IEEE/ACM Transactionson Computational Biologyand Bioinformatics, 17(6):2017–2028, November 2020.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic). URL https://dl.acm.org/doi/10.1109/TCBB.2019.2914208.

Haque:2013:GQB

[HHSC13] Md. Muksitul Haque, Lawrence B.Holder, Michael K. Skinner,and Diane J. Cook. Gen-eralized query-based active

REFERENCES 166

learning to identify differen-tially methylated regions inDNA. IEEE/ACM Trans-actions on ComputationalBiology and Bioinformatics,10(3):632–644, May 2013.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Ho:2007:ITS

[HHYH07] Shinn-Ying Ho, Chih-HungHsieh, Fu-Chieh Yu, andHui-Ling Huang. An in-telligent two-stage evolu-tionary algorithm for dy-namic pathway identificationfrom gene expression pro-files. IEEE/ACM Transac-tions on Computational Bi-ology and Bioinformatics, 4(4):648–704, October 2007.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Hodgkinson:2012:ADM

[HK12] Luqman Hodgkinson andRichard M. Karp. Algo-rithms to detect multiproteinmodularity conserved dur-ing evolution. IEEE/ACMTransactions on Computa-tional Biology and Bioinfor-matics, 9(4):1046–1058, July2012. CODEN ITCBCY.ISSN 1545-5963 (print),1557-9964 (electronic).

Hsu:2015:CNE

[HK15] Yi-Yu Hsu and Hung-YuKao. Curatable named-entity recognition using se-

mantic relations. IEEE/ACM Transactions on Com-putational Biology and Bioin-formatics, 12(4):785–792,July 2015. CODEN ITCBCY.ISSN 1545-5963 (print),1557-9964 (electronic).

Habibi:2020:DPC

[HK20] Mahnaz Habibi and Pe-gah Khosravi. Disrup-tion of protein complexesfrom weighted complex net-works. IEEE/ACM Transac-tions on Computational Bi-ology and Bioinformatics, 17(1):102–109, January 2020.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic). URL https://dl.acm.org/doi/abs/10.1109/TCBB.2018.2859952.

Handl:2007:MOB

[HKK07] Julia Handl, Douglas B. Kell,and Joshua Knowles. Mul-tiobjective optimization inbioinformatics and computa-tional biology. IEEE/ACMTransactions on Computa-tional Biology and Bioinfor-matics, 4(2):279–292, April2007. CODEN ITCBCY.ISSN 1545-5963 (print),1557-9964 (electronic).

Huffner:2014:PBN

[HKLN14] Falk Huffner, Christian Ko-musiewicz, Adrian Liebtrau,and Rolf Niedermeier. Par-titioning biological networksinto highly connected clus-ters with maximum edge cov-

REFERENCES 167

erage. IEEE/ACM Trans-actions on ComputationalBiology and Bioinformatics,11(3):455–467, May 2014.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Hujdurovic:2018:CAF

[HKM+18] Ademir Hujdurovic, UrsaKacar, Martin Milanic,Bernard Ries, and Alexan-dru I. Tomescu. Com-plexity and algorithms forfinding a perfect phylogenyfrom mixed tumor sam-ples. IEEE/ACM Transac-tions on Computational Bi-ology and Bioinformatics, 15(1):96–108, January 2018.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Hafemeister:2011:SOP

[HKS11] Christoph Hafemeister, RolandKrause, and AlexanderSchliep. Selecting oligonu-cleotide probes for whole-genome tiling arrays witha cross-hybridization poten-tial. IEEE/ACM Transac-tions on Computational Bi-ology and Bioinformatics,8(6):1642–1652, November2011. CODEN ITCBCY.ISSN 1545-5963 (print),1557-9964 (electronic).

Hirose:2018:SCT

[HKT+18] Osamu Hirose, ShotaroKawaguchi, Terumasa Toku-naga, Yu Toyoshima, Takayuki

Teramoto, Sayuri Kuge,Takeshi Ishihara, YuichiIino, and Ryo Yoshida.SPF-CellTracker: Track-ing multiple cells withstrongly-correlated movesusing a spatial particle filter.IEEE/ACM Transactionson Computational Biologyand Bioinformatics, 15(6):1822–1831, November 2018.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Han:2016:GII

[HL16] Kyungsook Han and JeonghoonLee. GeneNetFinder2: Im-proved inference of dy-namic gene regulatory re-lations with multiple regu-lators. IEEE/ACM Trans-actions on ComputationalBiology and Bioinformatics,13(1):4–11, January 2016.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Hu:2017:GRS

[HLDZ17] Hailong Hu, Zhong Li,Hongwei Dong, and TianheZhou. Graphical represen-tation and similarity anal-ysis of protein sequencesbased on fractal interpola-tion. IEEE/ACM Transac-tions on Computational Bi-ology and Bioinformatics, 14(1):182–192, January 2017.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

REFERENCES 168

Huang:2010:HRR

[HLG10] Liang-Tsung Huang, Lien-Fu Lai, and M. MichaelGromiha. Human-readablerule generator for integratingamino acid sequence infor-mation and stability of mu-tant proteins. IEEE/ACMTransactions on Computa-tional Biology and Bioinfor-matics, 7(4):681–687, Octo-ber 2010. CODEN ITCBCY.ISSN 1545-5963 (print),1557-9964 (electronic).

Huang:2011:IHA

[HLH11] Chao-Wen Huang, Wun-Shiun Lee, and Sun-YuanHsieh. An improved heuris-tic algorithm for findingmotif signals in DNA se-quences. IEEE/ACM Trans-actions on ComputationalBiology and Bioinformat-ics, 8(4):959–975, July 2011.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Hind:2020:NAD

[HLHAJ20] Jade Hind, Paulo Lisboa,Abir J. Hussain, and DhiyaAl-Jumeily. A novel ap-proach to detecting epista-sis using random samplingregularisation. IEEE/ACMTransactions on Computa-tional Biology and Bioin-formatics, 17(5):1535–1545,September 2020. CODENITCBCY. ISSN 1545-5963(print), 1557-9964 (elec-tronic). URL https://

dl.acm.org/doi/10.1109/TCBB.2019.2948330.

He:2018:TSB

[HLL+18a] Xinyu He, Lishuang Li, YangLiu, Xiaoming Yu, and JunMeng. A two-stage biomed-ical event trigger detectionmethod integrating featureselection and word embed-dings. IEEE/ACM Transac-tions on Computational Bi-ology and Bioinformatics, 15(4):1325–1332, July 2018.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Hu:2018:CBG

[HLL18b] Meng Hu, Wu Li, andHualou Liang. A copula-based Granger causalitymeasure for the analysisof neural spike train data.IEEE/ACM Transactions onComputational Biology andBioinformatics, 15(2):562–569, March 2018. CODENITCBCY. ISSN 1545-5963(print), 1557-9964 (elec-tronic).

Harmer:2019:BCC

[HLLO19] Russ Harmer, Yves-Stan LeCornec, Sebastien Legare,and Eugenia Oshurko. Bio-curation for cellular sig-nalling: The KAMI Project.IEEE/ACM Transactionson Computational Biologyand Bioinformatics, 16(5):1562–1573, September 2019.CODEN ITCBCY. ISSN

REFERENCES 169


Halasz:2013:ASS

[HLM+13] Adam M. Halasz, Hong-Jian Lai, Meghan M. Mc-Cabe, Krishnan Radhakr-ishnan, and Jeremy S. Ed-wards. Analytical solu-tion of steady-state equa-tions for chemical reactionnetworks with bilinear ratelaws. IEEE/ACM Trans-actions on ComputationalBiology and Bioinformatics,10(4):957–969, July 2013.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Lin:2011:DMF

[hLMBJ11] Tien ho Lin, Robert F.Murphy, and Ziv Bar-Joseph. Discriminative mo-tif finding for predictingprotein subcellular localiza-tion. IEEE/ACM Trans-actions on ComputationalBiology and Bioinformatics,8(2):441–451, March 2011.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

He:2020:DSJ

[HLN20] Yicheng He, Junfeng Liu,and Xia Ning. Drug selectionvia joint push and learning torank. IEEE/ACM Transac-tions on Computational Bi-ology and Bioinformatics, 17(1):110–123, January 2020.CODEN ITCBCY. ISSN

1545-5963 (print), 1557-9964(electronic). URL https://dl.acm.org/doi/abs/10.1109/TCBB.2018.2848908.

Hu:2018:ARE

[HLSR18] Bin Hu, Xiaowei Li, Shut-ing Sun, and Martyn Rat-cliffe. Attention recogni-tion in EEG-based affec-tive learning research us-ing CFS + KNN algo-rithm. IEEE/ACM Trans-actions on ComputationalBiology and Bioinformatics,15(1):38–45, January 2018.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Hakenberg:2010:EEP

[HLV+10] Jorg Hakenberg, Robert Lea-man, Nguyen Ha Vo, Sid-dhartha Jonnalagadda, RyanSullivan, Christopher Miller,Luis Tari, Chitta Baral, andGraciela Gonzalez. Efficientextraction of protein-proteininteractions from full-text ar-ticles. IEEE/ACM Trans-actions on ComputationalBiology and Bioinformat-ics, 7(3):481–494, July 2010.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Huang:2015:EMS

[HLW15] Lei Huang, Li Liao, andCathy H. Wu. Evolutionarymodel selection and param-eter estimation for protein–protein interaction network

REFERENCES 170

based on differential evolu-tion algorithm. IEEE/ACMTransactions on Computa-tional Biology and Bioinfor-matics, 12(3):622–631, May2015. CODEN ITCBCY.ISSN 1545-5963 (print),1557-9964 (electronic).

Hsiao:2016:PGI

[HLY+16] Yu-Ting Hsiao, Wei-Po Lee,Wei Yang, Stefan Muller,Christoph Flamm, Ivo Ho-facker, and Philipp Ku-gler. Practical guidelinesfor incorporating knowledge-based and data-driven strate-gies into the inference ofgene regulatory networks.IEEE/ACM Transactions onComputational Biology andBioinformatics, 13(1):64–75,January 2016. CODENITCBCY. ISSN 1545-5963(print), 1557-9964 (elec-tronic).

Hu:2017:PPD

[HLZ+17] Jun Hu, Yang Li, MingZhang, Xibei Yang, Hong-Bin Shen, and Dong-JunYu. Predicting protein-DNAbinding residues by weight-edly combining sequence-based features and boostingmultiple SVMs. IEEE/ACMTransactions on Computa-tional Biology and Bioin-formatics, 14(6):1389–1398,November 2017. CODENITCBCY. ISSN 1545-5963(print), 1557-9964 (elec-tronic).

Henzinger:2013:PAC

[HM13] Thomas A. Henzinger andMaria Mateescu. The propa-gation approach for comput-ing biochemical reaction net-works. IEEE/ACM Trans-actions on ComputationalBiology and Bioinformatics,10(2):310–322, March 2013.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Henriques:2015:BFP

[HM15] Rui Henriques and Sara C.Madeira. Biclustering withflexible plaid models tounravel interactions be-tween biological processes.IEEE/ACM Transactions onComputational Biology andBioinformatics, 12(4):738–752, July 2015. CODENITCBCY. ISSN 1545-5963(print), 1557-9964 (elec-tronic).

Huang:2007:PPP

[HMK+07] Chengbang Huang, FaruckMorcos, Simon P. Kanaan,Stefan Wuchty, Danny Z.Chen, and Jesus A. Iza-guirre. Predicting protein-protein interactions fromprotein domains using a setcover approach. IEEE/ACMTransactions on Computa-tional Biology and Bioinfor-matics, 4(1):78–87, January2007. CODEN ITCBCY.ISSN 1545-5963 (print),1557-9964 (electronic).

REFERENCES 171

Huson:2009:SSP

[HMS09] Daniel H. Huson, VincentMoulton, and Mike Steel.Special section: Phyloge-netics. IEEE/ACM Trans-actions on ComputationalBiology and Bioinformat-ics, 6(1):4–6, January 2009.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Hopfensitz:2012:MBG

[HMW+12] Martin Hopfensitz, ChristophMussel, Christian Wawra,Markus Maucher, MichaelKuhl, Heiko Neumann, andHans A. Kestler. Multi-scale binarization of geneexpression data for recon-structing Boolean networks.IEEE/ACM Transactions onComputational Biology andBioinformatics, 9(2):487–498, March 2012. CODENITCBCY. ISSN 1545-5963(print), 1557-9964 (elec-tronic).

Harrison:2017:GEI

[HMZ17] Robert W. Harrison, Ion I.Mandoiu, and Alexander Ze-likovsky. Guest editors’introduction to the spe-cial section on bioinformat-ics research and applica-tions. IEEE/ACM Trans-actions on ComputationalBiology and Bioinformatics,14(3):576–577, May 2017.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Handoko:2012:EQA

[HOS+12a] Stephanus Daniel Handoko,Xuchang Ouyang, ChinhTran To Su, Chee KeongKwoh, and Yew SoonOng. Erratum to “QuickV-ina: Accelerating AutoDockVina Using Gradient-BasedHeuristics for Global Op-timization”. IEEE/ACMTransactions on Computa-tional Biology and Bioinfor-matics, 9(6):1853, Novem-ber 2012. CODEN ITCBCY.ISSN 1545-5963 (print),1557-9964 (electronic).

Handoko:2012:QAA

[HOS+12b] Stephanus Daniel Handoko,Xuchang Ouyang, ChinhTran To Su, Chee KeongKwoh, and Yew SoonOng. QuickVina: Accel-erating AutoDock Vina us-ing gradient-based heuris-tics for global optimization.IEEE/ACM Transactionson Computational Biologyand Bioinformatics, 9(5):1266–1272, September 2012.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Howison:2013:HTC

[How13] Mark Howison. High-throughput compression ofFASTQ data with SeqDB.IEEE/ACM Transactions onComputational Biology andBioinformatics, 10(1):213–218, January 2013. CODENITCBCY. ISSN 1545-5963

REFERENCES 172


Hsu:2015:SBF

[HPH+15] Chih-Yuan Hsu, Zhen-MingPan, Rei-Hsing Hu, Chih-Chun Chang, Hsiao-ChunCheng, Che Lin, and Bor-Sen Chen. Systematic bio-logical filter design with a de-sired I/O filtering responsebased on promoter-RBS li-braries. IEEE/ACM Trans-actions on ComputationalBiology and Bioinformatics,12(3):712–725, May 2015.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Hossain:2013:IMS

[HPL+13] K. S. M. Tozammel Hos-sain, Debprakash Patnaik,Srivatsan Laxman, PrateekJain, Chris Bailey-Kellogg,and Naren Ramakrishnan.Improved multiple sequencealignments using coupledpattern mining. IEEE/ACMTransactions on Computa-tional Biology and Bioin-formatics, 10(5):1098–1112,September 2013. CODENITCBCY. ISSN 1545-5963(print), 1557-9964 (elec-tronic).

Hulsman:2009:EOK

[HRdR09] Marc Hulsman, Marcel J. T.Reinders, and Dick de Rid-der. Evolutionary opti-mization of kernel weightsimproves protein complex

comembership prediction.IEEE/ACM Transactions onComputational Biology andBioinformatics, 6(3):427–437, July 2009. CODENITCBCY. ISSN 1545-5963(print), 1557-9964 (elec-tronic).

He:2016:MMI

[HRHP16] Dan He, Irina Rish, DavidHaws, and Laxmi Parida.MINT: mutual informationbased transductive featureselection for genetic traitprediction. IEEE/ACMTransactions on Computa-tional Biology and Bioinfor-matics, 13(3):578–583, May2016. CODEN ITCBCY.ISSN 1545-5963 (print),1557-9964 (electronic).

Hendy:2008:HCK

[HS08] Michael D. Hendy and SagiSnir. Hadamard conjuga-tion for the Kimura 3STmodel: Combinatorial proofusing path sets. IEEE/ACMTransactions on Computa-tional Biology and Bioinfor-matics, 5(3):461–471, July2008. CODEN ITCBCY.ISSN 1545-5963 (print),1557-9964 (electronic).

Heath:2009:MNS

[HS09a] Lenwood S. Heath and Al-lan A. Sioson. Multimodalnetworks: Structure and op-erations. IEEE/ACM Trans-actions on ComputationalBiology and Bioinformatics,

REFERENCES 173

6(2):321–332, April 2009.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Heath:2009:SMN

[HS09b] Lenwood S. Heath and Al-lan A. Sioson. Semanticsof multimodal network mod-els. IEEE/ACM Transac-tions on Computational Bi-ology and Bioinformatics,6(2):271–280, April 2009.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Hoksza:2015:MRS

[HS15] David Hoksza and DanielSvozil. Multiple 3D RNAstructure superposition us-ing neighbor joining. IEEE/ACM Transactions on Com-putational Biology and Bioin-formatics, 12(3):520–530,May 2015. CODEN ITCBCY.ISSN 1545-5963 (print),1557-9964 (electronic).

Huber:2011:MMT

[HSlSM11] Katharina T. Huber, An-dreas Spillner, Rados lawSuchecki, and Vincent Moul-ton. Metrics on multil-abeled trees: Interrelation-ships and diameter bounds.IEEE/ACM Transactions onComputational Biology andBioinformatics, 8(4):1029–1040, July 2011. CODENITCBCY. ISSN 1545-5963(print), 1557-9964 (elec-tronic).

Handl:2018:AAD

[HSS18] J. Handl, A. Shehu, and JoseSantos Reyes. Advances inthe application and devel-opment of non-linear globaloptimization techniques incomputational structural bi-ology. IEEE/ACM Trans-actions on ComputationalBiology and Bioinformatics,15(3):688–689, May 2018.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Hershkovitz:2006:SAR

[HSTW06] Eli Hershkovitz, GuillermoSapiro, Allen Tannenbaum,and Loren Dean Williams.Statistical analysis of RNAbackbone. IEEE/ACMTransactions on Computa-tional Biology and Bioinfor-matics, 3(1):33–46, January2006. CODEN ITCBCY.ISSN 1545-5963 (print),1557-9964 (electronic).

Hong:2009:HRD

[HT09] Changjin Hong and Ahmed H.Tewfik. Heuristic reusabledynamic programming: Ef-ficient updates of local se-quence alignment. IEEE/ACM Transactions on Com-putational Biology and Bioin-formatics, 6(4):570–582, Oc-tober 2009. CODENITCBCY. ISSN 1545-5963(print), 1557-9964 (elec-tronic).

REFERENCES 174

Huang:2012:PEL

[HTLL12] Qinghua Huang, DachengTao, Xuelong Li, and AlanLiew. Parallelized evolution-ary learning for detection ofbiclusters in gene expressiondata. IEEE/ACM Trans-actions on ComputationalBiology and Bioinformatics,9(2):560–570, March 2012.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Huson:2009:DRP

[Hus09] Daniel H. Huson. Draw-ing rooted phylogenetic net-works. IEEE/ACM Transac-tions on Computational Bi-ology and Bioinformatics, 6(1):103–109, January 2009.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Halioui:2018:BWE

[HVD18] Ahmed Halioui, Petko Valtchev,and Abdoulaye Banire Di-allo. Bioinformatic workflowextraction from scientifictexts based on word sensedisambiguation. IEEE/ACMTransactions on Computa-tional Biology and Bioin-formatics, 15(6):1979–1990,November 2018. CODENITCBCY. ISSN 1545-5963(print), 1557-9964 (elec-tronic).

Hochsmann:2004:PMR

[HVG04] Matthias Hochsmann, BjornVoss, and Robert Giegerich.

Pure multiple RNA sec-ondary structure alignments:a progressive profile ap-proach. IEEE/ACM Trans-actions on ComputationalBiology and Bioinformatics,1(1):53–62, January 2004.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Huber:2011:PAR

[HvIKS11] Katharina T. Huber, Leo vanIersel, Steven Kelk, and Ra-dos law Suchecki. A practicalalgorithm for reconstruct-ing level-1 phylogenetic net-works. IEEE/ACM Trans-actions on ComputationalBiology and Bioinformat-ics, 8(3):635–649, May/June2011. CODEN ITCBCY.ISSN 1545-5963 (print),1557-9964 (electronic).

Hu:2007:DMP

[HW07] Xiaohua Hu and Daniel D.Wu. Data mining and pre-dictive modeling of biomolec-ular network from biomed-ical literature databases.IEEE/ACM Transactions onComputational Biology andBioinformatics, 4(2):251–263, April 2007. CODENITCBCY. ISSN 1545-5963(print), 1557-9964 (elec-tronic).

Humphries:2013:NT

[HW13] Peter J. Humphries andTaoyang Wu. On theneighborhoods of trees.

REFERENCES 175

IEEE/ACM Transactions onComputational Biology andBioinformatics, 10(3):721–728, May 2013. CODENITCBCY. ISSN 1545-5963(print), 1557-9964 (elec-tronic).

Hsiao:2014:GND

[HWK14] Jui-Chen Hsiao, Chih-HsuanWei, and Hung-Yu Kao.Gene name disambiguationusing multi-scope species de-tection. IEEE/ACM Trans-actions on ComputationalBiology and Bioinformatics,11(1):55–62, January 2014.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

He:2017:IIP

[HWPE17] Dan He, Zhanyong Wang,Laxmi Parida, and EleazarEskin. IPED2: Inher-itance path based pedi-gree reconstruction algo-rithm for complicated pedi-grees. IEEE/ACM Trans-actions on ComputationalBiology and Bioinformatics,14(5):1094–1103, September2017. CODEN ITCBCY.ISSN 1545-5963 (print),1557-9964 (electronic).

Hartmann:2018:GRI

[HWS+18] Tom Hartmann, NicolasWieseke, Roded Sharan,Martin Middendorf, andMatthias Bernt. Genomerearrangement with ILP.IEEE/ACM Transactions


Hashemikhabir:2018:FIG

[HXXJ18] Seyedsasan Hashemikhabir,Ran Xia, Yang Xiang,and Sarath Chandra Janga.A framework for identify-ing genotypic informationfrom clinical records: Ex-ploiting integrated ontol-ogy structures to transferannotations between ICDcodes and gene ontologies.IEEE/ACM Transactions onComputational Biology andBioinformatics, 15(4):1259–1269, July 2018. CODENITCBCY. ISSN 1545-5963(print), 1557-9964 (elec-tronic).

Hennings-Yeomans:2012:IPC

[HYC12] Pablo H. Hennings-Yeomansand Gregory F. Cooper. Im-proving the prediction ofclinical outcomes from ge-nomic data using multireso-lution analysis. IEEE/ACMTransactions on Computa-tional Biology and Bioin-formatics, 9(5):1442–1450,September 2012. CODENITCBCY. ISSN 1545-5963(print), 1557-9964 (elec-tronic).

Hu:2019:EDP

[HYL+19] Lun Hu, Xiaohui Yuan, Xing

REFERENCES 176

Liu, Shengwu Xiong, andXin Luo. Efficiently de-tecting protein complexesfrom protein interaction net-works via alternating direc-tion method of multipliers.IEEE/ACM Transactionson Computational Biologyand Bioinformatics, 16(6):1922–1935, November 2019.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic). URL https://dl.acm.org/doi/abs/10.1109/TCBB.2018.2844256.

He:2020:IAC

[HYL+20] Zaobo He, Jiguo Yu, Ji Li,Qilong Han, GuangchunLuo, and Yingshu Li. In-ference attacks and controlson genotypes and pheno-types for individual genomicdata. IEEE/ACM Trans-actions on ComputationalBiology and Bioinformatics,17(3):930–937, May 2020.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic). URL https://dl.acm.org/doi/10.1109/TCBB.2018.2810180.

Hao:2019:ICG

[HYR+19] Xiaoke Hao, Xiaohui Yao,Shannon L. Risacher, An-drew J. Saykin, JintaiYu, Huifu Wang, LanTan, Li Shen, and Dao-qiang Zhang. Identifyingcandidate genetic associa-tions with MRI-derived AD-related ROI via tree-guidedsparse learning. IEEE/ACM

Transactions on Computa-tional Biology and Bioin-formatics, 16(6):1986–1996,November 2019. CODENITCBCY. ISSN 1545-5963(print), 1557-9964 (elec-tronic). URL https://dl.acm.org/doi/abs/10.1109/TCBB.2018.2833487.

Hsieh:2008:OAI

[HYW08] Yong-Hsiang Hsieh, Chih-Chiang Yu, and Biing-FengWang. Optimal algorithmsfor the interval locationproblem with range con-straints on length and av-erage. IEEE/ACM Trans-actions on ComputationalBiology and Bioinformatics,5(2):281–290, April 2008.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Han:2017:GSM

[HYW+17] Fei Han, Chun Yang, Ya-QiWu, Jian-Sheng Zhu, Qing-Hua Ling, Yu-Qing Song,and De-Shuang Huang. Agene selection method for mi-croarray data based on bi-nary PSO encoding gene-to-class sensitivity informa-tion. IEEE/ACM Trans-actions on ComputationalBiology and Bioinformatics,14(1):85–96, January 2017.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

REFERENCES 177

He:2011:PSC

[HYY11] Zengyou He, Can Yang,and Weichuan Yu. A par-tial set covering model forprotein mixture identifica-tion using mass spectrome-try data. IEEE/ACM Trans-actions on ComputationalBiology and Bioinformatics,8(2):368–380, March 2011.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Hua:2016:GSM

[HYZ16] Keru Hua, Qin Yu, andRuiming Zhang. A guaran-teed similarity metric learn-ing framework for biolog-ical sequence comparison.IEEE/ACM Transactionson Computational Biologyand Bioinformatics, 13(5):868–877, September 2016.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Hao:2019:ASS

[HZL19] FanChang Hao, MelvinZhang, and Hon Wai Leong.A 2-approximation schemefor sorting signed per-mutations by reversals,transpositions, transrever-sals, and block-interchanges.IEEE/ACM Transactionson Computational Biologyand Bioinformatics, 16(5):1702–1711, September 2019.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

He:2020:PCI

[HZL+20] Zengyou He, Can Zhao, HaoLiang, Bo Xu, and QuanZou. Protein complexesidentification with family-wise error rate control.IEEE/ACM Transactionson Computational Biologyand Bioinformatics, 17(6):2062–2073, November 2020.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic). URL https://dl.acm.org/doi/10.1109/TCBB.2019.2912602.

Haack:2019:CDS

[HZR+19] Jordan Haack, Eli Zupke,Andrew Ramirez, Yi-ChiehWu, and Ran Libeskind-Hadas. Computing the diam-eter of the space of maximumparsimony reconciliations inthe duplication–transfer–lossmodel. IEEE/ACM Trans-actions on ComputationalBiology and Bioinformatics,16(1):14–22, January 2019.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Hawkins:2012:RFP

[HZTP12] John C. Hawkins, HongboZhu, Joan Teyra, andM. Teresa Pisabarro. Re-duced false positives inPDZ binding prediction us-ing sequence and structuraldescriptors. IEEE/ACMTransactions on Computa-tional Biology and Bioin-formatics, 9(5):1492–1503,

REFERENCES 178

September 2012. CODENITCBCY. ISSN 1545-5963(print), 1557-9964 (elec-tronic).

He:2017:PNA

[HZW+17] Feng He, Guanghui Zhu,Yin-Ying Wang, Xing-MingZhao, and De-Shuang Huang.PCID: a novel approach forpredicting disease comorbid-ity by integrating multi-scaledata. IEEE/ACM Trans-actions on ComputationalBiology and Bioinformatics,14(3):678–686, May 2017.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Hu:2014:PRA

[HZZT14] Fei Hu, Jun Zhou, LingxiZhou, and Jijun Tang. Prob-abilistic reconstruction ofancestral gene orders withinsertions and deletions.IEEE/ACM Transactions onComputational Biology andBioinformatics, 11(4):667–672, July 2014. CODENITCBCY. ISSN 1545-5963(print), 1557-9964 (elec-tronic).

Hao:2016:NMU

[HZZY16] Xiao-Hu Hao, Gui-JunZhang, Xiao-Gen Zhou, andXu-Feng Yu. A novel methodusing abstract convex un-derestimation in ab-initioprotein structure predictionfor guiding search in con-formational feature space.


Azuma:2016:PAC

[iAOSS16] Shun ichi Azuma, KatsuyaOwaki, Nobuhiro Shinohara,and Toshiharu Sugie. Per-formance analysis of chemo-taxis controllers: Whichhas better chemotaxis con-troller, Escherichia colior Paramecium caudatum?IEEE/ACM Transactionson Computational Biologyand Bioinformatics, 13(4):730–741, 2016. CODENITCBCY. ISSN 1545-5963(print), 1557-9964 (elec-tronic).

Imani:2019:CGR

[IBN19] Mahdi Imani and Ulisses M.Braga-Neto. Control of generegulatory networks usingBayesian inverse reinforce-ment learning. IEEE/ACMTransactions on Computa-tional Biology and Bioin-formatics, 16(4):1250–1261,July 2019. CODEN ITCBCY.ISSN 1545-5963 (print),1557-9964 (electronic).

Irurozki:2011:PPH

[ICL11] Ekhine Irurozki, Borja Calvo,and Jose A. Lozano. Apreprocessing procedure forhaplotype inference by pure

REFERENCES 179

parsimony. IEEE/ACMTransactions on Computa-tional Biology and Bioin-formatics, 8(5):1183–1195,September 2011. CODENITCBCY. ISSN 1545-5963(print), 1557-9964 (elec-tronic).

Ivanov:2013:QPP

[IDD13] Stefan Ivanov, Ivan Dim-itrov, and Irina Doytchinova.Quantitative prediction ofpeptide binding to HLA-DP1protein. IEEE/ACM Trans-actions on ComputationalBiology and Bioinformatics,10(3):811–815, May 2013.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Staff:2005:RL

[IEE05] IEEE and ACM Trans-actions on ComputationalBiology and Bioinformat-ics staff. 2004 reviewerslist. IEEE/ACM Trans-actions on ComputationalBiology and Bioinformat-ics, 2(1):77, January 2005.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Staff:2007:RL

[IEE07] IEEE and ACM Trans-actions on ComputationalBiology and Bioinformat-ics staff. 2006 reviewerslist. IEEE/ACM Transac-tions on Computational Bi-ology and Bioinformatics, 4

(1):158–160, January 2007.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Iglesias:2018:IAF

[IGA18] Andres Iglesias, AkemiGalvez, and Andreina Avila.Immunological approach forfull NURBS reconstructionof outline curves from noisydata points in medical imag-ing. IEEE/ACM Transac-tions on Computational Bi-ology and Bioinformatics,15(6):1929–1942, November2018. CODEN ITCBCY.ISSN 1545-5963 (print),1557-9964 (electronic).

Igel:2007:GBO

[IGM+07] Christian Igel, Tobias Glas-machers, Britta Mersch,Nico Pfeifer, and PeterMeinicke. Gradient-basedoptimization of kernel-targetalignment for sequence ker-nels applied to bacterial genestart detection. IEEE/ACMTransactions on Computa-tional Biology and Bioinfor-matics, 4(2):216–226, April2007. CODEN ITCBCY.ISSN 1545-5963 (print),1557-9964 (electronic).

Ironi:2018:MBT

[IL18] Liliana Ironi and Ettore Lan-zarone. A model-based toolfor the analysis and de-sign of gene regulatory net-works. IEEE/ACM Transac-tions on Computational Bi-

REFERENCES 180


Ichikawa:2014:SPH

[IM14] Kazuki Ichikawa and ShinichiMorishita. A simple butpowerful heuristic methodfor accelerating k-meansclustering of large-scale datain life science. IEEE/ACMTransactions on Computa-tional Biology and Bioinfor-matics, 11(4):681–692, July2014. CODEN ITCBCY.ISSN 1545-5963 (print),1557-9964 (electronic).

Irigoien:2013:DPI

[IMA13] Itziar Irigoien, FrancescMestres, and ConcepcionArenas. The depth prob-lem: Identifying the mostrepresentative units in a datagroup. IEEE/ACM Transac-tions on Computational Bi-ology and Bioinformatics, 10(1):161–172, January 2013.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Ibrahim:2011:UQP

[INT11] Zina Ibrahim, Alioune Ngom,and Ahmed Y. Tawfik. Us-ing qualitative probabil-ity in reverse-engineeringgene regulatory networks.IEEE/ACM Transactions onComputational Biology andBioinformatics, 8(2):326–

334, March 2011. CODENITCBCY. ISSN 1545-5963(print), 1557-9964 (elec-tronic).

Ikram:2018:ICB

[IQA18] Najmul Ikram, Muham-mad Abdul Qadir, andMuhammad Tanvir Afzal.Investigating correlation be-tween protein sequence sim-ilarity and semantic similar-ity using gene ontology anno-tations. IEEE/ACM Trans-actions on ComputationalBiology and Bioinformatics,15(3):905–912, May 2018.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Ismail:2018:RNR

[ISK18] Hamid D. Ismail, HirotoSaigo, and Dukka B. KC.RF-NR: Random forestbased approach for improvedclassification of nuclear re-ceptors. IEEE/ACM Trans-actions on ComputationalBiology and Bioinformatics,15(6):1844–1852, November2018. CODEN ITCBCY.ISSN 1545-5963 (print),1557-9964 (electronic).

Irigoien:2011:MTC

[IVA11] Itziar Irigoien, Sergi Vives,and Concepcion Arenas. Mi-croarray time course ex-periments: Finding pro-files. IEEE/ACM Transac-tions on Computational Bi-ology and Bioinformatics, 8

REFERENCES 181

(2):464–475, March 2011.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Irsoy:2012:DAC

[IYA12] Ozan Irsoy, Olcay TanerYildiz, and Ethem Alpaydin.Design and analysis of clas-sifier learning experiments inbioinformatics: Survey andcase studies. IEEE/ACMTransactions on Computa-tional Biology and Bioin-formatics, 9(6):1663–1675,November 2012. CODENITCBCY. ISSN 1545-5963(print), 1557-9964 (elec-tronic).

Jamil:2013:DIC

[Jam13] Hasan M. Jamil. De-signing integrated computa-tional biology pipelines vi-sually. IEEE/ACM Trans-actions on ComputationalBiology and Bioinformatics,10(3):605–618, May 2013.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Jamil:2015:IIE

[Jam15] Hasan M. Jamil. Im-proving integration effective-ness of ID mapping basedbiological record linkage.IEEE/ACM Transactions onComputational Biology andBioinformatics, 12(2):473–486, March 2015. CODENITCBCY. ISSN 1545-5963


Jamil:2017:VIQ

[Jam17] Hasan M. Jamil. A vi-sual interface for query-ing heterogeneous phyloge-netic databases. IEEE/ACMTransactions on Computa-tional Biology and Bioin-formatics, 14(1):131–144,January 2017. CODENITCBCY. ISSN 1545-5963(print), 1557-9964 (elec-tronic).

Jamil:2018:OPQ

[Jam18] Hasan M. Jamil. Optimiz-ing phylogenetic queries forperformance. IEEE/ACMTransactions on Computa-tional Biology and Bioin-formatics, 15(5):1692–1705,September 2018. CODENITCBCY. ISSN 1545-5963(print), 1557-9964 (elec-tronic).

Jhee:2019:CSC

[JBgLS19] Jong Ho Jhee, Sunjoo Bang,Dong gi Lee, and HyunjungShin. Comorbidity scoringwith causal disease networks.IEEE/ACM Transactionson Computational Biologyand Bioinformatics, 16(5):1627–1634, September 2019.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

REFERENCES 182

Jeong:2008:ISP

[JBP08] Jieun Jeong, Piotr Berman,and Teresa M. Przyty-cka. Improving strand pair-ing prediction through ex-ploring folding cooperativ-ity. IEEE/ACM Transac-tions on Computational Bi-ology and Bioinformatics, 5(4):484–491, October 2008.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Jeong:2015:NSF

[JC15] Jong Cheol Jeong andXuewen Chen. A newsemantic functional simi-larity over gene ontology.IEEE/ACM Transactions onComputational Biology andBioinformatics, 12(2):322–334, March 2015. CODENITCBCY. ISSN 1545-5963(print), 1557-9964 (elec-tronic).

Jaskowiak:2013:PMC

[JCF13] Pablo A. Jaskowiak, RicardoJ. G. B. Campello, and IvanG. Costa Filho. Proxim-ity measures for clusteringgene expression microarraydata: a validation methodol-ogy and a comparative anal-ysis. IEEE/ACM Transac-tions on Computational Bi-ology and Bioinformatics,10(4):845–857, July 2013.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Jacklin:2012:NCO

[JDCC12] Neil Jacklin, Zhi Ding, WeiChen, and Chunqi Chang.Noniterative convex opti-mization methods for net-work component analysis.IEEE/ACM Transactionson Computational Biologyand Bioinformatics, 9(5):1472–1481, September 2012.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Jing:2020:AAE

[JDHL20] Xiaoyang Jing, Qiwen Dong,Daocheng Hong, and RuqianLu. Amino acid encod-ing methods for proteinsequences: a comprehen-sive review and assessment.IEEE/ACM Transactionson Computational Biologyand Bioinformatics, 17(6):1918–1931, November 2020.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic). URL https://dl.acm.org/doi/10.1109/TCBB.2019.2911677.

John:2011:CCP

[JFN11] David J. John, Jacquelyn S.Fetrow, and James L. Nor-ris. Continuous cotemporalprobabilistic modeling of sys-tems biology networks fromsparse data. IEEE/ACMTransactions on Computa-tional Biology and Bioin-formatics, 8(5):1208–1222,September 2011. CODENITCBCY. ISSN 1545-5963

REFERENCES 183


Jahanshad:2019:MSM

[JFR+19] Neda Jahanshad, JoshuaFaskowitz, Gennady Roshchup-kin, Derrek P. Hibar, Boris A.Gutman, Nicholas J. Tusti-son, Hieab H. H. Adams,Wiro J. Niessen, Meike W.Vernooij, M. Arfan Ikram,Marcel P. Zwiers, Alejan-dro Arias Vasquez, BarbaraFranke, Jennifer L. Kroll,Benson Mwangi, Jair C.Soares, Alex Ing, SylvaneDesrivieres, Gunter Schu-mann, Narelle K. Hansell,Greig I. de Zubicaray,Katie L. McMahon, Nicholas G.Martin, Margaret J. Wright,and Paul M. Thompson.Multi-site meta-analysis ofmorphometry. IEEE/ACMTransactions on Computa-tional Biology and Bioin-formatics, 16(5):1508–1514,September 2019. CODENITCBCY. ISSN 1545-5963(print), 1557-9964 (elec-tronic).

Jeannin-Girardon:2015:LST

[JGBR15] Anne Jeannin-Girardon, Pas-cal Ballet, and VincentRodin. Large scale tissuemorphogenesis simulation onheterogeneous systems basedon a flexible biomechani-cal cell model. IEEE/ACMTransactions on Computa-tional Biology and Bioin-formatics, 12(5):1021–1033,


Jiang:2019:SSL

[JHW+19] Yichen Jiang, Jenny Hamer,Chenghong Wang, XiaoqianJiang, Miran Kim, YongsooSong, Yuhou Xia, NomanMohammed, Md Nazmus Sa-dat, and Shuang Wang. Se-cureLR: Secure logistic re-gression model via a hy-brid cryptographic proto-col. IEEE/ACM Transac-tions on Computational Bi-ology and Bioinformatics, 16(1):113–123, January 2019.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Jiang:2017:MDR

[JHX17] Xingpeng Jiang, XiaohuaHu, and Weiwei Xu. Mi-crobiome data represen-tation by joint nonnega-tive matrix factorizationwith Laplacian regulariza-tion. IEEE/ACM Trans-actions on ComputationalBiology and Bioinformatics,14(2):353–359, March 2017.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Jiang:2015:PMI

[JHXP15] Xingpeng Jiang, XiaohuaHu, Weiwei Xu, and E. K.Park. Predicting micro-bial interactions using vec-

REFERENCES 184

tor autoregressive modelwith graph regularization.IEEE/ACM Transactions onComputational Biology andBioinformatics, 12(2):254–261, March 2015. CODENITCBCY. ISSN 1545-5963(print), 1557-9964 (elec-tronic).

Ju:2019:EDA

[JHZL19] Ronghui Ju, Chenhui Hu,Pan Zhou, and QuanzhengLi. Early diagnosis ofAlzheimer’s disease basedon resting-state brain net-works and deep learning.IEEE/ACM Transactions onComputational Biology andBioinformatics, 16(1):244–257, January 2019. CODENITCBCY. ISSN 1545-5963(print), 1557-9964 (elec-tronic).

Jiang:2010:AAP

[Jia10] Minghui Jiang. Approxima-tion algorithms for predict-ing RNA secondary struc-tures with arbitrary pseudo-knots. IEEE/ACM Trans-actions on ComputationalBiology and Bioinformatics,7(2):323–332, April 2010.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Jang:2012:CMP

[JJH12] Woo-Hyuk Jang, Suk-HoonJung, and Dong-Soo Han.A computational model forpredicting protein interac-

tions based on multidomaincollaboration. IEEE/ACMTransactions on Computa-tional Biology and Bioinfor-matics, 9(4):1081–1090, July2012. CODEN ITCBCY.ISSN 1545-5963 (print),1557-9964 (electronic).

Joseph:2012:CPT

[JKN+12] Shaini Joseph, ShreyasKarnik, Pravin Nilawe,V. K. Jayaraman, and Su-san Idicula-Thomas. Clas-sAMP: a prediction tool forclassification of antimicro-bial peptides. IEEE/ACMTransactions on Computa-tional Biology and Bioin-formatics, 9(5):1535–1538,September 2012. CODENITCBCY. ISSN 1545-5963(print), 1557-9964 (elec-tronic).

Jackups:2010:CAS

[JL10] Ronald Jackups, Jr. andJie Liang. Combinato-rial analysis for sequenceand spatial motif discov-ery in short sequence frag-ments. IEEE/ACM Trans-actions on ComputationalBiology and Bioinformat-ics, 7(3):524–536, July 2010.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Jiang:2016:UGB

[JLH16] Zhenchao Jiang, LishuangLi, and Degen Huang. Anunsupervised graph based

REFERENCES 185

continuous word representa-tion method for biomedicaltext mining. IEEE/ACMTransactions on Computa-tional Biology and Bioinfor-matics, 13(4):634–642, 2016.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Ji:2017:CIF

[JLW17] Hao Ji, Yaohang Li, andSeth H. Weinberg. Calciumion fluctuations alter chan-nel gating in a stochasticluminal calcium release sitemodel. IEEE/ACM Trans-actions on ComputationalBiology and Bioinformatics,14(3):611–619, May 2017.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Jeong:2011:PSS

[JLwC11] Jong Cheol Jeong, XiaotongLin, and Xue wen Chen. Onposition-specific scoring ma-trix for protein function pre-diction. IEEE/ACM Trans-actions on ComputationalBiology and Bioinformatics,8(2):308–315, March 2011.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Ji:2016:DFM

[JLYZ16] Junzhong Ji, Jiawei Luo,Cuicui Yang, and AidongZhang. Detecting functionalmodules based on a multiple-grain model in large-scale

protein-protein interactionnetworks. IEEE/ACMTransactions on Computa-tional Biology and Bioinfor-matics, 13(4):610–622, 2016.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Jiang:2012:PPF

[JM12] Jonathan Q. Jiang andLisa J. McQuay. Pre-dicting protein functionby multi-label correlatedsemi-supervised learning.IEEE/ACM Transactions onComputational Biology andBioinformatics, 9(4):1059–1069, July 2012. CODENITCBCY. ISSN 1545-5963(print), 1557-9964 (elec-tronic).

Jha:2017:GLB

[JMA17] Manjari Jha, Raunaq Malho-tra, and Raj Acharya. A gen-eralized lattice based proba-bilistic approach for metage-nomic clustering. IEEE/ACM Transactions on Com-putational Biology and Bioin-formatics, 14(4):749–761,July 2017. CODEN ITCBCY.ISSN 1545-5963 (print),1557-9964 (electronic).

Jin:2009:PSP

[JNST09] Guohua Jin, Luay Nakhleh,Sagi Snir, and Tamir Tuller.Parsimony score of phy-logenetic networks: Hard-ness results and a linear-time heuristic. IEEE/ACM

REFERENCES 186

Transactions on Computa-tional Biology and Bioinfor-matics, 6(3):495–505, July2009. CODEN ITCBCY.ISSN 1545-5963 (print),1557-9964 (electronic).

Jiang:2020:DSE

[JQH+20] Hao Jiang, Yushan Qiu,Wenpin Hou, XiaoqingCheng, Man Yi Yim, andWai-Ki Ching. Drugside-effect profiles predic-tion: From empirical tostructural risk minimiza-tion. IEEE/ACM Trans-actions on ComputationalBiology and Bioinformatics,17(2):402–410, March 2020.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic). URL https://dl.acm.org/doi/abs/10.1109/TCBB.2018.2850884.

Jauhari:2014:MGE

[JR14] Shaurya Jauhari and S. A. M.Rizvi. Mining gene ex-pression data focusing can-cer therapeutics: a digest.IEEE/ACM Transactions onComputational Biology andBioinformatics, 11(3):533–547, May 2014. CODENITCBCY. ISSN 1545-5963(print), 1557-9964 (elec-tronic).

Jiang:2018:BET

[JRN+18] Nan Jiang, Wenge Rong,Yifan Nie, Yikang Shen,and Zhang Xiong. Biolog-ical event trigger identifica-

tion with noise contrastiveestimation. IEEE/ACMTransactions on Computa-tional Biology and Bioin-formatics, 15(5):1549–1559,September 2018. CODENITCBCY. ISSN 1545-5963(print), 1557-9964 (elec-tronic).

Jansson:2018:AMR

[JRSS18] Jesper Jansson, Ramesh Ra-jaby, Chuanqi Shen, andWing-Kin Sung. Algorithmsfor the majority rule + con-sensus tree and the fre-quency difference consensustree. IEEE/ACM Trans-actions on ComputationalBiology and Bioinformatics,15(1):15–26, January 2018.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Jarvis:2012:MIP

[JS12] Peter Jarvis and JeremySumner. Markov invariantsfor phylogenetic rate ma-trices derived from embed-ded submodels. IEEE/ACMTransactions on Computa-tional Biology and Bioinfor-matics, 9(3):828–836, May2012. CODEN ITCBCY.ISSN 1545-5963 (print),1557-9964 (electronic).

Jackson:2008:CGM

[JSA08] Benjamin N. Jackson, Patrick S.Schnable, and Srinivas Aluru.Consensus genetic maps asmedian orders from incon-

REFERENCES 187

sistent sources. IEEE/ACMTransactions on Computa-tional Biology and Bioinfor-matics, 5(2):161–171, April2008. CODEN ITCBCY.ISSN 1545-5963 (print),1557-9964 (electronic).

Jiao:2018:FDA

[JSS+18] Hongmei Jiao, Michael Shi,Qikun Shen, Junwu Zhu,and Peng Shi. Filter de-sign with adaptation to time-delay parameters for ge-netic regulatory networks.IEEE/ACM Transactions onComputational Biology andBioinformatics, 15(1):323–329, January 2018. CODENITCBCY. ISSN 1545-5963(print), 1557-9964 (elec-tronic).

Jetten:2018:NTB

[JvI18] Laura Jetten and Leo vanIersel. Nonbinary tree-based phylogenetic networks.IEEE/ACM Transactions onComputational Biology andBioinformatics, 15(1):205–217, January 2018. CODENITCBCY. ISSN 1545-5963(print), 1557-9964 (elec-tronic).

Jia:2020:PIM

[JWZ+20] Huiqiang Jia, Haichao Wei,Daming Zhu, Jingjing Ma,Hai Yang, Ruizhi Wang, andXianzhong Feng. PASA:Identifying more crediblestructural variants of He-dou12. IEEE/ACM Trans-

actions on ComputationalBiology and Bioinformatics,17(5):1493–1503, September2020. CODEN ITCBCY.ISSN 1545-5963 (print),1557-9964 (electronic). URLhttps://dl.acm.org/doi/10.1109/TCBB.2019.2934463.

Jian:2016:MKF

[JXN+16] Ling Jian, Zhonghang Xia,Xinnan Niu, Xijun Liang,Parimal Samir, and An-drew J. Link. `2 multiplekernel fuzzy SVM-based datafusion for improving peptideidentification. IEEE/ACMTransactions on Computa-tional Biology and Bioinfor-matics, 13(4):804–809, 2016.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Janga:2015:KDU

[JZCZ15] Sarath Chandra Janga,Dongxiao Zhu, Jake Y.Chen, and Mohammed J.Zaki. Knowledge discoveryusing big data in biomedicalsystems. IEEE/ACM Trans-actions on ComputationalBiology and Bioinformatics,12(4):726–728, July 2015.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Ji:2013:PLS

[JZL13] Shuiwang Ji, Wenlu Zhang,and Rongjian Li. A proba-bilistic latent semantic anal-ysis model for cocluster-

REFERENCES 188

ing the mouse brain atlas.IEEE/ACM Transactionson Computational Biologyand Bioinformatics, 10(6):1460–1468, November 2013.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Jiao:2018:RGC

[JZS+18] Hongmei Jiao, Liping Zhang,Qikun Shen, Junwu Zhu, andPeng Shi. Robust gene cir-cuit control design for time-delayed genetic regulatorynetworks without SUM reg-ulatory logic. IEEE/ACMTransactions on Computa-tional Biology and Bioin-formatics, 15(6):2086–2093,November 2018. CODENITCBCY. ISSN 1545-5963(print), 1557-9964 (elec-tronic).

Jiang:2012:SFU

[JZSZ12] Haitao Jiang, ChunfangZheng, David Sankoff, andBinhai Zhu. Scaffold fillingunder the breakpoint and re-lated distances. IEEE/ACMTransactions on Computa-tional Biology and Bioinfor-matics, 9(4):1220–1229, July2012. CODEN ITCBCY.ISSN 1545-5963 (print),1557-9964 (electronic).

Ju:2017:EAC

[JZW17] Chelsea J. T. Ju, Zhuang-tian Zhao, and Wei Wang.Efficient approach to correctread alignment for pseudo-

gene abundance estimates.IEEE/ACM Transactions onComputational Biology andBioinformatics, 14(3):522–533, May 2017. CODENITCBCY. ISSN 1545-5963(print), 1557-9964 (elec-tronic).

Jiang:2019:FNN

[JZZQ19] Xue Jiang, Han Zhang, ZhaoZhang, and Xiongwen Quan.Flexible non-negative ma-trix factorization to un-ravel disease-related genes.IEEE/ACM Transactionson Computational Biologyand Bioinformatics, 16(6):1948–1957, November 2019.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic). URL https://dl.acm.org/doi/abs/10.1109/TCBB.2018.2823746.

Kolchinsky:2010:CPP

[KAHK+10] Artemy Kolchinsky, AlaaAbi-Haidar, Jasleen Kaur,Ahmed Abdeen Hamed, andLuis M. Rocha. Classifica-tion of protein-protein in-teraction full-text documentsusing text and citation net-work features. IEEE/ACMTransactions on Computa-tional Biology and Bioinfor-matics, 7(3):400–411, July2010. CODEN ITCBCY.ISSN 1545-5963 (print),1557-9964 (electronic).

Keller:2017:ISL

[KAL+17] Anne Florence Keller, Nico-

REFERENCES 189

las Ambert, Arnaud Legen-dre, Mathieu Bedez, Jean-Marie Bouteiller, SergeBischoff, Michel Baudry,and Saliha Moussaoui. Im-pact of synaptic localizationand subunit composition ofionotropic glutamate recep-tors on synaptic function:Modeling and simulationstudies. IEEE/ACM Trans-actions on ComputationalBiology and Bioinformatics,14(4):892–904, July 2017.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Kountouris:2012:CSF

[KAP+12] Petros Kountouris, MichalisAgathocleous, Vasilis J.Promponas, Georgia Christ-odoulou, Simos Hadjicostas,Vassilis Vassiliades, andChris Christodoulou. Acomparative study on filter-ing protein secondary struc-ture prediction. IEEE/ACMTransactions on Computa-tional Biology and Bioinfor-matics, 9(3):731–739, May2012. CODEN ITCBCY.ISSN 1545-5963 (print),1557-9964 (electronic).

Karacali:2012:HMV

[Kar12a] Bilge Karacali. Hierarchi-cal motif vectors for predic-tion of functional sites inamino acid sequences usingquasi-supervised learning.IEEE/ACM Transactionson Computational Biology


Karafyllidis:2012:QGC

[Kar12b] Ioannis G. Karafyllidis.Quantum gate circuit modelof signal integration inbacterial quorum sensing.IEEE/ACM Transactions onComputational Biology andBioinformatics, 9(2):571–579, March 2012. CODENITCBCY. ISSN 1545-5963(print), 1557-9964 (elec-tronic).

Kordi:2017:CDT

[KB17] Misagh Kordi and Mukul S.Bansal. On the complexity ofduplication-transfer-loss rec-onciliation with non-binarygene trees. IEEE/ACMTransactions on Computa-tional Biology and Bioinfor-matics, 14(3):587–599, May2017. CODEN ITCBCY.ISSN 1545-5963 (print),1557-9964 (electronic).

Kordi:2019:EAD

[KB19] Misagh Kordi and Mukul S.Bansal. Exact algorithms forduplication-transfer-loss rec-onciliation with non-binarygene trees. IEEE/ACMTransactions on Computa-tional Biology and Bioin-formatics, 16(4):1077–1090,July 2019. CODEN ITCBCY.

REFERENCES 190


Karimnezhad:2020:IPK

[KB20] Ali Karimnezhad and David R.Bickel. Incorporating priorknowledge about geneticvariants into the analy-sis of genetic associationdata: an empirical Bayes ap-proach. IEEE/ACM Trans-actions on ComputationalBiology and Bioinformatics,17(2):635–646, March 2020.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic). URL https://dl.acm.org/doi/abs/10.1109/TCBB.2018.2865420.

Kifer:2017:OAD

[KBBD+17] Ilona Kifer, Rui M. Branca,Amir Ben-Dor, Linhui Zhai,Ping Xu, Janne Lehtio, andZohar Yakhini. Optimizinganalytical depth and cost ef-ficiency of IEF-LC/MS pro-teomics. IEEE/ACM Trans-actions on ComputationalBiology and Bioinformatics,14(2):272–281, March 2017.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Karbalayghareh:2019:CSC

[KBND19] Alireza Karbalayghareh, UlissesBraga-Neto, and Edward R.Dougherty. Classificationof single-cell gene expres-sion trajectories from in-complete and noisy data.IEEE/ACM Transactions on

Computational Biology andBioinformatics, 16(1):193–207, January 2019. CODENITCBCY. ISSN 1545-5963(print), 1557-9964 (elec-tronic).

Karbalayghareh:2018:CST

[KBNHD18] Alireza Karbalayghareh, UlissesBraga-Neto, Jianping Hua,and Edward Russell Dough-erty. Classification of statetrajectories in gene regula-tory networks. IEEE/ACMTransactions on Computa-tional Biology and Bioinfor-matics, 15(1):68–82, January2018. CODEN ITCBCY.ISSN 1545-5963 (print),1557-9964 (electronic).

Kuruppu:2012:IDC

[KBSCZ12] Shanika Kuruppu, BryanBeresford-Smith, ThomasConway, and Justin Zo-bel. Iterative dictionaryconstruction for compres-sion of large DNA datasets. IEEE/ACM Transac-tions on Computational Bi-ology and Bioinformatics, 9(1):137–149, January 2012.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Kim:2011:PMS

[KC11] Jong Kyoung Kim and Se-ungjin Choi. Probabilis-tic models for semisuper-vised discriminative motifdiscovery in DNA sequences.IEEE/ACM Transactions

REFERENCES 191


Kim:2015:IGN

[KCCC15] Jeong-Rae Kim, Sang-MokChoo, Hyung-Seok Choi, andKwang-Hyun Cho. Iden-tification of gene networkswith time delayed regulationbased on temporal expres-sion profiles. IEEE/ACMTransactions on Computa-tional Biology and Bioin-formatics, 12(5):1161–1168,September 2015. CODENITCBCY. ISSN 1545-5963(print), 1557-9964 (elec-tronic).

Kamath:2012:EAA

[KCD+12] Uday Kamath, Jack Comp-ton, Rezarta Islamaj Do-gan, Kenneth De Jong, andAmarda Shehu. An evolu-tionary algorithm approachfor feature generation fromsequence data and its ap-plication to DNA splice siteprediction. IEEE/ACMTransactions on Computa-tional Biology and Bioin-formatics, 9(5):1387–1398,September 2012. CODENITCBCY. ISSN 1545-5963(print), 1557-9964 (elec-tronic).

Kim:2018:GNA

[KCP18] Hyunjin Kim, Sang-Min

Choi, and Sanghyun Park.GSEH: a novel approachto select prostate cancer-associated genes using geneexpression heterogeneity.IEEE/ACM Transactions onComputational Biology andBioinformatics, 15(1):129–146, January 2018. CODENITCBCY. ISSN 1545-5963(print), 1557-9964 (elec-tronic).

K:2019:PDL

[KCP19] MD Aksam V. K., V. M.Chandrasekaran, and Sun-daramurthy Pandurangan.Protein domain level can-cer drug targets in the net-work of MAPK pathways.IEEE/ACM Transactionson Computational Biologyand Bioinformatics, 16(6):2057–2065, November 2019.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic). URL https://dl.acm.org/doi/abs/10.1109/TCBB.2018.2829507.

Kang:2015:ISO

[KCZ+15] Hao Kang, Kwang-HyunCho, Xiaohua Douglas Zhang,Tao Zeng, and Luonan Chen.Inferring sequential order ofsomatic mutations during tu-morgenesis based on Markovchain model. IEEE/ACMTransactions on Computa-tional Biology and Bioin-formatics, 12(5):1094–1103,September 2015. CODENITCBCY. ISSN 1545-5963

REFERENCES 192


Koneru:2015:DCA

[KD15] Suvarna Vani Koneru andBhavani S. Durga. Divideand conquer approach tocontact map overlap prob-lem using 2D-pattern min-ing of protein contact net-works. IEEE/ACM Trans-actions on ComputationalBiology and Bioinformatics,12(4):729–737, July 2015.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Knox:2016:MFG

[KD16] David A. Knox and Robin D.Dowell. A modeling frame-work for generation of posi-tional and temporal simula-tions of transcriptional regu-lation. IEEE/ACM Trans-actions on ComputationalBiology and Bioinformatics,13(3):459–471, May 2016.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Kapoor:2020:GMM

[KDS+20] Rajan Kapoor, AniruddhaDatta, Chao Sima, Jian-ping Hua, Rosana Lopes,and Michael L. Bittner. AGaussian mixture-model ex-ploiting pathway knowledgefor dissecting cancer hetero-geneity. IEEE/ACM Trans-actions on ComputationalBiology and Bioinformatics,

17(2):459–468, March 2020.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic). URL https://dl.acm.org/doi/abs/10.1109/TCBB.2018.2869813.

Krotzky:2014:EGB

[KFHK14] Timo Krotzky, ThomasFober, Eyke Hullermeier,and Gerhard Klebe. Ex-tended graph-based mod-els for enhanced similar-ity search in Cavbase.IEEE/ACM Transactionson Computational Biologyand Bioinformatics, 11(5):878–890, September 2014.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Kim:2012:SGE

[KG12] Haseong Kim and Erol Ge-lenbe. Stochastic geneexpression modeling withHill function for switch-likegene responses. IEEE/ACMTransactions on Computa-tional Biology and Bioinfor-matics, 9(4):973–979, July2012. CODEN ITCBCY.ISSN 1545-5963 (print),1557-9964 (electronic).

Konur:2015:PDM

[KG15] Savas Konur and MarianGheorghe. A property-drivenmethodology for formal anal-ysis of synthetic biology sys-tems. IEEE/ACM Trans-actions on ComputationalBiology and Bioinformatics,

REFERENCES 193

12(2):360–371, March 2015.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Kazemi:2020:MSA

[KG20] Ehsan Kazemi and MatthiasGrossglauser. MPGM: Scal-able and accurate mul-tiple network alignment.IEEE/ACM Transactionson Computational Biologyand Bioinformatics, 17(6):2040–2052, November 2020.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic). URL https://dl.acm.org/doi/10.1109/TCBB.2019.2914050.

Kong:2014:BSD

[KGF+14] Ao Kong, Chinmaya Gupta,Mauro Ferrari, Marco Agos-tini, Chiara Bedin, AliBouamrani, Ennio Tas-ciotti, and Robert Azencott.Biomarker signature discov-ery from mass spectrometrydata. IEEE/ACM Trans-actions on ComputationalBiology and Bioinformatics,11(4):766–772, July 2014.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Kasarapu:2014:RPF

[KGK14] Parthan Kasarapu, MariaGarcia De La Banda, andArun S. Konagurthu. Onrepresenting protein fold-ing patterns using non-linear parametric curves.


Kobayashi:2014:ISB

[KH14] Koichi Kobayashi and Ku-nihiko Hiraishi. ILP/SMT-based method for de-sign of Boolean networksbased on singleton attrac-tors. IEEE/ACM Trans-actions on ComputationalBiology and Bioinformatics,11(6):1253–1259, November2014. CODEN ITCBCY.ISSN 1545-5963 (print),1557-9964 (electronic).

Karim:2020:BNB

[KHO+20] Mohammad Bozlul Karim,Ming Huang, Naoaki Ono,Shigehiko Kanaya, and Md.Altaf-Ul-Amin. BiClusO:a novel biclustering ap-proach and its application tospecies-VOC relational data.IEEE/ACM Transactionson Computational Biologyand Bioinformatics, 17(6):1955–1965, November 2020.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic). URL https://dl.acm.org/doi/10.1109/TCBB.2019.2914901.

Kazmi:2012:HCA

[KHP12] N. Kazmi, M. A. Hossain,and R. M. Phillips. A hybrid

REFERENCES 194

cellular automaton modelof solid tumor growth andbioreductive drug transport.IEEE/ACM Transactionson Computational Biologyand Bioinformatics, 9(6):1595–1606, November 2012.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Kim:2018:ESP

[Kim18] Sun Kim. Editorial for se-lected papers of a Joint Con-ferences, Genome Informat-ics Workshop/InternationalConference on Bioinfor-matics GIW/InCoB 2015.IEEE/ACM Transactions onComputational Biology andBioinformatics, 15(6):1821,November 2018. CODENITCBCY. ISSN 1545-5963(print), 1557-9964 (elec-tronic).

Kim:2004:GEW

[KJ04] Junhyong Kim and IngeJonassen. Guest editorial:WABI special section part1. IEEE/ACM Transac-tions on Computational Bi-ology and Bioinformatics, 1(4):137–138, October 2004.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Kim:2005:GEW

[KJ05] Junhyong Kim and IngeJonassen. Guest edito-rial: WABI special section.Part II. IEEE/ACM Trans-

actions on ComputationalBiology and Bioinformat-ics, 2(1):1–2, January 2005.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Kim:2008:LSS

[KK08] Eagu Kim and John Ke-cecioglu. Learning scoringschemes for sequence align-ment from partial exam-ples. IEEE/ACM Transac-tions on Computational Bi-ology and Bioinformatics, 5(4):546–556, October 2008.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Krejnik:2012:EEA

[KK12] Milos Krejnik and JiriKlema. Empirical evidenceof the applicability of func-tional clustering throughgene expression classifica-tion. IEEE/ACM Trans-actions on ComputationalBiology and Bioinformat-ics, 9(3):788–798, May 2012.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Kimura:2019:PCB

[KK19] Kouichi Kimura and AsakoKoike. Parallel compu-tation of the Burrows–Wheeler transform of shortreads using prefix paral-lelism. IEEE/ACM Trans-actions on ComputationalBiology and Bioinformatics,

REFERENCES 195

16(1):3–13, January 2019.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Kim:2014:MLS

[KKC+14] Chang-Kug Kim, Jin-AKim, Ji-Weon Choi, In-Seon Jeong, Yi-Seul Moon,Dong-Suk Park, Young-Joo Seol, Yong-Kab Kim,Yong-Hwan Kim, and Yeon-Ki Kim. A multi-layeredscreening method to iden-tify plant regulatory genes.IEEE/ACM Transactions onComputational Biology andBioinformatics, 11(2):293–303, March 2014. CODENITCBCY. ISSN 1545-5963(print), 1557-9964 (elec-tronic).

Kwon:2016:DRA

[KKC16] Yung-Keun Kwon, JunilKim, and Kwang-HyunCho. Dynamical robust-ness against multiple muta-tions in signaling networks.IEEE/ACM Transactionson Computational Biologyand Bioinformatics, 13(5):996–1002, September 2016.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Kawano:2020:SFB

[KKI20] Keisuke Kawano, SatoshiKoide, and Chie Imamura.Seq2seq fingerprint withbyte-pair encoding for pre-dicting changes in pro-

tein stability upon singlepoint mutation. IEEE/ACMTransactions on Computa-tional Biology and Bioin-formatics, 17(5):1762–1772,September 2020. CODENITCBCY. ISSN 1545-5963(print), 1557-9964 (elec-tronic). URL https://dl.acm.org/doi/10.1109/TCBB.2019.2908641.

Kim:2019:SDG

[KKK19] Man-Sun Kim, DongsanKim, and Jeong-Rae Kim.Stage-dependent gene ex-pression profiling in colorec-tal cancer. IEEE/ACMTransactions on Computa-tional Biology and Bioin-formatics, 16(5):1685–1692,September 2019. CODENITCBCY. ISSN 1545-5963(print), 1557-9964 (elec-tronic).

Kc:2011:TIP

[KL11a] Dukka B. Kc and Den-nis R. Livesay. Topologyimproves phylogenetic mo-tif functional site predic-tions. IEEE/ACM Transac-tions on Computational Bi-ology and Bioinformatics, 8(1):226–233, January 2011.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Krishnamurthy:2011:TRL

[KL11b] Vikram Krishnamurthy andKai-Yiu Luk. 2010 TCBBreviewers list. IEEE/ACM

REFERENCES 196

Transactions on Computa-tional Biology and Bioinfor-matics, 8(1):282–284, Jan-uary 2011. CODEN ITCBCY.ISSN 1545-5963 (print),1557-9964 (electronic).

Krishnamurthy:2011:SMM

[KL11c] Vikram Krishnamurthy andKai-Yiu Luk. Semi-Markovmodels for Brownian dynam-ics permeation in biologicalion channels. IEEE/ACMTransactions on Computa-tional Biology and Bioinfor-matics, 8(1):273–281, Jan-uary 2011. CODEN ITCBCY.ISSN 1545-5963 (print),1557-9964 (electronic).

Kaiser:2019:UDG

[KL19] Florian Kaiser and DirkLabudde. Unsuperviseddiscovery of geometricallycommon structural mo-tifs and long-range con-tacts in protein 3D struc-tures. IEEE/ACM Trans-actions on ComputationalBiology and Bioinformatics,16(2):671–680, March 2019.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic). URL https://dl.acm.org/doi/abs/10.1109/TCBB.2017.2786250.

Kocak:2020:ABP

[KM20] Mehmet Kocak and Khy-obeni Mozhui. An applica-tion of the Bayesian peri-odicity test to identify di-urnal rhythm genes in the

brain. IEEE/ACM Trans-actions on ComputationalBiology and Bioinformatics,17(1):47–55, January 2020.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic). URL https://dl.acm.org/doi/abs/10.1109/TCBB.2018.2859971.

Kundaje:2005:CST

[KMG+05] Anshul Kundaje, ManuelMiddendorf, Feng Gao, ChrisWiggins, and ChristinaLeslie. Combining sequenceand time series expressiondata to learn transcriptionalmodules. IEEE/ACM Trans-actions on ComputationalBiology and Bioinformat-ics, 2(3):194–202, July 2005.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Kang:2020:CGW

[KMSY20] Qiwen Kang, Neil Moore,Christopher L. Schardl, andRuriko Yoshida. CURa-tio: Genome-wide phyloge-nomic analysis method us-ing ratios of total branchlengths. IEEE/ACM Trans-actions on ComputationalBiology and Bioinformatics,17(3):981–989, May 2020.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic). URL https://dl.acm.org/doi/10.1109/TCBB.2018.2878564.

Keedwell:2005:DGN

[KN05] Edward Keedwell and Ajit

REFERENCES 197

Narayanan. Discoveringgene networks with a neural-genetic hybrid. IEEE/ACMTransactions on Computa-tional Biology and Bioinfor-matics, 2(3):231–242, July2005. CODEN ITCBCY.ISSN 1545-5963 (print),1557-9964 (electronic).

Kucherov:2005:MLF

[KNR05] Gregory Kucherov, LaurentNoe, and Mikhail Royt-berg. Multiseed lossless fil-tration. IEEE/ACM Trans-actions on ComputationalBiology and Bioinformatics,2(1):51–61, January 2005.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Kaski:2005:ACE

[KNS+05] Samuel Kaski, Janne Nikkila,Janne Sinkkonen, Leo Lahti,Juha E. A. Knuuttila, andChristophe Roos. Associa-tive clustering for explor-ing dependencies betweenfunctional genomics datasets. IEEE/ACM Trans-actions on ComputationalBiology and Bioinformat-ics, 2(3):203–216, July 2005.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Khan:2018:RPR

[KNTB18] Shujaat Khan, Imran Naseem,Roberto Togneri, and Mo-hammed Bennamoun. RAFP-Pred: Robust prediction of

antifreeze proteins using lo-calized analysis of n-peptidecompositions. IEEE/ACMTransactions on Computa-tional Biology and Bioin-formatics, 15(1):244–250,January 2018. CODENITCBCY. ISSN 1545-5963(print), 1557-9964 (elec-tronic).

Keijsper:2015:TCB

[KO15] Judith Keijsper and TimOosterwijk. Tractable casesof (∗, 2)-bounded parsimonyhaplotyping. IEEE/ACMTransactions on Computa-tional Biology and Bioin-formatics, 12(1):234–247,January 2015. CODENITCBCY. ISSN 1545-5963(print), 1557-9964 (elec-tronic).

Kentzoglanakis:2012:SIF

[KP12] Kyriakos Kentzoglanakisand Matthew Poole. Aswarm intelligence frame-work for reconstructing genenetworks: Searching for bi-ologically plausible architec-tures. IEEE/ACM Trans-actions on ComputationalBiology and Bioinformatics,9(2):358–371, March 2012.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Kalathiya:2014:MME

[KPB14] Umesh Kalathiya, MonikabenPadariya, and Maciej Ba-ginski. Molecular model-

REFERENCES 198

ing and evaluation of noveldibenzopyrrole derivatives astelomerase inhibitors and po-tential drug for cancer ther-apy. IEEE/ACM Transac-tions on Computational Bi-ology and Bioinformatics,11(6):1196–1207, November2014. CODEN ITCBCY.ISSN 1545-5963 (print),1557-9964 (electronic).

Kang:2017:MBB

[KPK+17] Mingon Kang, JuyoungPark, Dong-Chul Kim,Ashis K. Biswas, ChunyuLiu, and Jean Gao. Multi-block bipartite graph for in-tegrative genomic analysis.IEEE/ACM Transactionson Computational Biologyand Bioinformatics, 14(6):1350–1358, November 2017.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Kaloudas:2019:EEB

[KPP19] Dimitrios Kaloudas, NikoletPavlova, and Robert Pen-chovsky. EBWS: Essen-tial bioinformatics Web ser-vices for sequence analy-ses. IEEE/ACM Transac-tions on Computational Bi-ology and Bioinformatics,16(3):942–953, May 2019.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Kaddi:2013:MHS

[KPW13] Chanchala D. Kaddi, R. Mitchell

Parry, and May D. Wang.Multivariate hypergeometricsimilarity measure. IEEE/ACM Transactions on Com-putational Biology and Bioin-formatics, 10(6):1505–1516,November 2013. CODENITCBCY. ISSN 1545-5963(print), 1557-9964 (elec-tronic).

Kahveci:2013:GEA

[KS13] Tamer Kahveci and MonaSingh. Guest editorial forACM BCB. IEEE/ACMTransactions on Computa-tional Biology and Bioin-formatics, 10(5):1089–1090,September 2013. CODENITCBCY. ISSN 1545-5963(print), 1557-9964 (elec-tronic).

Kirkpatrick:2014:PPP

[KS14] Bonnie Kirkpatrick and Kris-tian Stevens. Perfect phy-logeny problems with miss-ing values. IEEE/ACMTransactions on Computa-tional Biology and Bioin-formatics, 11(5):928–941,September 2014. CODENITCBCY. ISSN 1545-5963(print), 1557-9964 (elec-tronic).

Khalid:2018:PHD

[KS18] Zoya Khalid and Osman UgurSezerman. Prediction ofHIV drug resistance by com-bining sequence and struc-tural properties. IEEE/ACMTransactions on Computa-

REFERENCES 199

tional Biology and Bioinfor-matics, 15(3):966–973, May2018. CODEN ITCBCY.ISSN 1545-5963 (print),1557-9964 (electronic).

Kocabas:2016:ESM

[KSA16] Ovunc Kocabas, TolgaSoyata, and Mehmet K.Aktas. Emerging secu-rity mechanisms for medi-cal cyber physical systems.IEEE/ACM Transactions onComputational Biology andBioinformatics, 13(3):401–416, May 2016. CODENITCBCY. ISSN 1545-5963(print), 1557-9964 (elec-tronic).

Klarner:2012:TSD

[KSB12] Hannes Klarner, HeikeSiebert, and AlexanderBockmayr. Time seriesdependent analysis of un-parametrized Thomas net-works. IEEE/ACM Trans-actions on ComputationalBiology and Bioinformatics,9(5):1338–1351, September2012. CODEN ITCBCY.ISSN 1545-5963 (print),1557-9964 (electronic).

Kulandaisamy:2018:IAK

[KSK+18] A. Kulandaisamy, AmbujSrivastava, Pradeep Kumar,R. Nagarajan, S. BinnyPriya, and M. MichaelGromiha. Identificationand analysis of key residuesin protein-RNA complexes.IEEE/ACM Transactions


Kayano:2014:DDC

[KSM14] Mitsunori Kayano, MotokiShiga, and Hiroshi Mamit-suka. Detecting differen-tially coexpressed genes fromlabeled expression data: abrief review. IEEE/ACMTransactions on Computa-tional Biology and Bioin-formatics, 11(1):154–167,January 2014. CODENITCBCY. ISSN 1545-5963(print), 1557-9964 (elec-tronic).

Kapilevich:2019:CRC

[KSMT19] Viacheslav Kapilevich, ShigetoSeno, Hideo Matsuda, andYoichi Takenaka. Chromatin3D reconstruction from chro-mosomal contacts using a ge-netic algorithm. IEEE/ACMTransactions on Computa-tional Biology and Bioin-formatics, 16(5):1620–1626,September 2019. CODENITCBCY. ISSN 1545-5963(print), 1557-9964 (elec-tronic).

Kawano:2012:IGP

[KSN+12] Shuichi Kawano, TeppeiShimamura, Atsushi Ni-ida, Seiya Imoto, Rui Ya-maguchi, Masao Nagasaki,Ryo Yoshida, Cristin Print,

REFERENCES 200

and Satoru Miyano. Identify-ing gene pathways associatedwith cancer characteristicsvia sparse statistical meth-ods. IEEE/ACM Trans-actions on ComputationalBiology and Bioinformat-ics, 9(4):966–972, July 2012.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Kumozaki:2015:MLB

[KSS15] Shotaro Kumozaki, KengoSato, and Yasubumi Sakak-ibara. A machine learn-ing based approach to denovo sequencing of glycansfrom tandem mass spectrom-etry spectrum. IEEE/ACMTransactions on Computa-tional Biology and Bioin-formatics, 12(6):1267–1274,November 2015. CODENITCBCY. ISSN 1545-5963(print), 1557-9964 (elec-tronic).

Kelk:2012:EC

[KSvI12] Steven Kelk, Celine Scor-navacca, and Leo van Iersel.On the elusiveness of clus-ters. IEEE/ACM Transac-tions on Computational Bi-ology and Bioinformatics, 9(2):517–534, March 2012.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Korodi:2007:CAN

[KT07] Gergely Korodi and IoanTabus. Compression of anno-

tated nucleotide sequences.IEEE/ACM Transactions onComputational Biology andBioinformatics, 4(3):447–457, July 2007. CODENITCBCY. ISSN 1545-5963(print), 1557-9964 (elec-tronic).

Kleftogiannis:2015:YNE

[KTLM15] Dimitrios Kleftogiannis, Kon-stantinos Theofilatos, SpirosLikothanassis, and SeferinaMavroudi. YamiPred: anovel evolutionary methodfor predicting Pre-miRNAsand selecting relevant fea-tures. IEEE/ACM Trans-actions on ComputationalBiology and Bioinformatics,12(5):1183–1192, September2015. CODEN ITCBCY.ISSN 1545-5963 (print),1557-9964 (electronic).

Kuksa:2013:BSC

[Kuk13] Pavel P. Kuksa. Biologicalsequence classification withmultivariate string kernels.IEEE/ACM Transactionson Computational Biologyand Bioinformatics, 10(5):1201–1210, September 2013.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Kuroshu:2013:NCP

[Kur13] Reginaldo M. Kuroshu.Nonoverlapping clone pool-ing for high-throughput se-quencing. IEEE/ACMTransactions on Computa-

REFERENCES 201


Kulekci:2012:EMR

[KVX12] M. Oguzhan Kulekci, Jef-frey Scott Vitter, and Bo-jian Xu. Efficient max-imal repeat finding us-ing the Burrows-Wheelertransform and wavelet tree.IEEE/ACM Transactions onComputational Biology andBioinformatics, 9(2):421–429, March 2012. CODENITCBCY. ISSN 1545-5963(print), 1557-9964 (elec-tronic).

Kim:2007:AAD

[KWL07] Jong Hyun Kim, Michael S.Waterman, and Lei M.Li. Accuracy assessmentof diploid consensus se-quences. IEEE/ACM Trans-actions on ComputationalBiology and Bioinformatics,4(1):88–97, January 2007.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Kwon:2019:EER

[KY19] Sunyoung Kwon and Sun-groh Yoon. End-to-endrepresentation learning forchemical-chemical interac-tion prediction. IEEE/ACMTransactions on Computa-tional Biology and Bioin-


Kustra:2010:DFC

[KZ10] Rafal Kustra and Adam Za-gdanski. Data-fusion inclustering microarray data:Balancing discovery and in-terpretability. IEEE/ACMTransactions on Computa-tional Biology and Bioinfor-matics, 7(1):50–63, January2010. CODEN ITCBCY.ISSN 1545-5963 (print),1557-9964 (electronic).

Kim:2018:CPP

[KZW+18] Mansuck Kim, Huan Zhang,Charles Woloshuk, Won-BoShim, and Byung-Jun Yoon.Computational prediction ofpathogenic network mod-ules in fusarium verticil-lioides. IEEE/ACM Trans-actions on ComputationalBiology and Bioinformatics,15(2):506–515, March 2018.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Labarre:2006:NBT

[Lab06] Anthony Labarre. Newbounds and tractable in-stances for the transpositiondistance. IEEE/ACM Trans-actions on ComputationalBiology and Bioinformatics,3(4):380–394, October 2006.CODEN ITCBCY. ISSN

REFERENCES 202


Limpiti:2014:IIN

[LAI+14] Tulaya Limpiti, ChainarongAmornbunchornvej, ApichartIntarapanich, Anunchai As-sawamakin, and SissadesTongsima. iNJclust: iter-ative neighbor-joining treeclustering framework for in-ferring population structure.IEEE/ACM Transactionson Computational Biologyand Bioinformatics, 11(5):903–914, September 2014.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Li:2019:IRF

[LB19] Lei Li and Mukul S. Bansal.An integrated reconcilia-tion framework for domain,gene, and species level evo-lution. IEEE/ACM Trans-actions on ComputationalBiology and Bioinformatics,16(1):63–76, January 2019.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Lushbough:2010:BSI

[LBL+10] Carol Lushbough, Michael K.Bergman, Carolyn J. Lawrence,Doug Jennewein, and VolkerBrendel. BioExtract Server— an integrated workflow-enabling system to ac-cess and analyze heteroge-neous, distributed biomolec-ular data. IEEE/ACM

Transactions on Computa-tional Biology and Bioinfor-matics, 7(1):12–24, January2010. CODEN ITCBCY.ISSN 1545-5963 (print),1557-9964 (electronic).

Li:2012:CPS

[LBL12a] Shuai Cheng Li, Dongbo Bu,and Ming Li. Clustering100,000 protein structure de-coys in minutes. IEEE/ACMTransactions on Computa-tional Biology and Bioinfor-matics, 9(3):765–773, May2012. CODEN ITCBCY.ISSN 1545-5963 (print),1557-9964 (electronic).

Li:2012:RSH

[LBL12b] Shuai Cheng Li, DongboBu, and Ming Li. Residueswith similar hexagon neigh-borhoods share similar side-chain conformations. IEEE/ACM Transactions on Com-putational Biology and Bioin-formatics, 9(1):240–248, Jan-uary 2012. CODEN ITCBCY.ISSN 1545-5963 (print),1557-9964 (electronic).

Leale:2018:IUB

[LBM+18] Guillermo Leale, Ariel EmilioBaya, Diego H. Milone,Pablo M. Granitto, andGeorgina Stegmayer. In-ferring unknown biologicalfunction by integration ofGO annotations and gene ex-pression data. IEEE/ACMTransactions on Computa-tional Biology and Bioin-

REFERENCES 203

formatics, 15(1):168–180,January 2018. CODENITCBCY. ISSN 1545-5963(print), 1557-9964 (elec-tronic).

Lorenz:2013:MQR

[LBQ+13] Ronny Lorenz, Stephan H.Bernhart, Jing Qin, Chris-tian Honer zu Siederdissen,Andrea Tanzer, Fabian Am-man, Ivo L. Hofacker, andPeter F. Stadler. 2D meets4G: G-quadruplexes in RNAsecondary structure predic-tion. IEEE/ACM Trans-actions on ComputationalBiology and Bioinformatics,10(4):832–844, July 2013.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Lonardi:2010:DMB

[LC10] Stefano Lonardi and JakeChen. Data mining in bioin-formatics: Selected papersfrom BIOKDD. IEEE/ACMTransactions on Computa-tional Biology and Bioinfor-matics, 7(2):195–196, April2010. CODEN ITCBCY.ISSN 1545-5963 (print),1557-9964 (electronic).

Li:2019:DTP

[LC19] Limin Li and Menglan Cai.Drug target prediction bymulti-view low rank embed-ding. IEEE/ACM Trans-actions on ComputationalBiology and Bioinformatics,16(5):1712–1721, September


Lovato:2017:SNR

[LCB17] Pietro Lovato, Marco Cristani,and Manuele Bicego. SoftNgram representation andmodeling for protein re-mote homology detection.IEEE/ACM Transactionson Computational Biologyand Bioinformatics, 14(6):1482–1488, November 2017.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Luo:2011:LTA

[LCC+11] Cheng-Wei Luo, Ming-Chiang Chen, Yi-ChingChen, Roger W. L. Yang,Hsiao-Fei Liu, and Kun-Mao Chao. Linear-timealgorithms for the multi-ple gene duplication prob-lems. IEEE/ACM Transac-tions on Computational Bi-ology and Bioinformatics, 8(1):260–265, January 2011.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Lafond:2018:GTC

[LCEMO18] Manuel Lafond, CedricChauve, Nadia El-Mabrouk,and Aida Ouangraoua. Genetree construction and cor-rection using SuperTree andreconciliation. IEEE/ACMTransactions on Computa-tional Biology and Bioin-

REFERENCES 204


Liu:2019:PRH

[LCGW19] Bin Liu, Junjie Chen,Mingyue Guo, and Xiao-long Wang. Protein re-mote homology detectionand fold recognition basedon sequence-order frequencymatrix. IEEE/ACM Trans-actions on ComputationalBiology and Bioinformat-ics, 16(1):292–300, January2019. CODEN ITCBCY.ISSN 1545-5963 (print),1557-9964 (electronic).

Lopez-Caamal:2019:SAI

[LCH19] Fernando Lopez-Caamal andHeinrich J. Huber. Stable IL-1β1β-activation in an inflam-masome signalling model de-pends on positive and nega-tive feedbacks and tight reg-ulation of protein produc-tion. IEEE/ACM Trans-actions on ComputationalBiology and Bioinformatics,16(2):627–637, March 2019.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic). URL https://dl.acm.org/doi/abs/10.1109/TCBB.2018.2794971.

Li:2010:CRA

[LCLL10] Gang Li, Tak-Ming Chan,Kwong-Sak Leung, and Kin-Hong Lee. A cluster refine-

ment algorithm for motif dis-covery. IEEE/ACM Trans-actions on ComputationalBiology and Bioinformatics,7(4):654–668, October 2010.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Lopez-Caamal:2014:SQC

[LCOMG14] Fernando Lopez-Caamal,Diego A. Oyarzun, Richard H.Middleton, and Mıriam R.Garcıa. Spatial quantifica-tion of cytosolic Ca2+ ac-cumulation in nonexcitablecells: an analytical study.IEEE/ACM Transactions onComputational Biology andBioinformatics, 11(3):592–603, May 2014. CODENITCBCY. ISSN 1545-5963(print), 1557-9964 (elec-tronic).

Luhmann:2018:SAC

[LCSW18] Nina Luhmann, CedricChauve, Jens Stoye, andRoland Wittler. Scaffold-ing of ancient contigs andancestral reconstruction ina phylogenetic framework.IEEE/ACM Transactionson Computational Biologyand Bioinformatics, 15(6):2094–2100, November 2018.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Lacroix:2008:IMN

[LCTS08] Vincent Lacroix, LudovicCottret, Patricia Thebault,

REFERENCES 205

and Marie-France Sagot. Anintroduction to metabolicnetworks and their structuralanalysis. IEEE/ACM Trans-actions on ComputationalBiology and Bioinformatics,5(4):594–617, October 2008.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Liu:2018:LRS

[LCW+18] Jian Liu, Yuhu Cheng,Xuesong Wang, Xiaoluo Cui,Yi Kong, and Junping Du.Low rank subspace cluster-ing via discrete constraintand hypergraph regulariza-tion for tumor molecular pat-tern discovery. IEEE/ACMTransactions on Computa-tional Biology and Bioin-formatics, 15(5):1500–1512,September 2018. CODENITCBCY. ISSN 1545-5963(print), 1557-9964 (elec-tronic).

Li:2013:MLI

[LCWZ13] Si Li, Kwok Pui Choi,Taoyang Wu, and LouxinZhang. Maximum likelihoodinference of the evolution-ary history of a PPI networkfrom the duplication historyof its proteins. IEEE/ACMTransactions on Computa-tional Biology and Bioin-formatics, 10(6):1412–1421,November 2013. CODENITCBCY. ISSN 1545-5963(print), 1557-9964 (elec-tronic).

Li:2016:MMH

[LCZN16] Yifeng Li, Haifen Chen, JieZheng, and Alioune Ngom.The max-min high-order dy-namic Bayesian network forlearning gene regulatory net-works with time-delayed reg-ulations. IEEE/ACM Trans-actions on ComputationalBiology and Bioinformat-ics, 13(4):792–803, 2016.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Luo:2017:CPD

[LDL+17] Jiawei Luo, Pingjian Ding,Cheng Liang, Buwen Cao,and Xiangtao Chen. Col-lective prediction of disease-associated miRNAs basedon transduction learning.IEEE/ACM Transactionson Computational Biologyand Bioinformatics, 14(6):1468–1475, November 2017.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Li:2018:GGS

[LDM18] Juntao Li, Wenpeng Dong,and Deyuan Meng. Groupedgene selection of cancer viaadaptive sparse group lassobased on conditional mutualinformation. IEEE/ACMTransactions on Computa-tional Biology and Bioin-formatics, 15(6):2028–2038,November 2018. CODENITCBCY. ISSN 1545-5963

REFERENCES 206


Lasker:2007:EDH

[LDS+07] Keren Lasker, Oranit Dror,Maxim Shatsky, Ruth Nussi-nov, and Haim J. Wolf-son. EMatch: Discoveryof high resolution struc-tural homologues of pro-tein domains in interme-diate resolution cryo-EMmaps. IEEE/ACM Trans-actions on ComputationalBiology and Bioinformatics,4(1):28–39, January 2007.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Lahti:2011:PAP

[LEAK11] Leo Lahti, Laura L. Elo,Tero Aittokallio, and SamuelKaski. Probabilistic analysisof probe reliability in differ-ential gene expression stud-ies with short oligonucleotidearrays. IEEE/ACM Trans-actions on ComputationalBiology and Bioinformatics,8(1):217–225, January 2011.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Leinweber:2018:GBP

[LFF18] Matthias Leinweber, ThomasFober, and Bernd Freisleben.GPU-Based point cloud su-perpositioning for structuralcomparisons of protein bind-ing sites. IEEE/ACM Trans-actions on Computational


Land:2016:MCS

[LFK16] Tyler A. Land, Perry Fiz-zano, and Robin B. Kod-ner. Measuring cluster sta-bility in a large scale phylo-genetic analysis of functionalgenes in metagenomes us-ing pplacer. IEEE/ACMTransactions on Computa-tional Biology and Bioin-formatics, 13(2):341–349,March 2016. CODENITCBCY. ISSN 1545-5963(print), 1557-9964 (elec-tronic).

Lacroix:2006:MSG

[LFS06] Vincent Lacroix, Cristina G.Fernandes, and Marie-FranceSagot. Motif search ingraphs: Application tometabolic networks. IEEE/ACM Transactions on Com-putational Biology and Bioin-formatics, 3(4):360–368, Oc-tober 2006. CODENITCBCY. ISSN 1545-5963(print), 1557-9964 (elec-tronic).

Li:2019:AIC

[LFZ+19] Min Li, Zhihui Fei, MinZeng, Fang-Xiang Wu, Yao-hang Li, Yi Pan, andJianxin Wang. Auto-mated ICD-9 coding viaa deep learning approach.

REFERENCES 207


Lovato:2015:MAP

[LGB15] Pietro Lovato, AlejandroGiorgetti, and ManueleBicego. A multimodalapproach for protein re-mote homology detection.IEEE/ACM Transactionson Computational Biologyand Bioinformatics, 12(5):1193–1198, September 2015.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Luck:2019:HMM

[LGN+19] Alexander Luck, PascalGiehr, Karl Nordstrom, JornWalter, and Verena Wolf.Hidden Markov modellingreveals neighborhood de-pendence of Dnmt3a and3b activity. IEEE/ACMTransactions on Computa-tional Biology and Bioin-formatics, 16(5):1598–1609,September 2019. CODENITCBCY. ISSN 1545-5963(print), 1557-9964 (elec-tronic).

Li:2020:DDM

[LGW20] Feng Li, Lin Gao, andBingbo Wang. Detec-tion of driver modules withrarely mutated genes in can-

cers. IEEE/ACM Trans-actions on ComputationalBiology and Bioinformatics,17(2):390–401, March 2020.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic). URL https://dl.acm.org/doi/abs/10.1109/TCBB.2018.2846262.

Lu:2010:RNM

[LGX10] Xin Lu, Anthony Gamst,and Ronghui Xu. RD-Curve: a nonparametricmethod to evaluate thestability of ranking proce-dures. IEEE/ACM Transac-tions on Computational Bi-ology and Bioinformatics, 7(4):719–726, October 2010.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Liu:2017:SNH

[LGZ+17] Yuxin Liu, Chao Gao, ZiliZhang, Yuxiao Lu, ShiChen, Mingxin Liang, andLi Tao. Solving NP-hardproblems with Physarum-based ant colony system.IEEE/ACM Transactions onComputational Biology andBioinformatics, 14(1):108–120, January 2017. CODENITCBCY. ISSN 1545-5963(print), 1557-9964 (elec-tronic).

Leung:2010:MFM

[LH10] Yukyee Leung and Ye-ungsam Hung. A multiple-filter-multiple-wrapper ap-

REFERENCES 208

proach to gene selection andmicroarray data classifica-tion. IEEE/ACM Transac-tions on Computational Bi-ology and Bioinformatics, 7(1):108–117, January 2010.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Lee:2020:CPP

[LH20] Wook Lee and KyungsookHan. Constructive predic-tion of potential RNA ap-tamers for a protein target.IEEE/ACM Transactionson Computational Biologyand Bioinformatics, 17(5):1476–1482, September 2020.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic). URL https://dl.acm.org/doi/10.1109/TCBB.2019.2951114.

Luo:2018:NAI

[LHC18] Jiawei Luo, Wei Huang,and Buwen Cao. A novelapproach to identify themiRNA–mRNA causal reg-ulatory modules in can-cer. IEEE/ACM Transac-tions on Computational Bi-ology and Bioinformatics, 15(1):309–315, January 2018.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Li:2020:DNN

[LHCL20] Yujie Li, Heng Huang,Hanbo Chen, and TianmingLiu. Deep neural networks

for In Situ hybridizationgrid completion and clus-tering. IEEE/ACM Trans-actions on ComputationalBiology and Bioinformatics,17(2):536–546, March 2020.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic). URL https://dl.acm.org/doi/abs/10.1109/TCBB.2018.2864262.

Liu:2018:PWT

[LHDS18] Ke Liu, Sha Hou, Jun-biao Dai, and Zhirong Sun.PyMut: a Web tool foroverlapping gene loss-of-function mutation design.IEEE/ACM Transactions onComputational Biology andBioinformatics, 15(4):1107–1110, July 2018. CODENITCBCY. ISSN 1545-5963(print), 1557-9964 (elec-tronic).

Ling:2016:MTH

[LHG+16] Cheng Ling, Tsuyoshi Hamada,Jingyang Gao, GuoguangZhao, Donghong Sun, andWeifeng Shi. MrBayes tgMC3++: a high performanceand resource-efficient GPU-oriented phylogenetic anal-ysis method. IEEE/ACMTransactions on Computa-tional Biology and Bioin-formatics, 13(5):845–854,September 2016. CODENITCBCY. ISSN 1545-5963(print), 1557-9964 (elec-tronic).

REFERENCES 209

Le:2013:CRT

[LHH13] Ngoc Tu Le, Tu Bao Ho,and Bich Hai Ho. Com-putational reconstructionof transcriptional relation-ships from ChIP-chip data.IEEE/ACM Transactions onComputational Biology andBioinformatics, 10(2):300–307, March 2013. CODENITCBCY. ISSN 1545-5963(print), 1557-9964 (elec-tronic).

Liu:2019:TBP

[LHH19] Hongyu Liu, Qinmin Vi-vian Hu, and Liang He.Term-based personalizationfor feature selection in clin-ical handover form auto-filling. IEEE/ACM Transac-tions on Computational Bi-ology and Bioinformatics, 16(4):1219–1230, July 2019.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Li:2019:IFI

[LHHL19] Ying Li, Ye He, SiyuHan, and Yanchun Liang.Identification and func-tional inference for tumor-associated long non-codingRNA. IEEE/ACM Trans-actions on ComputationalBiology and Bioinformatics,16(4):1288–1301, July 2019.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Liu:2017:UBM

[LHKL17] Yun Liu, Tao Hou, BingKang, and Fu Liu. Unsu-pervised binning of metage-nomic assembled contigs us-ing improved fuzzy C-meansmethod. IEEE/ACM Trans-actions on ComputationalBiology and Bioinformatics,14(6):1459–1467, November2017. CODEN ITCBCY.ISSN 1545-5963 (print),1557-9964 (electronic).

Le:2019:FPA

[LHL+19a] Thuc Duy Le, Tao Hoang, Ji-uyong Li, Lin Liu, HuawenLiu, and Shu Hu. A fast PCalgorithm for high dimen-sional causal discovery withmulti-core PCs. IEEE/ACMTransactions on Computa-tional Biology and Bioin-formatics, 16(5):1483–1495,September 2019. CODENITCBCY. ISSN 1545-5963(print), 1557-9964 (elec-tronic).

Liu:2019:CPS

[LHL+19b] Bingqiang Liu, Ling Han, Xi-angrong Liu, Jichang Wu,and Qin Ma. Computationalprediction of sigma-54 pro-moters in bacterial genomesby integrating motif findingand machine learning strate-gies. IEEE/ACM Transac-tions on Computational Bi-ology and Bioinformatics, 16(4):1211–1218, July 2019.CODEN ITCBCY. ISSN

REFERENCES 210


Li:2011:FSF

[LHLY11] Yanpeng Li, Xiaohua Hu,Hongfei Lin, and ZhiahiYang. A framework forsemisupervised feature gen-eration and its applicationsin biomedical literature min-ing. IEEE/ACM Transac-tions on Computational Bi-ology and Bioinformatics, 8(2):294–307, March 2011.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Li:2014:RSA

[LHN+14] Jing Li, Jun Hu, MatthewNewman, Kejun Liu, andHuanying Ge. RNA-seq anal-ysis pipeline based on Oshellenvironment. IEEE/ACMTransactions on Computa-tional Biology and Bioin-formatics, 11(5):973–978,September 2014. CODENITCBCY. ISSN 1545-5963(print), 1557-9964 (elec-tronic).

Liu:2018:CPT

[LHQ+18] Min Liu, Yue He, Weili Qian,Yangliu Wei, and XiaoyanLiu. Cell population trackingin a honeycomb structure us-ing an IMM filter based 3Dlocal graph matching model.IEEE/ACM Transactionson Computational Biologyand Bioinformatics, 15(5):1706–1717, September 2018.


Liu:2016:PSE

[LHS16] Yongchao Liu, Thomas Han-keln, and Bertil Schmidt.Parallel and space-efficientconstruction of Burrows–Wheeler transform and suf-fix array for big genomedata. IEEE/ACM Trans-actions on ComputationalBiology and Bioinformatics,13(3):592–598, May 2016.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

LeFaucheur:2011:NCS

[LHTT11] Xavier Le Faucheur, EliHershkovits, Rina Tannen-baum, and Allen Tannen-baum. Nonparametric clus-tering for studying RNAconformations. IEEE/ACMTransactions on Computa-tional Biology and Bioin-formatics, 8(6):1604–1619,November 2011. CODENITCBCY. ISSN 1545-5963(print), 1557-9964 (elec-tronic).

Li:2015:BLC

[LHWL15] Zhenhua Li, Ying He, Lim-soon Wong, and Jinyan Li.Burial level change definesa high energetic relevancefor protein binding inter-faces. IEEE/ACM Trans-actions on ComputationalBiology and Bioinformatics,

REFERENCES 211


Luo:2011:ICE

[LHY+11] Lin-Kai Luo, Deng-FengHuang, Ling-Jun Ye, Qi-Feng Zhou, Gui-Fang Shao,and Hong Peng. Improv-ing the computational effi-ciency of recursive clusterelimination for gene selec-tion. IEEE/ACM Transac-tions on Computational Bi-ology and Bioinformatics, 8(1):122–129, January 2011.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Lin:2019:RCM

[LHZ+19] Xiaohui Lin, Xin Huang,Lina Zhou, Weijie Ren,Jun Zeng, Weihong Yao,and Xingyuan Wang. Therobust classification modelbased on combinatorial fea-tures. IEEE/ACM Trans-actions on ComputationalBiology and Bioinformatics,16(2):650–657, March 2019.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic). URL https://dl.acm.org/doi/abs/10.1109/TCBB.2017.2779512.

Li:2020:ILM

[LJ20] Lishuang Li and YuxinJiang. Integrating lan-guage model and readingcontrol gate in BLSTM-CRF

for biomedical named en-tity recognition. IEEE/ACMTransactions on Computa-tional Biology and Bioinfor-matics, 17(3):841–846, May2020. CODEN ITCBCY.ISSN 1545-5963 (print),1557-9964 (electronic). URLhttps://dl.acm.org/doi/10.1109/TCBB.2018.2868346.

Li:2012:DGE

[LJK+12] Ying-Xin Li, Shuiwang Ji,Sudhir Kumar, JiepingYe, and Zhi-Hua Zhou.Drosophila gene expressionpattern annotation throughmulti-instance multi-labellearning. IEEE/ACM Trans-actions on ComputationalBiology and Bioinformatics,9(1):98–112, January 2012.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Liao:2014:GSU

[LJL+14] Bo Liao, Yan Jiang, WeiLiang, Wen Zhu, Lijun Cai,and Zhi Cao. Gene selec-tion using locality sensitiveLaplacian score. IEEE/ACMTransactions on Computa-tional Biology and Bioin-formatics, 11(6):1146–1156,November 2014. CODENITCBCY. ISSN 1545-5963(print), 1557-9964 (elec-tronic).

Liao:2015:EFR

[LJL+15] Bo Liao, Yan Jiang, WeiLiang, Lihong Peng, Li Peng,

REFERENCES 212

Damien Hanyurwimfura, Ze-jun Li, and Min Chen.On efficient feature rankingmethods for high-throughputdata analysis. IEEE/ACMTransactions on Computa-tional Biology and Bioin-formatics, 12(6):1374–1384,November 2015. CODENITCBCY. ISSN 1545-5963(print), 1557-9964 (elec-tronic).

Liu:2013:IAA

[LJZZ13] Nan Liu, Haitao Jiang,Daming Zhu, and BinhaiZhu. An improved ap-proximation algorithm forscaffold filling to maximizethe common adjacencies.IEEE/ACM Transactions onComputational Biology andBioinformatics, 10(4):905–913, July 2013. CODENITCBCY. ISSN 1545-5963(print), 1557-9964 (elec-tronic).

Li:2011:CED

[LK11] Qi Li and Chandra Kamb-hamettu. Contour extrac-tion of Drosophila embryos.IEEE/ACM Transactionson Computational Biologyand Bioinformatics, 8(6):1509–1521, November 2011.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Lo:2014:SCR

[LKLB14] Christine Lo, Boyko Kakaradov,Daniel Lokshtanov, and

Christina Boucher. SeeSite:characterizing relationshipsbetween splice junctionsand splicing enhancers.IEEE/ACM Transactions onComputational Biology andBioinformatics, 11(4):648–656, July 2014. CODENITCBCY. ISSN 1545-5963(print), 1557-9964 (elec-tronic).

Li:2019:CIC

[LKW+19] Donghe Li, Wonji Kim,Longfei Wang, Kyong-AhYoon, Boyoung Park, CharnyPark, Sun-Young Kong,Yongdeuk Hwang, DaehyunBaek, Eun Sook Lee, andSungho Won. Comparisonof INDEL calling tools withsimulation data and realshort-read data. IEEE/ACMTransactions on Computa-tional Biology and Bioin-formatics, 16(5):1635–1644,September 2019. CODENITCBCY. ISSN 1545-5963(print), 1557-9964 (elec-tronic).

Li:2011:HHT

[LKY+11] Helong Li, Sam Kwong, Li-hua Yang, Daren Huang, andDongping Xiao. Hilbert–Huang Transform for analy-sis of heart rate variability incardiac health. IEEE/ACMTransactions on Computa-tional Biology and Bioin-formatics, 8(6):1557–1567,November 2011. CODENITCBCY. ISSN 1545-5963

REFERENCES 213


Li:2011:DAN

[LL11] Ping Li and James Lam.Disturbance analysis ofnonlinear differential equa-tion models of geneticSUM regulatory networks.IEEE/ACM Transactions onComputational Biology andBioinformatics, 8(1):253–259, January 2011. CODENITCBCY. ISSN 1545-5963(print), 1557-9964 (elec-tronic).

Liu:2019:PCP

[LL19] Bin Liu and Shumin Li.ProtDet-CCH: Protein re-mote homology detection bycombining long short-termmemory and ranking meth-ods. IEEE/ACM Transac-tions on Computational Bi-ology and Bioinformatics, 16(4):1203–1210, July 2019.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Lopez-Lopera:2019:SLF

[LLA19] Andres F. Lopez-Loperaand Mauricio A. Alvarez.Switched latent force modelsfor reverse-engineering tran-scriptional regulation in geneexpression data. IEEE/ACMTransactions on Computa-tional Biology and Bioin-formatics, 16(1):322–335,January 2019. CODENITCBCY. ISSN 1545-5963


Liu:2020:BLE

[LLBL20] Yuansheng Liu, ChaowangLan, Michael Blumenstein,and Jinyan Li. Bi-level errorcorrection for PacBio longreads. IEEE/ACM Trans-actions on ComputationalBiology and Bioinformatics,17(3):899–905, May 2020.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic). URL https://dl.acm.org/doi/10.1109/TCBB.2017.2780832.

Li:2013:ISS

[LLC+13] Xiong Li, Bo Liao, LijunCai, Zhi Cao, and WenZhu. Informative SNPs se-lection based on two-locusand multilocus linkage dis-equilibrium: Criteria ofmax-correlation and min-redundancy. IEEE/ACMTransactions on Computa-tional Biology and Bioinfor-matics, 10(3):688–695, May2013. CODEN ITCBCY.ISSN 1545-5963 (print),1557-9964 (electronic).

Liao:2015:HCM

[LLC+15] Bo Liao, Xiong Li, LijunCai, Zhi Cao, and HaowenChen. A hierarchical clus-tering method of select-ing kernel SNP to unifyinformative SNP and tagSNP. IEEE/ACM Transac-tions on Computational Bi-

REFERENCES 214

ology and Bioinformatics, 12(1):113–122, January 2015.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Liang:2015:IDA

[LLCZ15] Muxuan Liang, Zhizhong Li,Ting Chen, and JianyangZeng. Integrative dataanalysis of multi-platformcancer data with a mul-timodal deep learning ap-proach. IEEE/ACM Trans-actions on ComputationalBiology and Bioinformatics,12(4):928–937, July 2015.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Lin:2018:MGD

[LLES18] Congping Lin, LaurentLemarchand, Reinhardt Eu-ler, and Imogen Sparkes.Modeling the geometry anddynamics of the endo-plasmic reticulum network.IEEE/ACM Transactions onComputational Biology andBioinformatics, 15(2):377–386, March 2018. CODENITCBCY. ISSN 1545-5963(print), 1557-9964 (elec-tronic).

Li:2007:DSD

[LLH+07] Wenyuan Li, Ying Liu,Hung-Chung Huang, Yanx-iong Peng, Yongjing Lin,Wee-Keong Ng, and Kok-Leong Ong. Dynamical sys-tems for discovering protein

complexes and functionalmodules from biological net-works. IEEE/ACM Trans-actions on ComputationalBiology and Bioinformatics,4(2):233–250, April 2007.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Lu:2014:LPC

[LLH+14] Meng Lu, Hye-Seung Lee,David Hadley, Jianhua Z.Huang, and Xiaoning Qian.Logistic principal componentanalysis for rare variantsin gene-environment interac-tion analysis. IEEE/ACMTransactions on Computa-tional Biology and Bioin-formatics, 11(6):1020–1028,November 2014. CODENITCBCY. ISSN 1545-5963(print), 1557-9964 (elec-tronic).

Li:2017:IIS

[LLH+17] Min Li, Zhongxiang Liao,Yiming He, Jianxin Wang,Junwei Luo, and Yi Pan.ISEA: Iterative seed-extensionalgorithm for De Novo as-sembly using paired-end in-formation and insert sizedistribution. IEEE/ACMTransactions on Computa-tional Biology and Bioinfor-matics, 14(4):916–925, July2017. CODEN ITCBCY.ISSN 1545-5963 (print),1557-9964 (electronic).

REFERENCES 215

Liu:2018:PTB

[LLH18] Chengyu Liu, Rainer Lehto-nen, and Sampsa Hau-taniemi. PerPAS: Topology-based single sample path-way analysis method. IEEE/ACM Transactions on Com-putational Biology and Bioin-formatics, 15(3):1022–1027,May 2018. CODEN ITCBCY.ISSN 1545-5963 (print),1557-9964 (electronic).

Li:2015:RBC

[LLHF15] Han Li, Chun Li, Jie Hu,and Xiaodan Fan. A resam-pling based clustering algo-rithm for replicated gene ex-pression data. IEEE/ACMTransactions on Computa-tional Biology and Bioin-formatics, 12(6):1295–1303,November 2015. CODENITCBCY. ISSN 1545-5963(print), 1557-9964 (elec-tronic).

Lo:2015:ITD

[LLL15] Leung-Yau Lo, Kwong-Sak Leung, and Kin-HongLee. Inferring time-delayedcausal gene network usingtime-series expression data.IEEE/ACM Transactionson Computational Biologyand Bioinformatics, 12(5):1169–1182, September 2015.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Liang:2016:NMD

[LLL16a] Cheng Liang, Yue Li, and Ji-awei Luo. A novel methodto detect functional mi-croRNA regulatory mod-ules by bicliques merging.IEEE/ACM Transactions onComputational Biology andBioinformatics, 13(3):549–556, May 2016. CODENITCBCY. ISSN 1545-5963(print), 1557-9964 (elec-tronic).

Liu:2016:DDS

[LLL16b] Yang Liu, Bowen Li, andJungang Lou. Distur-bance decoupling of singu-lar Boolean control networks.IEEE/ACM Transactionson Computational Biologyand Bioinformatics, 13(6):1194–1200, November 2016.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Liao:2020:ILI

[LLL+20] Xingyu Liao, Min Li, Jun-wei Luo, You Zou, Fang-Xiang Wu, Yi Pan, FengLuo, and Jianxin Wang.Improving de novo assem-bly based on read classifica-tion. IEEE/ACM Transac-tions on Computational Bi-ology and Bioinformatics, 17(1):177–188, January 2020.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic). URL https://dl.acm.org/doi/abs/10.1109/TCBB.2018.2861380.

REFERENCES 216

Li:2017:UCC

[LLNW17] Min Li, Yu Lu, ZhibeiNiu, and Fang-Xiang Wu.United complex centralityfor identification of essen-tial proteins from PPI net-works. IEEE/ACM Trans-actions on ComputationalBiology and Bioinformatics,14(2):370–380, March 2017.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Li:2016:EBE

[LLQ+16] Lishuang Li, Shanshan Liu,Meiyue Qin, Yiwen Wang,and Degen Huang. Ex-tracting biomedical eventwith dual decomposition in-tegrating word embeddings.IEEE/ACM Transactionson Computational Biologyand Bioinformatics, 13(4):669–677, 2016. CODENITCBCY. ISSN 1545-5963(print), 1557-9964 (elec-tronic).

Li:2020:EBE

[LLQ20] Lishuang Li, Yang Liu,and Meiyue Qin. Ex-tracting biomedical eventswith parallel multi-poolingconvolutional neural net-works. IEEE/ACM Trans-actions on ComputationalBiology and Bioinformatics,17(2):599–607, March 2020.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic). URL https:/

/dl.acm.org/doi/abs/10.1109/TCBB.2018.2868078.

Li:2015:PIR

[LLRZ15] Hui Li, Xiaoyi Li, MuraliRamanathan, and AidongZhang. Prediction and infor-mative risk factor selection ofbone diseases. IEEE/ACMTransactions on Computa-tional Biology and Bioinfor-matics, 12(1):79–91, January2015. CODEN ITCBCY.ISSN 1545-5963 (print),1557-9964 (electronic).

Liu:2010:SSV

[LLT10] Zhenqiu Liu, Shili Lin, andMing Tan. Sparse sup-port vector machines with Lppenalty for biomarker identi-fication. IEEE/ACM Trans-actions on ComputationalBiology and Bioinformatics,7(1):100–107, January 2010.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Luhmann:2019:SSP

[LLT+19] Nina Luhmann, Manuel La-fond, Annelyse Thevenin,Aida Ouangraoua, RolandWittler, and Cedric Chauve.The SCJ small parsimonyproblem for weighted geneadjacencies. IEEE/ACMTransactions on Computa-tional Biology and Bioin-formatics, 16(4):1364–1373,July 2019. CODEN ITCBCY.ISSN 1545-5963 (print),1557-9964 (electronic).

REFERENCES 217

Lin:2019:ISP

[LLTC19] Hao Lin, Zhi-Yong Liang,Hua Tang, and Wei Chen.Identifying sigma70 promot-ers with novel pseudo nu-cleotide composition. IEEE/ACM Transactions on Com-putational Biology and Bioin-formatics, 16(4):1316–1321,July 2019. CODEN ITCBCY.ISSN 1545-5963 (print),1557-9964 (electronic).

Liu:2010:MPI

[LLW10] Xiaowen Liu, Jinyan Li, andLusheng Wang. Modelingprotein interacting groupsby quasi-bicliques: Complex-ity, algorithm, and applica-tion. IEEE/ACM Trans-actions on ComputationalBiology and Bioinformatics,7(2):354–364, April 2010.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Leung:2011:DMD

[LLW+11] KwongSak Leung, KinHongLee, JinFeng Wang, Ed-die YT Ng, Henry LYChan, Stephen KW Tsui,Tony SK Mok, Pete Chi-Hang Tse, and Joseph JYSung. Data mining on DNAsequences of Hepatitis Bvirus. IEEE/ACM Trans-actions on ComputationalBiology and Bioinformatics,8(2):428–440, March 2011.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Li:2015:TPB

[LLW+15] Min Li, Yu Lu, JianxinWang, Fang-Xiang Wu,and Yi Pan. A topol-ogy potential-based methodfor identifying essential pro-teins from PPI networks.IEEE/ACM Transactions onComputational Biology andBioinformatics, 12(2):372–383, March 2015. CODENITCBCY. ISSN 1545-5963(print), 1557-9964 (elec-tronic).

Li:2011:RUP

[LLX+11] Hong-Dong Li, Yi-ZengLiang, Qing-Song Xu, Dong-Sheng Cao, Bin-Bin Tan,Bai-Chuan Deng, and Chen-Chen Lin. Recipe for un-covering predictive genes us-ing support vector machinesbased on model popula-tion analysis. IEEE/ACMTransactions on Computa-tional Biology and Bioin-formatics, 8(6):1633–1641,November 2011. CODENITCBCY. ISSN 1545-5963(print), 1557-9964 (elec-tronic).

Li:2016:PSS

[LLX+16] Liqi Li, Jinhui Li, Wei-dong Xiao, Yongsheng Li,Yufang Qin, Shiwen Zhou,and Hua Yang. Predictionthe substrate specificities ofmembrane transport pro-teins based on support vectormachine and hybrid features.

REFERENCES 218


Liu:2013:RSN

[LLZ+13] Wei Liu, Dong Li, Yun-ping Zhu, Hongwei Xie, andFuchu He. Reconstruc-tion of signaling networkfrom protein interactionsbased on function annota-tions. IEEE/ACM Trans-actions on ComputationalBiology and Bioinformatics,10(2):514–521, March 2013.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Liao:2020:ETA

[LLZ+20a] Xingyu Liao, Min Li,You Zou, Fang-Xiang Wu,Yi Pan, and Jianxin Wang.An efficient trimming algo-rithm based on multi-featurefusion scoring model for NGSdata. IEEE/ACM Trans-actions on ComputationalBiology and Bioinformatics,17(3):728–738, May 2020.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic). URL https://dl.acm.org/doi/10.1109/TCBB.2019.2897558.

Liu:2020:EMX

[LLZ+20b] Jian Liu, Qiuru Liu, LeiZhang, Shuhui Su, and

Yongzhuang Liu. Enablingmassive XML-based bio-logical data managementin HBase. IEEE/ACMTransactions on Computa-tional Biology and Bioin-formatics, 17(6):1994–2004,November 2020. CODENITCBCY. ISSN 1545-5963(print), 1557-9964 (elec-tronic). URL https://dl.acm.org/doi/10.1109/TCBB.2019.2915811.

Liao:2012:NMS

[LLZC12] Bo Liao, Xiong Li, WenZhu, and Zhi Cao. A novelmethod to select informa-tive SNPs and their appli-cation in genetic associa-tion studies. IEEE/ACMTransactions on Computa-tional Biology and Bioin-formatics, 9(5):1529–1534,September 2012. CODENITCBCY. ISSN 1545-5963(print), 1557-9964 (elec-tronic).

Leitner:2010:OBI

[LMK+10] Florian Leitner, Scott A.Mardis, Martin Krallinger,Gianni Cesareni, Lynette A.Hirschman, and Alfonso Va-lencia. An overview ofBioCreative II.5. IEEE/ACM Transactions on Com-putational Biology and Bioin-formatics, 7(3):385–399, July2010. CODEN ITCBCY.ISSN 1545-5963 (print),1557-9964 (electronic).

REFERENCES 219

Leoncini:2015:CCT

[LMPT15] Mauro Leoncini, ManuelaMontangero, Marco Pelle-grini, and Karina PanuciaTillan. CMStalker: a com-binatorial tool for compositemotif discovery. IEEE/ACMTransactions on Computa-tional Biology and Bioin-formatics, 12(5):1123–1136,September 2015. CODENITCBCY. ISSN 1545-5963(print), 1557-9964 (elec-tronic).

Li:2014:OSM

[LMZ14] Weiming Li, Bin Ma, andKaizhong Zhang. Opti-mizing spaced k-mer neigh-bors for efficient filtrationin protein similarity search.IEEE/ACM Transactions onComputational Biology andBioinformatics, 11(2):398–406, March 2014. CODENITCBCY. ISSN 1545-5963(print), 1557-9964 (elec-tronic).

Li:2020:IPC

[LMZ+20] Min Li, Xiangmao Meng,Ruiqing Zheng, Fang-XiangWu, Yaohang Li, Yi Pan,and Jianxin Wang. Iden-tification of protein com-plexes by using a spatialand temporal active pro-tein interaction network.IEEE/ACM Transactions onComputational Biology andBioinformatics, 17(3):817–827, May 2020. CODENITCBCY. ISSN 1545-5963


Liu:2017:API

[LMZL17] Yi Liu, Bin Ma, KaizhongZhang, and Gilles Lajoie. Anapproach for peptide iden-tification by De Novo se-quencing of mixture spec-tra. IEEE/ACM Transac-tions on Computational Bi-ology and Bioinformatics,14(2):326–336, March 2017.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Li:2013:NLS

[LN13] Yifeng Li and Alioune Ngom.Nonnegative least-squaresmethods for the classificationof high-dimensional biologi-cal data. IEEE/ACM Trans-actions on ComputationalBiology and Bioinformatics,10(2):447–456, March 2013.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

L:2017:BDW

[LN17] Biji C. L. and Achuth-sankar S. Nair. Bench-mark dataset for wholegenome sequence compres-sion. IEEE/ACM Trans-actions on ComputationalBiology and Bioinformatics,14(6):1228–1236, November2017. CODEN ITCBCY.ISSN 1545-5963 (print),1557-9964 (electronic).

REFERENCES 220

Liu:2005:TMB

[LNC+05] Ying Liu, Shamkant B.Navathe, Jorge Civera,Venu Dasigi, Ashwin Ram,Brian J. Ciliax, and RayDingledine. Text miningbiomedical literature for dis-covering gene-to-gene re-lationships: a compara-tive study of algorithms.IEEE/ACM Transactions onComputational Biology andBioinformatics, 2(1):62–76,January 2005. CODENITCBCY. ISSN 1545-5963(print), 1557-9964 (elec-tronic).

Li:2019:CRP

[LNC+19] Min Li, Peng Ni, XiaopeiChen, Jianxin Wang, Fang-Xiang Wu, and Yi Pan.Construction of refined pro-tein interaction network forpredicting essential proteins.IEEE/ACM Transactions onComputational Biology andBioinformatics, 16(4):1386–1397, July 2019. CODENITCBCY. ISSN 1545-5963(print), 1557-9964 (elec-tronic).

Liu:2009:BWT

[LNR+09] Kevin Liu, Serita Nelesen,Sindhu Raghavan, C. RandalLinder, and Tandy Warnow.Barking up the wrong tree-length: The impact of gappenalty on alignment andtree accuracy. IEEE/ACMTransactions on Computa-

tional Biology and Bioinfor-matics, 6(1):7–21, January2009. CODEN ITCBCY.ISSN 1545-5963 (print),1557-9964 (electronic).

Liu:2020:MDN

[LNW20] Ye Liu, Michael K. Ng,and Stephen Wu. Multi-domain networks associa-tion for biological data us-ing block signed graph clus-tering. IEEE/ACM Trans-actions on ComputationalBiology and Bioinformatics,17(2):435–448, March 2020.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic). URL https://dl.acm.org/doi/abs/10.1109/TCBB.2018.2848904.

Ling:2005:GEIb

[LNY05a] C. X. Ling, W. S. Noble,and Q. Yang. Guest Edi-tor’s introduction to the Spe-cial Issue: Machine Learn-ing for Bioinformatics—Part2. IEEE/ACM Transac-tions on Computational Bi-ology and Bioinformatics,2(3):177–178, July 2005.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Ling:2005:GEIa

[LNY05b] Charles X. Ling, William StaffordNoble, and Qiang Yang.Guest Editors’ introduc-tion to the Special Is-sue: Machine Learningfor Bioinformatics—Part 1.

REFERENCES 221

IEEE/ACM Transactionson Computational Biologyand Bioinformatics, 2(2):81–82, April 2005. CODENITCBCY. ISSN 1545-5963(print), 1557-9964 (elec-tronic).

Liu:2015:IDN

[LP15] Xueming Liu and LinqiangPan. Identifying drivernodes in the human sig-naling network using struc-tural controllability analy-sis. IEEE/ACM Transac-tions on Computational Bi-ology and Bioinformatics,12(2):467–472, March 2015.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Liu:2013:CFS

[LPH+13] Hsi-Che Liu, Pei-Chen Peng,Tzung-Chien Hsieh, Ting-Chi Yeh, Chih-Jen Lin,Chien-Yu Chen, Jen-YinHou, Lee-Yung Shih, andDer-Cherng Liang. Com-parison of feature selec-tion methods for cross-laboratory microarray anal-ysis. IEEE/ACM Transac-tions on Computational Bi-ology and Bioinformatics,10(3):593–604, May 2013.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Lee:2018:SBP

[LPH18] Wook Lee, Byungkyu Park,and Kyungsook Han. Sequence-

based prediction of putativetranscription factor bindingsites in DNA sequences ofany length. IEEE/ACMTransactions on Computa-tional Biology and Bioin-formatics, 15(5):1461–1469,September 2018. CODENITCBCY. ISSN 1545-5963(print), 1557-9964 (elec-tronic).

Lozano:2008:STA

[LPR+08] Antoni Lozano, Ron Y. Pin-ter, Oleg Rokhlenko, GabrielValiente, and Michal Ziv-Ukelson. Seeded tree align-ment. IEEE/ACM Transac-tions on Computational Bi-ology and Bioinformatics, 5(4):503–513, October 2008.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Lamiable:2013:AGT

[LQV+13] Alexis Lamiable, FranckQuessette, Sandrine Vial,Dominique Barth, and AlainDenise. An algorith-mic game-theory approachfor coarse-grain predictionof RNA 3D structure.IEEE/ACM Transactions onComputational Biology andBioinformatics, 10(1):193–199, January 2013. CODENITCBCY. ISSN 1545-5963(print), 1557-9964 (elec-tronic).

Liu:2020:JIV

[LQY+20] Jian Liu, Zhi Qu, Mo Yang,

REFERENCES 222

Jialiang Sun, Shuhui Su, andLei Zhang. Jointly inte-grating VCF-based variantsand OWL-based biomedi-cal ontologies in MongoDB.IEEE/ACM Transactionson Computational Biologyand Bioinformatics, 17(5):1504–1515, September 2020.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic). URL https://dl.acm.org/doi/10.1109/TCBB.2019.2951137.

Lecca:2020:RBM

[LR20] Paola Lecca and Angela Re.A reaction-based model ofthe state space of chem-ical reaction systems en-ables efficient simulations.IEEE/ACM Transactions onComputational Biology andBioinformatics, 17(2):469–482, March 2020. CODENITCBCY. ISSN 1545-5963(print), 1557-9964 (elec-tronic). URL https://dl.acm.org/doi/abs/10.1109/TCBB.2019.2894699.

Lee:2008:IEN

[LRM08] George Lee, Carlos Ro-driguez, and Anant Madab-hushi. Investigating the ef-ficacy of nonlinear dimen-sionality reduction schemesin classifying gene andprotein expression studies.IEEE/ACM Transactions onComputational Biology andBioinformatics, 5(3):368–384, July 2008. CODENITCBCY. ISSN 1545-5963


Lin:2012:MPT

[LRM12] Yu Lin, Vaibhav Rajan,and Bernard M. E. Moret.A metric for phylogenetictrees based on matching.IEEE/ACM Transactions onComputational Biology andBioinformatics, 9(4):1014–1022, July 2012. CODENITCBCY. ISSN 1545-5963(print), 1557-9964 (elec-tronic).

Lancia:2008:HDA

[LRR08] Giuseppe Lancia, R. Ravi,and Romeo Rizzi. Haplo-typing for disease associa-tion: a combinatorial ap-proach. IEEE/ACM Trans-actions on ComputationalBiology and Bioinformatics,5(2):245–251, April 2008.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Linz:2009:HNT

[LS09] Simone Linz and CharlesSemple. Hybridization innonbinary trees. IEEE/ACMTransactions on Computa-tional Biology and Bioinfor-matics, 6(1):30–45, January2009. CODEN ITCBCY.ISSN 1545-5963 (print),1557-9964 (electronic).

Lan:2010:EIF

[LS10] Man Lan and Jian Su. Em-pirical investigations into

REFERENCES 223

full-text protein interactionarticle categorization task(ACT) in the BioCreativeII.5 challenge. IEEE/ACMTransactions on Computa-tional Biology and Bioinfor-matics, 7(3):421–427, July2010. CODEN ITCBCY.ISSN 1545-5963 (print),1557-9964 (electronic).

Loriot:2011:CSD

[LSB+11] Sebastien Loriot, SushantSachdeva, Karine Bastard,Chantal Prevost, and Fred-eric Cazals. On the charac-terization and selection of di-verse conformational ensem-bles with applications to flex-ible docking. IEEE/ACMTransactions on Computa-tional Biology and Bioinfor-matics, 8(2):487–498, March2011. CODEN ITCBCY.ISSN 1545-5963 (print),1557-9964 (electronic).

Lamers:2008:PRX

[LSMF08] Susanna L. Lamers, MarcoSalemi, Michael S. McGrath,and Gary B. Fogel. Pre-diction of R5, X4, andR5X4 HIV-1 coreceptor us-age with evolved neural net-works. IEEE/ACM Trans-actions on ComputationalBiology and Bioinformatics,5(2):291–300, April 2008.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Liu:2011:CBA

[LSMW11] Weiguo Liu, Bertil Schmidt,and Wolfgang Muller-Wittig.CUDA-BLASTP: Accelerat-ing BLASTP on CUDA-enabled graphics hardware.IEEE/ACM Transactionson Computational Biologyand Bioinformatics, 8(6):1678–1684, November 2011.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Lee:2017:DPD

[LSTW+17] En-Shiun Annie Lee, Ho-Yin Antonio Sze-To, Man-Hon Wong, Kwong-Sak Le-ung, Terrence Chi-KongLau, and Andrew K. C.Wong. Discovering protein-DNA binding cores byaligned pattern clustering.IEEE/ACM Transactions onComputational Biology andBioinformatics, 14(2):254–263, March 2017. CODENITCBCY. ISSN 1545-5963(print), 1557-9964 (elec-tronic).

Li:2020:UWE

[LSY+20] Jianqiang Li, Xiaofeng Shi,Zhu-Hong You, Hai-ChengYi, Zhuangzhuang Chen,Qiuzhen Lin, and MinFang. Using weighted ex-treme learning machine com-bined with scale-invariantfeature transform to pre-dict protein-protein interac-tions from protein evolution-ary information. IEEE/ACM

REFERENCES 224

Transactions on Computa-tional Biology and Bioin-formatics, 17(5):1546–1554,September 2020. CODENITCBCY. ISSN 1545-5963(print), 1557-9964 (elec-tronic). URL https://dl.acm.org/doi/10.1109/TCBB.2020.2965919.

Lones:2007:RMD

[LT07] Michael Lones and AndyTyrrell. Regulatory motifdiscovery using a populationclustering evolutionary algo-rithm. IEEE/ACM Trans-actions on ComputationalBiology and Bioinformat-ics, 4(3):403–414, July 2007.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Li:2017:RRB

[LT17] Fangfei Li and Yang Tang.Robust reachability of Booleancontrol networks. IEEE/ACM Transactions on Com-putational Biology and Bioin-formatics, 14(3):740–745,May 2017. CODEN ITCBCY.ISSN 1545-5963 (print),1557-9964 (electronic).

Lei:2013:CRC

[LTaS13] Jikai Lei, Prapaporn Techa-angkoon, and Yanni Sun.Chain-RNA: a comparativencRNA search tool based onthe two-dimensional chain al-gorithm. IEEE/ACM Trans-actions on ComputationalBiology and Bioinformatics,


Lu:2007:ISL

[LTL+07] Yijuan Lu, Qi Tian, FengLiu, Maribel Sanchez, andYufeng Wang. Interac-tive semisupervised learn-ing for microarray analy-sis. IEEE/ACM Transac-tions on Computational Bi-ology and Bioinformatics,4(2):190–203, April 2007.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Li:2019:NSA

[LTL+19] Min Li, Li Tang, Zhongxi-ang Liao, Junwei Luo, Fang-Xiang Wu, Yi Pan, andJianxin Wang. A novel scaf-folding algorithm based oncontig error correction andpath extension. IEEE/ACMTransactions on Computa-tional Biology and Bioinfor-matics, 16(3):764–773, May2019. CODEN ITCBCY.ISSN 1545-5963 (print),1557-9964 (electronic).

Lazar:2012:SFT

[LTM+12] Cosmin Lazar, JonatanTaminau, Stijn Meganck,David Steenhoff, Alain Co-letta, Colin Molter, Vir-ginie de Schaetzen, RobinDuque, Hugues Bersini, andAnn Nowe. A survey onfilter techniques for fea-

REFERENCES 225

ture selection in gene ex-pression microarray analy-sis. IEEE/ACM Transac-tions on Computational Bi-ology and Bioinformatics, 9(4):1106–1119, July 2012.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Lazar:2013:GNA

[LTM+13] Cosmin Lazar, JonatanTaminau, Stijn Meganck,David Steenhoff, Alain Co-letta, David Y. Weiss So-lis, Colin Molter, RobinDuque, Hugues Bersini, andAnn Nowe. GENESHIFT:a nonparametric approachfor integrating microarraygene expression data basedon the inner product as adistance measure betweenthe distributions of genes.IEEE/ACM Transactions onComputational Biology andBioinformatics, 10(2):383–392, March 2013. CODENITCBCY. ISSN 1545-5963(print), 1557-9964 (elec-tronic).

Luo:2019:DGP

[LTRW19] Ping Luo, Li-Ping Tian,Jishou Ruan, and Fang-Xiang Wu. Disease geneprediction by integratingPPI networks, clinical RNA-seq data and OMIM data.IEEE/ACM Transactions onComputational Biology andBioinformatics, 16(1):222–232, January 2019. CODEN


Lieberman:2011:VEA

[LTwG+11] Michael D. Lieberman, SimaTaheri, whatever Guo, Fate-meh Mirrashed, Inbal Yahav,Aleks Aris, and Ben Shnei-derman. Visual explorationacross biomedical databases.IEEE/ACM Transactions onComputational Biology andBioinformatics, 8(2):536–550, March 2011. CODENITCBCY. ISSN 1545-5963(print), 1557-9964 (elec-tronic).

Langdon:2010:SSD

[LUdSCH10] W. B. Langdon, G. J. G.Upton, R. da Silva Ca-margo, and A. P. Harri-son. A survey of spa-tial defects in Homo Sapi-ens Affymetrix GeneChips.IEEE/ACM Transactions onComputational Biology andBioinformatics, 7(4):647–653, October 2010. CODENITCBCY. ISSN 1545-5963(print), 1557-9964 (elec-tronic).

Labarre:2014:MPL

[LV14] Anthony Labarre and SiccoVerwer. Merging partially la-belled trees: hardness and adeclarative programming so-lution. IEEE/ACM Trans-actions on ComputationalBiology and Bioinformatics,11(2):389–397, March 2014.

REFERENCES 226


Liu:2013:NBC

[LW13a] Kuan-Liang Liu and Tzu-Tsung Wong. Naıve Bayesianclassifiers with multinomialmodels for rRNA taxonomicassignment. IEEE/ACMTransactions on Computa-tional Biology and Bioinfor-matics, 10(5):1, September2013. CODEN ITCBCY.ISSN 1545-5963 (print),1557-9964 (electronic).

Luo:2013:ARA

[LW13b] Chao Luo and XingyuanWang. Algebraic repre-sentation of asynchronousmultiple-valued networksand its dynamics. IEEE/ACM Transactions on Com-putational Biology and Bioin-formatics, 10(4):927–938,July 2013. CODEN ITCBCY.ISSN 1545-5963 (print),1557-9964 (electronic).

Luo:2015:GES

[LW15] Feng Luo and Xintao Wu.Guest editorial for spe-cial section on BIBM 2013.IEEE/ACM Transactions onComputational Biology andBioinformatics, 12(2):252–253, March 2015. CODENITCBCY. ISSN 1545-5963(print), 1557-9964 (elec-tronic).

Li:2017:TUG

[LW17] Jianqiang Li and Fei Wang.Towards unsupervised geneselection: a matrix factoriza-tion framework. IEEE/ACMTransactions on Computa-tional Biology and Bioinfor-matics, 14(3):514–521, May2017. CODEN ITCBCY.ISSN 1545-5963 (print),1557-9964 (electronic).

Li:2018:CSI

[LW18] Xiangtao Li and Ka-ChunWong. A comparativestudy for identifying thechromosome-wide spatialclusters from high-throughputchromatin conformation cap-ture data. IEEE/ACMTransactions on Computa-tional Biology and Bioinfor-matics, 15(3):774–787, May2018. CODEN ITCBCY.ISSN 1545-5963 (print),1557-9964 (electronic).

Li:2019:EGW

[LW19a] Xiangtao Li and Ka-ChunWong. Elucidating genome-wide protein-RNA interac-tions using differential evolu-tion. IEEE/ACM Transac-tions on Computational Bi-ology and Bioinformatics, 16(1):272–282, January 2019.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Liu:2019:SPL

[LW19b] Cheng Liu and Hau SanWong. Structured penalized

REFERENCES 227

logistic regression for geneselection in gene expressiondata analysis. IEEE/ACMTransactions on Computa-tional Biology and Bioin-formatics, 16(1):312–321,January 2019. CODENITCBCY. ISSN 1545-5963(print), 1557-9964 (elec-tronic).

Liu:2014:MCP

[LWG+14] Xiaoqing Liu, Jun Wu,Haipeng Gong, ShengchunDeng, and Zengyou He. Min-ing conditional phosphory-lation motifs. IEEE/ACMTransactions on Computa-tional Biology and Bioin-formatics, 11(5):915–927,September 2014. CODENITCBCY. ISSN 1545-5963(print), 1557-9964 (elec-tronic).

Liu:2018:RNN

[LWG+18] Jin-Xing Liu, Dong Wang,Ying-Lian Gao, Chun-HouZheng, Yong Xu, and JiguoYu. Regularized non-negative matrix factoriza-tion for identifying differen-tially expressed genes andclustering samples: a sur-vey. IEEE/ACM Transac-tions on Computational Bi-ology and Bioinformatics,15(3):974–987, May 2018.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Lan:2018:PMD

[LWL+18] Wei Lan, Jianxin Wang, MinLi, Jin Liu, Fang-Xiang Wu,and Yi Pan. PredictingMicroRNA-disease associa-tions based on improved Mi-croRNA and disease simi-larities. IEEE/ACM Trans-actions on ComputationalBiology and Bioinformatics,15(6):1774–1782, November2018. CODEN ITCBCY.ISSN 1545-5963 (print),1557-9964 (electronic).

Luo:2019:CDR

[LWL+19] Huimin Luo, Jianxin Wang,Min Li, Junwei Luo, PengNi, Kaijie Zhao, Fang-XiangWu, and Yi Pan. Com-putational drug reposition-ing with random walk ona heterogeneous network.IEEE/ACM Transactionson Computational Biologyand Bioinformatics, 16(6):1890–1900, November 2019.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic). URL https://dl.acm.org/doi/abs/10.1109/TCBB.2018.2832078.

Liu:2020:SSS

[LWL+20] Yong Liu, Min Wu, Cheng-hao Liu, Xiao-Li Li, andJie Zheng. SL2MF: Pre-dicting synthetic lethalityin human cancers via lo-gistic matrix factorization.IEEE/ACM Transactions onComputational Biology and

REFERENCES 228

Bioinformatics, 17(3):748–757, May 2020. CODENITCBCY. ISSN 1545-5963(print), 1557-9964 (elec-tronic). URL https://dl.acm.org/doi/10.1109/TCBB.2019.2909908.

Loohuis:2014:IDD

[LWM14] Loes Olde Loohuis, AndreasWitzel, and Bud Mishra. Im-proving detection of drivergenes: power-law null modelof copy number variationin cancer. IEEE/ACMTransactions on Computa-tional Biology and Bioin-formatics, 11(6):1260–1263,November 2014. CODENITCBCY. ISSN 1545-5963(print), 1557-9964 (elec-tronic).

Luo:2020:GGF

[LWS+20] Junwei Luo, Jianxin Wang,Juan Shang, Huimin Luo,Min Li, Fang-Xiang Wu, andYi Pan. GapReduce: agap filling algorithm basedon partitioned read sets.IEEE/ACM Transactions onComputational Biology andBioinformatics, 17(3):877–886, May 2020. CODENITCBCY. ISSN 1545-5963(print), 1557-9964 (elec-tronic). URL https://dl.acm.org/doi/10.1109/TCBB.2018.2789909.

Liu:2018:IAD

[LWT+18] Jin Liu, Jianxin Wang, Zhen-jun Tang, Bin Hu, Fang-Xiang Wu, and Yi Pan.

Improving Alzheimer’s dis-ease classification by com-bining multiple measures.IEEE/ACM Transactionson Computational Biologyand Bioinformatics, 15(5):1649–1659, September 2018.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Liu:2012:IBS

[LWZ12] Li-Zhi Liu, Fang-Xiang Wu,and W. J. Zhang. Inferenceof biological S-system us-ing the separable estimationmethod and the genetic al-gorithm. IEEE/ACM Trans-actions on ComputationalBiology and Bioinformat-ics, 9(4):955–965, July 2012.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Liu:2016:CIB

[LXG+16] Jin-Xing Liu, Yong Xu,Ying-Lian Gao, Chun-HouZheng, Dong Wang, andQi Zhu. A class-information-based sparse componentanalysis method to iden-tify differentially expressedgenes on RNA-Seq data.IEEE/ACM Transactions onComputational Biology andBioinformatics, 13(2):392–398, March 2016. CODENITCBCY. ISSN 1545-5963(print), 1557-9964 (elec-tronic).

REFERENCES 229

Liu:2015:RBT

[LXZ+15] Jin-Xing Liu, Yong Xu,Chun-Hou Zheng, HengKong, and Zhi-Hui Lai.RPCA-based tumor classifi-cation using gene expressiondata. IEEE/ACM Trans-actions on ComputationalBiology and Bioinformatics,12(4):964–970, July 2015.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Li:2016:EDP

[LYH+16] Cong Li, Can Yang, GregHather, Ray Liu, andHongyu Zhao. Efficient drug-pathway association anal-ysis via integrative penal-ized matrix decomposition.IEEE/ACM Transactions onComputational Biology andBioinformatics, 13(3):531–540, May 2016. CODENITCBCY. ISSN 1545-5963(print), 1557-9964 (elec-tronic).

Lerner:2007:CSI

[LYK07] Boaz Lerner, Josepha Yeshaya,and Lev Koushnir. Onthe classification of a smallimbalanced cytogenetic im-age database. IEEE/ACMTransactions on Computa-tional Biology and Bioinfor-matics, 4(2):204–215, April2007. CODEN ITCBCY.ISSN 1545-5963 (print),1557-9964 (electronic).

Li:2017:PSP

[LYL+17] Jian-Qiang Li, Zhu-HongYou, Xiao Li, Zhong Ming,and Xing Chen. PSPEL:In silico prediction of self-interacting proteins fromamino acids sequences usingensemble learning. IEEE/ACM Transactions on Com-putational Biology and Bioin-formatics, 14(5):1165–1172,September 2017. CODENITCBCY. ISSN 1545-5963(print), 1557-9964 (elec-tronic).

Lei:2020:AFS

[LYW20] Xiujuan Lei, Xiaoqin Yang,and Fang-Xiang Wu. Ar-tificial fish swarm opti-mization based method toidentify essential proteins.IEEE/ACM Transactions onComputational Biology andBioinformatics, 17(2):495–505, March 2020. CODENITCBCY. ISSN 1545-5963(print), 1557-9964 (elec-tronic). URL https://dl.acm.org/doi/abs/10.1109/TCBB.2018.2865567.

Liu:2019:UMJ

[LYY+19] Kefei Liu, Jieping Ye, YangYang, Li Shen, and HuiJiang. A unified model forjoint normalization and dif-ferential gene expression de-tection in RNA-seq data.IEEE/ACM Transactions onComputational Biology andBioinformatics, 16(2):442–454, March 2019. CODEN

REFERENCES 230

ITCBCY. ISSN 1545-5963(print), 1557-9964 (elec-tronic). URL https://dl.acm.org/doi/abs/10.1109/TCBB.2018.2790918.

Li:2018:FWI

[LZ18a] Youyuan Li and YingpingZhuang. fmpRPMF: aWeb implementation for pro-tein identification by robustpeptide mass fingerprinting.IEEE/ACM Transactionson Computational Biologyand Bioinformatics, 15(5):1728–1731, September 2018.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Lin:2018:PHR

[LZ18b] Xiaoli Lin and XiaolongZhang. Prediction ofhot regions in PPIs basedon improved local com-munity structure detecting.IEEE/ACM Transactionson Computational Biologyand Bioinformatics, 15(5):1470–1479, September 2018.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Liao:2014:NUB

[LZGZ14] Ruiqi Liao, Ruichang Zhang,Jihong Guan, and ShuigengZhou. A new unsu-pervised binning approachfor metagenomic sequencesbased on N -grams and au-tomatic feature weighting.IEEE/ACM Transactions on

Computational Biology andBioinformatics, 11(1):42–54,January 2014. CODENITCBCY. ISSN 1545-5963(print), 1557-9964 (elec-tronic).

Liang:2018:OGS

[LZH18] Xianpeng Liang, Lin Zhu,and De-Shuang Huang. Op-timization of gene set anno-tations using robust trace-norm multitask learning.IEEE/ACM Transactions onComputational Biology andBioinformatics, 15(3):1016–1021, May 2018. CODENITCBCY. ISSN 1545-5963(print), 1557-9964 (elec-tronic).

Liu:2017:IMD

[LZHZ17] Yuansheng Liu, XiangxiangZeng, Zengyou He, and QuanZou. Inferring MicroRNA-disease associations by ran-dom walk on a heterogeneousnetwork with multiple datasources. IEEE/ACM Trans-actions on ComputationalBiology and Bioinformatics,14(4):905–915, July 2017.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Li:2019:MSM

[LZL+19] Min Li, Ruiqing Zheng, Yao-hang Li, Fang-Xiang Wu,and Jianxin Wang. MGT–SM: a method for construct-ing cellular signal transduc-tion networks. IEEE/ACM

REFERENCES 231

Transactions on Computa-tional Biology and Bioin-formatics, 16(2):417–424,March 2019. CODENITCBCY. ISSN 1545-5963(print), 1557-9964 (elec-tronic). URL https://dl.acm.org/doi/abs/10.1109/TCBB.2017.2705143.

Li:2020:MMT

[LZL+20] Tao Li, Xiankai Zhang, FengLuo, Fang-Xiang Wu, andJianxin Wang. MultiMo-tifMaker: a multi-thread toolfor identifying DNA methy-lation motifs from Pacbioreads. IEEE/ACM Transac-tions on Computational Bi-ology and Bioinformatics, 17(1):220–225, January 2020.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic). URL https://dl.acm.org/doi/abs/10.1109/TCBB.2018.2861399.

Liu:2020:BBP

[LZQ+20] Guang-Hui Liu, Bei-WeiZhang, Gang Qian, BinWang, Bo Mao, and IsabelleBichindaritz. Bioimage-based prediction of proteinsubcellular location in hu-man tissue with ensemblefeatures and deep networks.IEEE/ACM Transactionson Computational Biologyand Bioinformatics, 17(6):1966–1980, November 2020.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic). URL https://


Li:2020:NIM

[LZW20] Xiangtao Li, Shixiong Zhang,and Ka-Chun Wong. Nature-inspired multiobjective epis-tasis elucidation from genome-wide association studies.IEEE/ACM Transactions onComputational Biology andBioinformatics, 17(1):226–237, January 2020. CO-DEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic). URL https://dl.acm.org/doi/abs/10.1109/TCBB.2018.2849759.

Lin:2019:IBE

[LZX+19] Yan Lin, Fa-Zhan Zhang,Kai Xue, Yi-Zhou Gao, andFeng-Biao Guo. Identify-ing bacterial essential genesbased on a feature-integratedmethod. IEEE/ACM Trans-actions on ComputationalBiology and Bioinformatics,16(4):1274–1279, July 2019.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Lin:2020:ECH

[LZX20] Xiaoli Lin, Xiaolong Zhang,and Xin Xu. Efficient clas-sification of hot spots andhub protein interfaces byrecursive feature elimina-tion and gradient boosting.IEEE/ACM Transactionson Computational Biologyand Bioinformatics, 17(5):1525–1534, September 2020.

REFERENCES 232

CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic). URL https://dl.acm.org/doi/10.1109/TCBB.2019.2931717.

Liu:2016:NMP

[LZZ+16] Yuanning Liu, Qi Zhao, HaoZhang, Rui Xu, Yang Li,and Liyan Wei. A newmethod to predict RNAsecondary structure basedon RNA folding simulation.IEEE/ACM Transactionson Computational Biologyand Bioinformatics, 13(5):990–995, September 2016.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Mimaroglu:2012:DDC

[MA12] Selim Mimaroglu and EminAksehirli. DICLENS: Di-visive clustering ensemblewith automatic cluster num-ber. IEEE/ACM Transac-tions on Computational Bi-ology and Bioinformatics, 9(2):408–420, March 2012.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Mahata:2010:ECH

[Mah10] Pritha Mahata. Exploratoryconsensus of hierarchicalclusterings for melanomaand breast cancer. IEEE/ACM Transactions on Com-putational Biology and Bioin-formatics, 7(1):138–152, Jan-uary 2010. CODEN ITCBCY.


Maitra:2009:IPO

[Mai09] Ranjan Maitra. Initializingpartition-optimization algo-rithms. IEEE/ACM Trans-actions on ComputationalBiology and Bioinformatics,6(1):144–157, January 2009.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Mamitsuka:2005:ELK

[Mam05] Hiroshi Mamitsuka. Es-sential latent knowledgefor protein-protein inter-actions: Analysis by anunsupervised learning ap-proach. IEEE/ACM Trans-actions on ComputationalBiology and Bioinformatics,2(2):119–130, April 2005.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Matsen:2007:OCT

[Mat07] Frederick Matsen. Opti-mization over a class of treeshape statistics. IEEE/ACMTransactions on Computa-tional Biology and Bioinfor-matics, 4(3):506–512, July2007. CODEN ITCBCY.ISSN 1545-5963 (print),1557-9964 (electronic).

Matsen:2009:FTI

[Mat09] Frederick A. Matsen. Fouriertransform inequalities forphylogenetic trees. IEEE/

REFERENCES 233

ACM Transactions on Com-putational Biology and Bioin-formatics, 6(1):89–95, Jan-uary 2009. CODEN ITCBCY.ISSN 1545-5963 (print),1557-9964 (electronic).

Matthews:2015:HCL

[Mat15] Suzanne J. Matthews. Het-erogeneous compression oflarge collections of evolu-tionary trees. IEEE/ACMTransactions on Computa-tional Biology and Bioinfor-matics, 12(4):807–814, July2015. CODEN ITCBCY.ISSN 1545-5963 (print),1557-9964 (electronic).

Mazza:2012:HPC

[Maz12] Tommaso Mazza. High per-formance computational sys-tems biology. IEEE/ACMTransactions on Computa-tional Biology and Bioinfor-matics, 9(3):641–642, May2012. CODEN ITCBCY.ISSN 1545-5963 (print),1557-9964 (electronic).

Moore:2016:EMF

[MB16] Erin Jessica Moore and Thir-machos Bourlai. Expecta-tion maximization of fre-quent patterns, a specific,local, pattern-based biclus-tering algorithm for biolog-ical datasets. IEEE/ACMTransactions on Computa-tional Biology and Bioin-formatics, 13(5):812–824,September 2016. CODENITCBCY. ISSN 1545-5963


Mallik:2020:WWC

[MB20] Saurav Mallik and Sang-hamitra Bandyopadhyay.WeCoMXP: Weighted con-nectivity measure integrat-ing co-methylation, co-expression and protein-protein interactions for gene-module detection. IEEE/ACM Transactions on Com-putational Biology and Bioin-formatics, 17(2):690–703,March 2020. CODENITCBCY. ISSN 1545-5963(print), 1557-9964 (elec-tronic). URL https://dl.acm.org/doi/abs/10.1109/TCBB.2018.2868348.

Murugesan:2017:BMI

[MBB+17] Sugeerth Murugesan, Kristo-pher Bouchard, Jesse A.Brown, Bernd Hamann,William W. Seeley, AndrewTrujillo, and Gunther H. We-ber. Brain modulyzer: In-teractive visual analysis offunctional brain connectiv-ity. IEEE/ACM Transac-tions on Computational Bi-ology and Bioinformatics,14(4):805–818, July 2017.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Muselli:2011:MMV

[MBF+11] Marco Muselli, AlbertoBertoni, Marco Frasca,Alessandro Beghini, Francesca

REFERENCES 234

Ruffino, and Giorgio Valen-tini. A mathematicalmodel for the validationof gene selection methods.IEEE/ACM Transactionson Computational Biologyand Bioinformatics, 8(5):1385–1392, September 2011.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Murthy:2013:CAC

[MBF+13] Abhishek Murthy, Ezio Bar-tocci, Flavio H. Fenton,James Glimm, Richard A.Gray, Elizabeth M. Cherry,Scott A. Smolka, and RaduGrosu. Curvature analysisof cardiac excitation wave-fronts. IEEE/ACM Trans-actions on ComputationalBiology and Bioinformatics,10(2):323–336, March 2013.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Mazza:2012:RTP

[MBGP12] Tommaso Mazza, Paolo Bal-larini, Rosita Guido, andDavide Prandi. The rele-vance of topology in parallelsimulation of biological net-works. IEEE/ACM Trans-actions on ComputationalBiology and Bioinformat-ics, 9(3):911–923, May 2012.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Michels:2019:RBM

[MBJ19] Tim Michels, Dimitri Berh,and Xiaoyi Jiang. AnRJMCMC-based method fortracking and resolving col-lisions of Drosophila lar-vae. IEEE/ACM Transac-tions on Computational Bi-ology and Bioinformatics,16(2):465–474, March 2019.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic). URL https://dl.acm.org/doi/abs/10.1109/TCBB.2017.2779141.

Matsen:2018:TRT

[MBKK18] Frederick A. Matsen, Sara C.Billey, Arnold Kas, and Mat-jaz Konvalinka. Tangle-grams: a reduction toolfor mathematical phyloge-netics. IEEE/ACM Transac-tions on Computational Bi-ology and Bioinformatics, 15(1):343–349, January 2018.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Martins:2018:CMT

[MBP+18] Daniel P. Martins, Michael Tayn-nan Barros, MassimilianoPierobon, Meenakshisun-daram Kandhavelu, PietroLio’, and Sasitharan Bal-asubramaniam. Compu-tational models for trap-ping Ebola virus using engi-neered bacteria. IEEE/ACMTransactions on Computa-tional Biology and Bioin-formatics, 15(6):2017–2027,

REFERENCES 235

November 2018. CODENITCBCY. ISSN 1545-5963(print), 1557-9964 (elec-tronic).

Moon:2019:SIC

[MBP+19] SeongRyeol Moon, CurtBalch, Sungjin Park, Jin-hyuk Lee, Jiyong Sung, andSeungyoon Nam. System-atic inspection of the clinicalrelevance of TP53 missensemutations in gastric cancer.IEEE/ACM Transactionson Computational Biologyand Bioinformatics, 16(5):1693–1701, September 2019.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Mehmood:2015:PLS

[MBS15] Tahir Mehmood, Jon Bohlin,and Lars Snipen. A partialleast squares based proce-dure for upstream sequenceclassification in prokaryotes.IEEE/ACM Transactions onComputational Biology andBioinformatics, 12(3):560–567, May 2015. CODENITCBCY. ISSN 1545-5963(print), 1557-9964 (elec-tronic).

McIntosh:2007:HCR

[MC07] Tara McIntosh and SanjayChawla. High confidence rulemining for microarray anal-ysis. IEEE/ACM Transac-tions on Computational Bi-ology and Bioinformatics, 4(4):611–623, October 2007.


Masseroli:2016:IQG

[MCC16] Marco Masseroli, Arif Canakoglu,and Stefano Ceri. Integra-tion and querying of ge-nomic and proteomic seman-tic annotations for biomed-ical knowledge extraction.IEEE/ACM Transactions onComputational Biology andBioinformatics, 13(2):209–219, March 2016. CODENITCBCY. ISSN 1545-5963(print), 1557-9964 (elec-tronic).

Mena-Chalco:2008:IPC

[MCCZC08] Jesus Mena-Chalco, HelaineCarrer, Yossi Zana, andRoberto M. Cesar Jr. Iden-tification of protein cod-ing regions using the mod-ified Gabor-wavelet trans-form. IEEE/ACM Trans-actions on ComputationalBiology and Bioinformatics,5(2):198–207, April 2008.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Merelli:2011:IBS

[MCD+11] Ivan Merelli, Paolo Cozzi,Daniele D’Agostino, AndreaClematis, and Luciano Mi-lanesi. Image-based sur-face matching algorithm ori-ented to structural biol-ogy. IEEE/ACM Transac-tions on Computational Bi-

REFERENCES 236


Mirceva:2012:EAR

[MCDD12] Georgina Mirceva, IvanaCingovska, Zoran Dimov,and Danco Davcev. Effi-cient approaches for retriev-ing protein tertiary struc-tures. IEEE/ACM Transac-tions on Computational Bi-ology and Bioinformatics, 9(4):1166–1179, July 2012.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Mei:2015:ESN

[MCH+15] Yongguo Mei, Adria Carbo,Stefan Hoops, Raquel Honte-cillas, and Josep Bassaganya-Riera. ENISI SDE: a newweb-based tool for mod-eling stochastic processes.IEEE/ACM Transactions onComputational Biology andBioinformatics, 12(2):289–297, March 2015. CODENITCBCY. ISSN 1545-5963(print), 1557-9964 (elec-tronic).

Moskovitch:2017:PCO

[MCHT17] Robert Moskovitch, HyunmiChoi, George Hripcsak, andNicholas Tatonetti. Progno-sis of clinical outcomes withtemporal patterns and expe-riences with one class fea-ture selection. IEEE/ACM

Transactions on Computa-tional Biology and Bioinfor-matics, 14(3):555–563, May2017. CODEN ITCBCY.ISSN 1545-5963 (print),1557-9964 (electronic).

Mkrtchyan:2017:OLS

[MCRC17] Katya Mkrtchyan, AnirbanChakraborty, and Amit K.Roy-Chowdhury. Optimallandmark selection for reg-istration of 4D confocalimage stacks in Arabidop-sis . IEEE/ACM Transac-tions on Computational Bi-ology and Bioinformatics,14(2):457–467, March 2017.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Mohsenizadeh:2018:OOB

[MDD18] Daniel N. Mohsenizadeh,Roozbeh Dehghannasiri, andEdward R. Dougherty. Op-timal objective-based exper-imental design for uncer-tain dynamical gene net-works with experimental er-ror. IEEE/ACM Transac-tions on Computational Bi-ology and Bioinformatics, 15(1):218–230, January 2018.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Mitra:2011:GNS

[MDH11] Sushmita Mitra, RanajitDas, and Yoichi Hayashi. Ge-netic networks and soft com-puting. IEEE/ACM Trans-

REFERENCES 237

actions on ComputationalBiology and Bioinformatics,8(1):94–107, January 2011.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Mourad:2013:DPS

[MDM13] Ramy Mourad, Zaher Dawy,and Faruck Morcos. Design-ing pooling systems for noisyhigh-throughput protein-protein interaction experi-ments using Boolean com-pressed sensing. IEEE/ACMTransactions on Computa-tional Biology and Bioin-formatics, 10(6):1478–1490,November 2013. CODENITCBCY. ISSN 1545-5963(print), 1557-9964 (elec-tronic).

Mu:2018:OOC

[MDPR18] Chunyan Mu, Peter Dit-trich, David Parker, andJonathan E. Rowe. Organisation-oriented coarse graining andrefinement of stochastic reac-tion networks. IEEE/ACMTransactions on Computa-tional Biology and Bioin-formatics, 15(4):1152–1166,July 2018. CODEN ITCBCY.ISSN 1545-5963 (print),1557-9964 (electronic).

Markin:2019:CMP

[ME19a] Alexey Markin and OliverEulenstein. ComputingManhattan path-differencemedian trees: a practi-cal local search approach.


Markin:2019:CMT

[ME19b] Alexey Markin and OliverEulenstein. Cophenetic me-dian trees. IEEE/ACMTransactions on Computa-tional Biology and Bioin-formatics, 16(5):1459–1470,September 2019. CODENITCBCY. ISSN 1545-5963(print), 1557-9964 (elec-tronic).

Markin:2019:ELS

[ME19c] Alexey Markin and OliverEulenstein. Efficient lo-cal search for Euclideanpath-difference median trees.IEEE/ACM Transactions onComputational Biology andBioinformatics, 16(4):1374–1385, July 2019. CODENITCBCY. ISSN 1545-5963(print), 1557-9964 (elec-tronic).

Messaoudi:2014:BSS

[MEOL14] Imen Messaoudi, Afef Elloumi-Oueslati, and Zied Lachiri.Building specific signals fromfrequency chaos game and re-vealing periodicities using asmoothed Fourier analysis.IEEE/ACM Transactionson Computational Biologyand Bioinformatics, 11(5):

REFERENCES 238

863–877, September 2014.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Monteiro:2018:UML

[MFF+18] Miguel Monteiro, Ana Cata-rina Fonseca, Ana TeresaFreitas, Teresa Pinho eMelo, Alexandre P. Fran-cisco, Jose M. Ferro, andArlindo L. Oliveira. Us-ing machine learning to im-prove the prediction of func-tional outcome in ischemicstroke patients. IEEE/ACMTransactions on Computa-tional Biology and Bioin-formatics, 15(6):1953–1959,November 2018. CODENITCBCY. ISSN 1545-5963(print), 1557-9964 (elec-tronic).

Mazza:2015:FIA

[MFS+15] Tommaso Mazza, Cate-rina Fusilli, Chiara Sara-cino, Gianluigi Mazzoccoli,Francesca Tavano, ManlioVinciguerra, and ValerioPazienza. Functional impactof autophagy-related geneson the homeostasis and dy-namics of pancreatic cancercell lines. IEEE/ACM Trans-actions on ComputationalBiology and Bioinformatics,12(3):667–678, May 2015.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Mina:2014:IRL

[MG14] Marco Mina and Pietro Hi-ram Guzzi. Improvingthe robustness of local net-work alignment: design andextensive assessment of aMarkov clustering-based ap-proach. IEEE/ACM Trans-actions on ComputationalBiology and Bioinformatics,11(3):561–572, May 2014.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Mykowiecka:2019:CEE

[MG19] Agnieszka Mykowiecka andPawel Gorecki. Credibility ofevolutionary events in genetrees. IEEE/ACM Trans-actions on ComputationalBiology and Bioinformatics,16(3):713–726, May 2019.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Milano:2019:GNA

[MGC19] Marianna Milano, Pietro Hi-ram Guzzi, and Mario Can-nataro. GLAlign: a novelalgorithm for local networkalignment. IEEE/ACMTransactions on Computa-tional Biology and Bioin-formatics, 16(6):1958–1969,November 2019. CODENITCBCY. ISSN 1545-5963(print), 1557-9964 (elec-tronic). URL https://dl.acm.org/doi/abs/10.1109/TCBB.2018.2830323.

REFERENCES 239

Mak:2008:PPS

[MGK08] Man-Wai Mak, Jian Guo,and Sun-Yuan Kung. Pair-ProSVM: Protein subcellu-lar localization based on lo-cal pairwise profile align-ment and SVM. IEEE/ACMTransactions on Computa-tional Biology and Bioinfor-matics, 5(3):416–422, July2008. CODEN ITCBCY.ISSN 1545-5963 (print),1557-9964 (electronic).

Mohammadi:2017:TAT

[MGKG17] Shahin Mohammadi, David F.Gleich, Tamara G. Kolda,and Ananth Grama. Tri-angular alignment TAME:a tensor-based approach forhigher-order network align-ment. IEEE/ACM Trans-actions on ComputationalBiology and Bioinformatics,14(6):1446–1458, November2017. CODEN ITCBCY.ISSN 1545-5963 (print),1557-9964 (electronic).

Ma:2012:SBP

[MGL+12] Xin Ma, Jing Guo, Hong-DeLiu, Jian-Ming Xie, and XiaoSun. Sequence-based predic-tion of DNA-binding residuesin proteins with conservationand correlation information.IEEE/ACM Transactionson Computational Biologyand Bioinformatics, 9(6):1766–1775, November 2012.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Mottelet:2017:MFA

[MGS17] Stephane Mottelet, GilGaullier, and Georges Sadaka.Metabolic flux analysis inisotope labeling experimentsusing the adjoint approach.IEEE/ACM Transactions onComputational Biology andBioinformatics, 14(2):491–497, March 2017. CODENITCBCY. ISSN 1545-5963(print), 1557-9964 (elec-tronic).

Ma:2015:PPR

[MGXS15] Xin Ma, Jing Guo, Ke Xiao,and Xiao Sun. PRBP: Pre-diction of RNA-binding pro-teins using a random for-est algorithm combined withan RNA-binding residue pre-dictor. IEEE/ACM Trans-actions on ComputationalBiology and Bioinformatics,12(6):1385–1393, November2015. CODEN ITCBCY.ISSN 1545-5963 (print),1557-9964 (electronic).

Huang:2013:EEO

[mHB13] Yao ming Huang and ChrisBystroff. Expanded explo-rations into the optimiza-tion of an energy function forprotein design. IEEE/ACMTransactions on Computa-tional Biology and Bioin-formatics, 10(5):1176–1187,September 2013. CODENITCBCY. ISSN 1545-5963(print), 1557-9964 (elec-tronic).

REFERENCES 240

Ma:2020:CIH

[MHHJ20] Yuanyuan Ma, Xiaohua Hu,Tingting He, and Xing-peng Jiang. Clusteringand integrating of hetero-geneous microbiome databy joint symmetric nonneg-ative matrix factorizationwith Laplacian regulariza-tion. IEEE/ACM Trans-actions on ComputationalBiology and Bioinformatics,17(3):788–795, May 2020.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic). URL https://dl.acm.org/doi/10.1109/TCBB.2017.2756628.

Marschall:2012:PAA

[MHKR12] Tobias Marschall, InkeHerms, Hans-Michael Kaltenbach,and Sven Rahmann. Proba-bilistic arithmetic automataand their applications. IEEE/ACM Transactions on Com-putational Biology and Bioin-formatics, 9(6):1737–1750,November 2012. CODENITCBCY. ISSN 1545-5963(print), 1557-9964 (elec-tronic).

Michal:2007:FCM

[MIC+07] Shahar Michal, Tor Ivry,Omer Cohen, Moshe Sipper,and Danny Barash. Find-ing a common motif of RNAsequences using genetic pro-gramming: The GeRNAMosystem. IEEE/ACM Trans-actions on ComputationalBiology and Bioinformatics,

4(4):596–610, October 2007.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Mirzal:2014:NTR

[Mir14] Andri Mirzal. Nonpara-metric Tikhonov regular-ized NMF and its appli-cation in cancer clustering.IEEE/ACM Transactionson Computational Biologyand Bioinformatics, 11(6):1208–1217, November 2014.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Milenkovic:2018:GLB

[MJ18] Tijana Milenkovic and Sarath Chan-dra Janga. Great LakesBioinformatics ConferenceGLBIO 2015 special sectioneditorial. IEEE/ACM Trans-actions on ComputationalBiology and Bioinformatics,15(4):1229–1230, July 2018.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Marczyk:2020:GXA

[MJPP20] Michal Marczyk, RomanJaksik, Andrzej Polan-ski, and Joanna Polanska.GaMRed-adaptive filteringof high-throughput biologicaldata. IEEE/ACM Transac-tions on Computational Bi-ology and Bioinformatics, 17(1):149–157, January 2020.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964

REFERENCES 241


Marhon:2016:PPC

[MK16] Sajid A. Marhon and Ste-fan C. Kremer. Prediction ofprotein coding regions usinga wide-range wavelet win-dow method. IEEE/ACMTransactions on Computa-tional Biology and Bioinfor-matics, 13(4):742–753, 2016.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Mozaffari-Kermani:2016:ISS

[MKARB16] Mehran Mozaffari-Kermani,Reza Azarderakhsh, KuiRen, and Jean-Luc Beuchat.Introduction to the specialsection on emerging securitytrends for biomedical com-putations, devices, and in-frastructures: guest edito-rial. IEEE/ACM Transac-tions on Computational Bi-ology and Bioinformatics,13(3):399–400, May 2016.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Maji:2020:SEA

[MKG20] Ranjan Kumar Maji, Sunir-mal Khatua, and ZhumurGhosh. A supervised en-semble approach for sensi-tive microRNA target pre-diction. IEEE/ACM Trans-actions on ComputationalBiology and Bioinformatics,

17(1):37–46, January 2020.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic). URL https://dl.acm.org/doi/abs/10.1109/TCBB.2018.2858252.

Mernberger:2011:SSG

[MKH11] Marco Mernberger, GerhardKlebe, and Eyke Huller-meier. SEGA: Semiglobalgraph alignment for structure-based protein comparison.IEEE/ACM Transactionson Computational Biologyand Bioinformatics, 8(5):1330–1343, September 2011.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Miyawaki-Kuwakado:2020:PMC

[MKKS20] Atsuko Miyawaki-Kuwakado,Soichiro Komori, and Fumi-hide Shiraishi. A promis-ing method for calculatingtrue steady-state metaboliteconcentrations in large-scalemetabolic reaction networkmodels. IEEE/ACM Trans-actions on ComputationalBiology and Bioinformatics,17(1):27–36, January 2020.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic). URL https://dl.acm.org/doi/abs/10.1109/TCBB.2018.2853724.

Matsieva:2017:RSF

[MKS+17] Julia Matsieva, Steven Kelk,Celine Scornavacca, ChrisWhidden, and Dan Gus-field. A resolution of the

REFERENCES 242

static formulation questionfor the problem of com-puting the history bound.IEEE/ACM Transactions onComputational Biology andBioinformatics, 14(2):404–417, March 2017. CODENITCBCY. ISSN 1545-5963(print), 1557-9964 (elec-tronic).

Meyer:2018:MMP

[ML18] Karlene Nicole Meyer andMichelle R. Lacey. Mod-eling methylation patternswith long read sequencingdata. IEEE/ACM Transac-tions on Computational Bi-ology and Bioinformatics, 15(4):1379–1389, July 2018.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Mo:2017:NMB

[MLZ17] Hongwei Mo, Lili Liu, andJiao Zhao. A new magne-totactic bacteria optimiza-tion algorithm based on mo-ment migration. IEEE/ACMTransactions on Computa-tional Biology and Bioinfor-matics, 14(1):15–26, January2017. CODEN ITCBCY.ISSN 1545-5963 (print),1557-9964 (electronic).

Min:2018:NRS

[MLZ18] Wenwen Min, Juan Liu, andShihua Zhang. Network-regularized sparse logisticregression models for clin-ical risk prediction and

biomarker discovery. IEEE/ACM Transactions on Com-putational Biology and Bioin-formatics, 15(3):944–953,May 2018. CODEN ITCBCY.ISSN 1545-5963 (print),1557-9964 (electronic).

Moskon:2014:SAC

[MM14a] Miha Moskon and MihaMraz. Systematic approachto computational design ofgene regulatory networkswith information processingcapabilities. IEEE/ACMTransactions on Computa-tional Biology and Bioin-formatics, 11(2):431–440,March 2014. CODENITCBCY. ISSN 1545-5963(print), 1557-9964 (elec-tronic).

Mukhopadhyay:2014:INR

[MM14b] Anirban Mukhopadhyay andMonalisa Mandal. Iden-tifying non-redundant genemarkers from microarraydata: a multiobjective vari-able length PSO-based ap-proach. IEEE/ACM Trans-actions on ComputationalBiology and Bioinformatics,11(6):1170–1183, November2014. CODEN ITCBCY.ISSN 1545-5963 (print),1557-9964 (electronic).

Muki-Marttunen:2017:AMB

[MM17] Tuomo Muki-Marttunen. Analgorithm for motif-basednetwork design. IEEE/ACMTransactions on Computa-

REFERENCES 243


Maulik:2013:MQB

[MMB+13] Ujjwal Maulik, AnirbanMukhopadhyay, Malay Bhat-tacharyya, Lars Kaderali,Benedikt Brors, Sanghami-tra Bandyopadhyay, andRoland Eils. Mining quasi-bicliques from HIV-1-humanprotein interaction network:a multiobjective bicluster-ing approach. IEEE/ACMTransactions on Computa-tional Biology and Bioin-formatics, 10(2):423–435,March 2013. CODENITCBCY. ISSN 1545-5963(print), 1557-9964 (elec-tronic).

Meira:2014:AMA

[MMFD14] Luis A. A. Meira, Vinıcius R.Maximo, Alvaro L. Fazenda,and Arlindo F. Da Con-ceicao. Acc-Motif: accel-erated network motif detec-tion. IEEE/ACM Trans-actions on ComputationalBiology and Bioinformat-ics, 11(5):853–862, Septem-ber 2014. CODEN ITCBCY.ISSN 1545-5963 (print),1557-9964 (electronic).

Meng:2015:ICG

[MMH15] Nan Meng, Raghu Machi-raju, and Kun Huang. Iden-

tify critical genes in de-velopment with consistentH3K4me2 patterns acrossmultiple tissues. IEEE/ACMTransactions on Computa-tional Biology and Bioin-formatics, 12(5):1104–1111,September 2015. CODENITCBCY. ISSN 1545-5963(print), 1557-9964 (elec-tronic).

Miklos:2010:MPI

[MMS10] Istvan Miklos, Bence Melykuti,and Krister Swenson. TheMetropolized partial im-portance sampling MCMCmixes slowly on minimum re-versal rearrangement paths.IEEE/ACM Transactions onComputational Biology andBioinformatics, 7(4):763–767, October 2010. CODENITCBCY. ISSN 1545-5963(print), 1557-9964 (elec-tronic).

Metsis:2014:DCN

[MMSH14] Vangelis Metsis, Fillia Make-don, Dinggang Shen, andHeng Huang. DNA copynumber selection using ro-bust structured sparsity-inducing norms. IEEE/ACMTransactions on Computa-tional Biology and Bioin-formatics, 11(1):138–181,January 2014. CODENITCBCY. ISSN 1545-5963(print), 1557-9964 (elec-tronic).

REFERENCES 244

Marchiori:2014:GEP

[MNA14] Elena Marchiori, AliouneNgom, and Raj Acharya.Guest editorial: patternrecognition in bioinformat-ics. IEEE/ACM Transac-tions on Computational Bi-ology and Bioinformatics,11(3):498–499, May 2014.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Mneimneh:2009:AOS

[Mne09] Saad Mneimneh. On theapproximation of optimalstructures for RNA–RNAinteraction. IEEE/ACMTransactions on Computa-tional Biology and Bioinfor-matics, 6(4):682–688, Octo-ber 2009. CODEN ITCBCY.ISSN 1545-5963 (print),1557-9964 (electronic).

Meskin:2013:PEB

[MNND13] N. Meskin, H. Nounou,M. Nounou, and A. Datta.Parameter estimation of bio-logical phenomena: an un-scented Kalman filter ap-proach. IEEE/ACM Trans-actions on ComputationalBiology and Bioinformatics,10(2):537–543, March 2013.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Mandou:2010:GEI

[MNPZ10] Ion Mandou, Giri Narasimhan,Yi Pan, and Yanqing Zhang.

Guest Editors’ introductionto the special section onbioinformatics research andapplications. IEEE/ACMTransactions on Computa-tional Biology and Bioinfor-matics, 7(4):577–578, Octo-ber 2010. CODEN ITCBCY.ISSN 1545-5963 (print),1557-9964 (electronic).

Ma:2009:GCU

[MNR09] Jianmin Ma, Minh N.Nguyen, and Jagath C.Rajapakse. Gene classi-fication using codon us-age and support vector ma-chines. IEEE/ACM Transac-tions on Computational Bi-ology and Bioinformatics, 6(1):134–143, January 2009.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Moret:2004:PNM

[MNW+04] Bernard M. E. Moret, LuayNakhleh, Tandy Warnow,C. Randal Linder, AnnaTholse, Anneke Padolina,Jerry Sun, and Ruth Timme.Phylogenetic networks: Mod-eling, reconstructibility, andaccuracy. IEEE/ACMTransactions on Computa-tional Biology and Bioinfor-matics, 1(1):13–23, January2004. CODEN ITCBCY.ISSN 1545-5963 (print),1557-9964 (electronic).

Madeira:2004:BAB

[MO04] Sara C. Madeira and Ar-

REFERENCES 245

lindo L. Oliveira. Biclus-tering algorithms for biolog-ical data analysis: a sur-vey. IEEE/ACM Transac-tions on Computational Bi-ology and Bioinformatics,1(1):24–45, January 2004.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Mossel:2007:DMT

[Mos07] Elchanan Mossel. Dis-torted metrics on treesand phylogenetic forests.IEEE/ACM Transactions onComputational Biology andBioinformatics, 4(1):108–116, January 2007. CODENITCBCY. ISSN 1545-5963(print), 1557-9964 (elec-tronic).

Maji:2013:RFC

[MP13] Pradipta Maji and SushmitaPaul. Rough-fuzzy cluster-ing for grouping functionallysimilar genes from microar-ray data. IEEE/ACM Trans-actions on ComputationalBiology and Bioinformatics,10(2):286–299, March 2013.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Malik:2019:RCS

[MP19] Laraib Malik and Rob Patro.Rich chromatin structureprediction from Hi-C data.IEEE/ACM Transactionson Computational Biologyand Bioinformatics, 16(5):


Misra:2015:PMI

[MPA15] Sanchit Misra, Kiran Pam-nany, and Srinivas Aluru.Parallel mutual informa-tion based construction ofgenome-scale networks onthe Intel Xeon Phi copro-cessor. IEEE/ACM Trans-actions on ComputationalBiology and Bioinformatics,12(5):1008–1020, September2015. CODEN ITCBCY.ISSN 1545-5963 (print),1557-9964 (electronic).

Mahoney:2012:MOB

[MPF12] Arthur W. Mahoney, Gre-gory J. Podgorski, andNicholas S. Flann. Multiob-jective optimization based-approach for discoveringnovel cancer therapies. IEEE/ACM Transactions on Com-putational Biology and Bioin-formatics, 9(1):169–184, Jan-uary 2012. CODEN ITCBCY.ISSN 1545-5963 (print),1557-9964 (electronic).

Minh:2009:BPD

[MPKvH09] Bui Quang Minh, FabioPardi, Steffen Klaere, andArndt von Haeseler. Bud-geted phylogenetic diver-sity on circular split sys-tems. IEEE/ACM Trans-actions on ComputationalBiology and Bioinformatics,

REFERENCES 246


Mitrofanova:2011:PPF

[MPM11] Antonina Mitrofanova, VladimirPavlovic, and Bud Mishra.Prediction of protein func-tions with gene ontologyand interspecies protein ho-mology data. IEEE/ACMTransactions on Computa-tional Biology and Bioinfor-matics, 8(3):775–784, May/June 2011. CODENITCBCY. ISSN 1545-5963(print), 1557-9964 (elec-tronic).

Manica:2020:FAA

[MPP+20] Matteo Manica, RaphaelPolig, Mitra Purandare,Roland Mathis, ChristophHagleitner, and Marıa RodrıguezMartınez. FPGA accel-erated analysis of Booleangene regulatory networks.IEEE/ACM Transactionson Computational Biologyand Bioinformatics, 17(6):2141–2147, November 2020.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic). URL https://dl.acm.org/doi/10.1109/TCBB.2019.2936836.

Mizera:2019:TAA

[MPQY19] Andrzej Mizera, Jun Pang,Hongyang Qu, and QixiaYuan. Taming asynchronyfor attractor detection in

large Boolean networks.IEEE/ACM Transactions onComputational Biology andBioinformatics, 16(1):31–42,January 2019. CODENITCBCY. ISSN 1545-5963(print), 1557-9964 (elec-tronic).

Maximova:2018:SGP

[MPS18] Tatiana Maximova, ErionPlaku, and Amarda Shehu.Structure-guided proteintransition modeling with aprobabilistic roadmap algo-rithm. IEEE/ACM Trans-actions on ComputationalBiology and Bioinformatics,15(6):1783–1796, November2018. CODEN ITCBCY.ISSN 1545-5963 (print),1557-9964 (electronic).

Mizera:2018:APT

[MPSY18] Andrzej Mizera, Jun Pang,Cui Su, and Qixia Yuan.ASSA-PBN: a toolbox forprobabilistic Boolean net-works. IEEE/ACM Transac-tions on Computational Bi-ology and Bioinformatics, 15(4):1203–1216, July 2018.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Mandoiu:2009:GEI

[MPSZ09] Ion Mandoiu, Yi Pan, RajSunderraman, and Alexan-der Zelikovsky. Guest Ed-itors’ introduction to thespecial section on bioinfor-matics research and applica-

REFERENCES 247

tions. IEEE/ACM Trans-actions on ComputationalBiology and Bioinformatics,6(2):178–179, April 2009.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Mizera:2018:RTS

[MPY18] Andrzej Mizera, Jun Pang,and Qixia Yuan. Reviv-ing the two-state Markovchain approach. IEEE/ACMTransactions on Computa-tional Biology and Bioin-formatics, 15(5):1525–1537,September 2018. CODENITCBCY. ISSN 1545-5963(print), 1557-9964 (elec-tronic).

Mandoiu:2007:GEI

[MPZ07] Ion I. Mandoiu, Yi Pan, andAlexander Zelikovsky. GuestEditors’ introduction to theSpecial Section on Bioinfor-matics Research and Appli-cations. IEEE/ACM Trans-actions on ComputationalBiology and Bioinformatics,4(4):513–514, October 2007.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Mandoiu:2008:GEI

[MPZ08] Ion I. Mandoiu, Yi Pan, andAlexander Zelikovsky. GuestEditors’ introduction to thespecial section on bioinfor-matics research and applica-tions. IEEE/ACM Trans-actions on Computational

Biology and Bioinformat-ics, 5(3):321–322, July 2008.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Mossel:2010:ILS

[MR10] Elchanan Mossel and Se-bastien Roch. Incom-plete lineage sorting: Con-sistent phylogeny estima-tion from multiple loci.IEEE/ACM Transactions onComputational Biology andBioinformatics, 7(1):166–171, January 2010. CODENITCBCY. ISSN 1545-5963(print), 1557-9964 (elec-tronic).

Ma:2012:RNH

[MRB12] Lingyu Ma, Marco Reis-ert, and Hans Burkhardt.RENNSH: a novel α-helixidentification approach forintermediate resolution elec-tron density maps. IEEE/ACM Transactions on Com-putational Biology and Bioin-formatics, 9(1):228–239, Jan-uary 2012. CODEN ITCBCY.ISSN 1545-5963 (print),1557-9964 (electronic).

Ma:2018:MLR

[MRK18] Eddie Y. T. Ma, Sujee-van Ratnasingham, and Ste-fan C. Kremer. Machinelearned replacement of N -labels for basecalled se-quences in DNA barcod-ing. IEEE/ACM Transac-tions on Computational Bi-

REFERENCES 248


Mossel:2009:SEA

[MRS09] Elchanan Mossel, SebastienRoch, and Mike Steel.Shrinkage effect in ances-tral maximum likelihood.IEEE/ACM Transactions onComputational Biology andBioinformatics, 6(1):126–133, January 2009. CODENITCBCY. ISSN 1545-5963(print), 1557-9964 (elec-tronic).

Munoz:2010:RPG

[MS10] Adriana Munoz and DavidSankoff. Rearrangementphylogeny of genomes in con-tig form. IEEE/ACM Trans-actions on ComputationalBiology and Bioinformatics,7(4):579–587, October 2010.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Mauch:2011:EFE

[MS11] Sean Mauch and MarkStalzer. Efficient formula-tions for exact stochasticsimulation of chemical sys-tems. IEEE/ACM Trans-actions on ComputationalBiology and Bioinformatics,8(1):27–35, January 2011.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Maji:2017:SFS

[MS17] Pradipta Maji and EktaShah. Significance and func-tional similarity for iden-tification of disease genes.IEEE/ACM Transactionson Computational Biologyand Bioinformatics, 14(6):1419–1433, November 2017.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Mandal:2019:BIC

[MSB19] Koyel Mandal, Rosy Sarmah,and Dhruba Kumar Bhat-tacharyya. Biomarker iden-tification for cancer dis-ease using biclustering ap-proach: an empirical study.IEEE/ACM Transactions onComputational Biology andBioinformatics, 16(2):490–509, March 2019. CODENITCBCY. ISSN 1545-5963(print), 1557-9964 (elec-tronic). URL https://dl.acm.org/doi/abs/10.1109/TCBB.2018.2820695.

Mykowiecka:2018:IGS

[MSG18] Agnieszka Mykowiecka, PawelSzczesny, and Pawel Gorecki.Inferring gene-species as-signments in the presenceof horizontal gene transfer.IEEE/ACM Transactionson Computational Biologyand Bioinformatics, 15(5):1571–1578, September 2018.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

REFERENCES 249

Magni:2011:SPI

[MSH+11] Paolo Magni, Angela Sime-one, Sandra Healy, AntonellaIsacchi, and Roberta Bosotti.Summarizing probe intensi-ties of Affymetrix GeneChip3’ expression arrays tak-ing into account day-to-day variability. IEEE/ACMTransactions on Computa-tional Biology and Bioin-formatics, 8(5):1425–1430,September 2011. CODENITCBCY. ISSN 1545-5963(print), 1557-9964 (elec-tronic).

Malhotra:2019:PTE

[MSJP19] Anvita Gupta Malhotra,Sudha Singh, Mohit Jha,and Khushhali M. Pandey.A parametric targetabil-ity evaluation approachfor vitiligo proteome ex-tracted through integrationof gene ontologies and pro-tein interaction topologies.IEEE/ACM Transactionson Computational Biologyand Bioinformatics, 16(6):1830–1842, November 2019.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic). URL https://dl.acm.org/doi/abs/10.1109/TCBB.2018.2835459.

Mirzaei:2019:PSP

[MSKC19] Shokoufeh Mirzaei, TomerSidi, Chen Keasar, and SilviaCrivelli. Purely structuralprotein scoring functionsusing support vector ma-

chine and ensemble learning.IEEE/ACM Transactionson Computational Biologyand Bioinformatics, 16(5):1515–1523, September 2019.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Mandon:2019:ASR

[MSP+19] Hugues Mandon, Cui Su,Jun Pang, Soumya Paul, Ste-fan Haar, and Loic Pauleve.Algorithms for the sequentialreprogramming of Booleannetworks. IEEE/ACMTransactions on Computa-tional Biology and Bioin-formatics, 16(5):1610–1619,September 2019. CODENITCBCY. ISSN 1545-5963(print), 1557-9964 (elec-tronic).

Ma:2018:ICS

[MSQ18] Xiaoke Ma, Penggang Sun,and Guimin Qin. Identify-ing condition-specific mod-ules by clustering multi-ple networks. IEEE/ACMTransactions on Computa-tional Biology and Bioin-formatics, 15(5):1636–1648,September 2018. CODENITCBCY. ISSN 1545-5963(print), 1557-9964 (elec-tronic).

Meng:2013:WAC

[MSS+13a] Tao Meng, Ahmed T. Soli-man, Mei-Ling Shyu, YiminYang, Shu-Ching Chen, S. S.Iyengar, John Yordy, and

REFERENCES 250

Puneeth Iyengar. Waveletanalysis in current cancergenome research: a survey.IEEE/ACM Transactionson Computational Biologyand Bioinformatics, 10(6):1442–14359, November 2013.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Molloy:2013:PSE

[MSS13b] Kevin Molloy, Sameh Saleh,and Amarda Shehu. Prob-abilistic search and energyguidance for biased decoysampling in ab initio pro-tein structure prediction.IEEE/ACM Transactionson Computational Biologyand Bioinformatics, 10(5):1162–1175, September 2013.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Majumder:2019:CMD

[MSS19a] Aurpan Majumder, Mri-tyunjay Sarkar, and Pro-lay Sharma. A compositemode differential gene regu-latory architecture based ontemporal expression profiles.IEEE/ACM Transactionson Computational Biologyand Bioinformatics, 16(6):1785–1793, November 2019.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic). URL https://dl.acm.org/doi/abs/10.1109/TCBB.2018.2828418.

Meysman:2019:MES

[MSS+19b] Pieter Meysman, YvanSaeys, Ehsan Sabaghian,Wout Bittremieux, Yves Vande Peer, Bart Goethals, andKris Laukens. Mining the en-riched subgraphs for specificvertices in a biological graph.IEEE/ACM Transactionson Computational Biologyand Bioinformatics, 16(5):1496–1507, September 2019.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Ma:2019:IFP

[MSZ19a] Xiaoke Ma, Penggang Sun,and Zhong-Yuan Zhang. Anintegrative framework forprotein interaction networkand methylation data to dis-cover epigenetic modules.IEEE/ACM Transactionson Computational Biologyand Bioinformatics, 16(6):1855–1866, November 2019.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic). URL https://dl.acm.org/doi/abs/10.1109/TCBB.2018.2831666.

Mandoiu:2019:GEI

[MSZ19b] Ion I. Mandoiu, PavelSkums, and Alexander Ze-likovsky. Guest Editors’introduction to the spe-cial section on bioinformat-ics research and applica-tions. IEEE/ACM Transac-tions on Computational Bi-ology and Bioinformatics, 16

REFERENCES 251

(4):1362–1363, July 2019.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Mao:2011:RMS

[MT11] Kezhi Z. Mao and WenyinTang. Recursive Maha-lanobis separability mea-sure for gene subset selec-tion. IEEE/ACM Transac-tions on Computational Bi-ology and Bioinformatics, 8(1):266–272, January 2011.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Margaliot:2012:SSD

[MT12a] Michael Margaliot and TamirTuller. On the steady-statedistribution in the homoge-neous ribosome flow model.IEEE/ACM Transactionson Computational Biologyand Bioinformatics, 9(6):1724–1736, November 2012.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Margaliot:2012:SAR

[MT12b] Michael Margaliot and TamirTuller. Stability analysisof the ribosome flow model.IEEE/ACM Transactionson Computational Biologyand Bioinformatics, 9(5):1545–1552, September 2012.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Martinez:2015:CAS

[MTM+15] Hector Martinez, JoaquinTarraga, Ignacio Medina,Sergio Barrachina, MaribelCastillo, Joaquin Dopazo,and Enrique S. Quintana-Orti. Concurrent and ac-curate short read map-ping on multicore processors.IEEE/ACM Transactionson Computational Biologyand Bioinformatics, 12(5):995–1007, September 2015.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Mahjani:2017:FCF

[MTNH17] Behrang Mahjani, SalmanToor, Carl Nettelblad, andSverker Holmgren. A flexiblecomputational frameworkusing R and map-reduce forpermutation tests of massivegenetic analysis of complextraits. IEEE/ACM Trans-actions on ComputationalBiology and Bioinformatics,14(2):381–392, March 2017.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Madeira:2010:IRM

[MTSCO10] Sara C. Madeira, Miguel C.Teixeira, Isabel Sa-Correia,and Arlindo L. Oliveira.Identification of regulatorymodules in time series geneexpression data using a lin-ear time biclustering algo-rithm. IEEE/ACM Transac-tions on Computational Bi-

REFERENCES 252


Murali:2018:GE

[Mur18] T. M. Murali. Guest edi-torial. IEEE/ACM Trans-actions on ComputationalBiology and Bioinformat-ics, 15(4):1036, July 2018.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Milotti:2013:CAB

[MVS+13] Edoardo Milotti, VladislavVyshemirsky, Michela Sega,Sabrina Stella, FedericoDogo, and Roberto Chig-nola. Computer-aided bio-physical modeling: a quan-titative approach to com-plex biological systems.IEEE/ACM Transactions onComputational Biology andBioinformatics, 10(3):805–810, May 2013. CODENITCBCY. ISSN 1545-5963(print), 1557-9964 (elec-tronic).

Martin-Vide:2019:ACB

[MVVR19] Carlos Martin-Vide andMiguel A. Vega-Rodriguez.Algorithms for computa-tional biology: Third edi-tion. IEEE/ACM Trans-actions on ComputationalBiology and Bioinformatics,16(3):701–702, May 2019.CODEN ITCBCY. ISSN


Martin-Vide:2020:ACB

[MVVR20] Carlos Martın-Vide andMiguel A. Vega-Rodrıguez.Algorithms for computa-tional biology: Fifth edi-tion. IEEE/ACM Trans-actions on ComputationalBiology and Bioinformat-ics, 17(1):1, January 2020.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic). URL https://dl.acm.org/doi/abs/10.1109/TCBB.2019.2949851.

Muraro:2013:IGN

[MVW+13] Daniele Muraro, Ute Vob,Michael Wilson, MalcolmBennett, Helen Byrne, IveDe Smet, Charlie Hodgman,and John King. Inferenceof the genetic network reg-ulating lateral root initia-tion in Arabidopsis thaliana.IEEE/ACM Transactions onComputational Biology andBioinformatics, 10(1):50–60,January 2013. CODENITCBCY. ISSN 1545-5963(print), 1557-9964 (elec-tronic).

Mirzaei:2016:FCN

[MW16] Sajad Mirzaei and YufengWu. Fast constructionof near parsimonious hy-bridization networks formultiple phylogenetic trees.IEEE/ACM Transactions onComputational Biology and

REFERENCES 253

Bioinformatics, 13(3):565–570, May 2016. CODENITCBCY. ISSN 1545-5963(print), 1557-9964 (elec-tronic).

Mazrouee:2020:PMF

[MW20] Sepideh Mazrouee and WeiWang. PolyCluster: Mini-mum fragment disagreementclustering for polyploid phas-ing. IEEE/ACM Transac-tions on Computational Bi-ology and Bioinformatics, 17(1):264–277, January 2020.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic). URL https://dl.acm.org/doi/abs/10.1109/TCBB.2018.2858803.

Murphy:2011:TAP

[MWD11] James T. Murphy, Ray Wal-she, and Marc Devocelle. Atheoretical analysis of theProdrug delivery system fortreating antibiotic-resistantbacteria. IEEE/ACM Trans-actions on ComputationalBiology and Bioinformat-ics, 8(3):650–658, May/June2011. CODEN ITCBCY.ISSN 1545-5963 (print),1557-9964 (electronic).

Ma:2012:EAA

[MWL+12] Christopher Ma, ThomasK. F. Wong, T. W. Lam,W. K. Hon, K. Sadakane,and S. M. Yiu. An ef-ficient alignment algorithmfor searching simple pseudo-knots over long genomic se-

quence. IEEE/ACM Trans-actions on ComputationalBiology and Bioinformatics,9(6):1629–1638, November2012. CODEN ITCBCY.ISSN 1545-5963 (print),1557-9964 (electronic).

Mukund:2018:CEN

[MWLS18] Kavitha Mukund, Samuel R.Ward, Richard L. Lieber,and Shankar Subramaniam.Co-expression network ap-proach to studying the ef-fects of Botulinum Neurotoxin-A. IEEE/ACM Transactionson Computational Biologyand Bioinformatics, 15(6):2009–2016, November 2018.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Mooney:2012:GGU

[MWSM12] Michael Mooney, Beth Wilmot,The Bipolar Genome Study,and Shannon McWeeney.The GA and the GWAS:Using genetic algorithms tosearch for multilocus associ-ations. IEEE/ACM Trans-actions on ComputationalBiology and Bioinformat-ics, 9(3):899–910, May 2012.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Mandoiu:2013:GEI

[MWZ13] Ion I. Mandoiu, JianxinWang, and Alexander Ze-likovsky. Guest Editors’introduction to the special

REFERENCES 254

section on bioinformaticsresearch and applications.IEEE/ACM Transactionson Computational Biologyand Bioinformatics, 10(6):1345–1346, November 2013.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

McDermott:2020:DLB

[MWZ+20] Matthew B. A. McDermott,Jennifer Wang, Wen-NingZhao, Steven D. Sheridan,Peter Szolovits, Isaac Ko-hane, Stephen J. Haggarty,and Roy H. Perlis. Deeplearning benchmarks onl1000 gene expression data.IEEE/ACM Transactionson Computational Biologyand Bioinformatics, 17(6):1846–1857, November 2020.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic). URL https://dl.acm.org/doi/10.1109/TCBB.2019.2910061.

Ma:2017:EBS

[MWZY17] Lichun Ma, Debby D. Wang,Bin Zou, and Hong Yan.An eigen-binding site basedmethod for the analysis ofanti-EGFR drug resistancein lung cancer treatment.IEEE/ACM Transactionson Computational Biologyand Bioinformatics, 14(5):1187–1194, September 2017.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Ma:2012:MRD

[MYCW12] Wenji Ma, Yong Yang, Zhi-Zhong Chen, and LushengWang. Mutation regiondetection for closely re-lated individuals without aknown pedigree. IEEE/ACMTransactions on Computa-tional Biology and Bioinfor-matics, 9(2):499–510, March2012. CODEN ITCBCY.ISSN 1545-5963 (print),1557-9964 (electronic).

Ma:2017:OIS

[MZ17] Tianle Ma and AidongZhang. Omics informatics:From scattered individualsoftware tools to integratedworkflow management sys-tems. IEEE/ACM Trans-actions on ComputationalBiology and Bioinformatics,14(4):926–946, July 2017.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Meng:2015:GSI

[MZL15] Jun Meng, Jing Zhang, andYushi Luan. Gene selec-tion integrated with biologi-cal knowledge for plant stressresponse using neighborhoodsystem and rough set the-ory. IEEE/ACM Transac-tions on Computational Bi-ology and Bioinformatics,12(2):433–444, March 2015.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

REFERENCES 255

Macwan:2016:RSC

[MZS+16] Isaac G. Macwan, Zihe Zhao,Omar T. Sobh, Ishita Muk-erji, Bhushan Dharmad-hikari, and Prabir K. Patra.Residue specific and chiralitydependent interactions be-tween carbon nanotubes andflagellin. IEEE/ACM Trans-actions on ComputationalBiology and Bioinformatics,13(3):541–548, May 2016.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Mao:2019:MEP

[MZSL19] Chengsheng Mao, YuanZhao, Mengxin Sun, andYuan Luo. Are my EHRsprivate enough? Event-level privacy protection.IEEE/ACM Transactions onComputational Biology andBioinformatics, 16(1):103–112, January 2019. CODENITCBCY. ISSN 1545-5963(print), 1557-9964 (elec-tronic).

Nebel:2011:AFE

[NA11] Markus E. Nebel and ScheidAnika. Analysis of the freeenergy in a stochastic RNAsecondary structure model.IEEE/ACM Transactionson Computational Biologyand Bioinformatics, 8(6):1468–1482, November 2011.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Noriega-Atala:2020:EIS

[NAHT+20] Enrique Noriega-Atala, Paul D.Hein, Shraddha S. Thumsi,Zechy Wong, Xia Wang,Sean M. Hendryx, and Clay-ton T. Morrison. Extractinginter-sentence relations forassociating biological con-text with events in biomed-ical texts. IEEE/ACMTransactions on Computa-tional Biology and Bioin-formatics, 17(6):1895–1906,November 2020. CODENITCBCY. ISSN 1545-5963(print), 1557-9964 (elec-tronic). URL https://dl.acm.org/doi/10.1109/TCBB.2019.2904231.

Nakhleh:2010:MSR

[Nak10] Luay Nakhleh. A metric onthe space of reduced phyloge-netic networks. IEEE/ACMTransactions on Computa-tional Biology and Bioinfor-matics, 7(2):218–222, April2010. CODEN ITCBCY.ISSN 1545-5963 (print),1557-9964 (electronic).

Nanni:2019:BCH

[NBGL19] Loris Nanni, Sheryl Brah-nam, Stefano Ghidoni, andAlessandra Lumini. Bioim-age classification with hand-crafted and learned fea-tures. IEEE/ACM Trans-actions on ComputationalBiology and Bioinformatics,16(3):874–885, May 2019.CODEN ITCBCY. ISSN

REFERENCES 256


Nepomuceno-Chamorro:2015:BTA

[NCMCAR15] Isabel A. Nepomuceno-Chamorro, Alfonso Marquez-Chamorro, and Jesus S.Aguilar-Ruiz. Building tran-scriptional association net-works in cytoscape with Reg-NetC. IEEE/ACM Trans-actions on ComputationalBiology and Bioinformatics,12(4):823–824, July 2015.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Norkus:2012:AAL

[NFM+12] Mindaugas Norkus, DamienFay, Mary J. Murphy, FrankBarry, Gearoid OLaighin,and Liam Kilmartin. On theapplication of active learn-ing and Gaussian processesin postcryopreservation cellmembrane integrity experi-ments. IEEE/ACM Trans-actions on ComputationalBiology and Bioinformat-ics, 9(3):846–856, May 2012.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Ni:2016:PME

[NGY+16] Xumin Ni, Wei Guo, KaiYuan, Xiong Yang, ZhimingMa, Shuhua Xu, and Shi-hua Zhang. A probabilis-tic method for estimating thesharing of identity by descentfor populations with migra-

tion. IEEE/ACM Trans-actions on ComputationalBiology and Bioinformatics,13(2):281–290, March 2016.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Nguyen:2017:NSC

[NHH+17] Van-Nui Nguyen, Kai-YaoHuang, Chien-Hsun Huang,K. Robert Lai, and Tzong-Yi Lee. A new schemeto characterize and iden-tify protein ubiquitinationsites. IEEE/ACM Trans-actions on ComputationalBiology and Bioinformatics,14(2):393–403, March 2017.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Niu:2017:SBA

[NHTD17] Ben Niu, Huali Huang, Li-jing Tan, and Qiqi Duan.Symbiosis-based alternativelearning multi-swarm par-ticle swarm optimization.IEEE/ACM Transactions onComputational Biology andBioinformatics, 14(1):4–14,January 2017. CODENITCBCY. ISSN 1545-5963(print), 1557-9964 (elec-tronic).

Noman:2007:IGR

[NI07] Nasimul Noman and Hi-toshi Iba. Inferring generegulatory networks us-ing differential evolutionwith local search heuris-

REFERENCES 257

tics. IEEE/ACM Transac-tions on Computational Bi-ology and Bioinformatics, 4(4):634–647, October 2007.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Najafi:2019:SAM

[NJMF19] Amir Najafi, Sepehr Janghor-bani, Seyed Abolfazl Mo-tahari, and Emad Fatem-izadeh. Statistical associa-tion mapping of population-structured genetic data.IEEE/ACM Transactions onComputational Biology andBioinformatics, 16(2):638–649, March 2019. CODENITCBCY. ISSN 1545-5963(print), 1557-9964 (elec-tronic). URL https://dl.acm.org/doi/abs/10.1109/TCBB.2017.2786239.

Nanni:2012:IBV

[NLGG12] Loris Nanni, Alessandra Lu-mini, Dinesh Gupta, andAarti Garg. Identifying bac-terial virulent proteins byfusing a set of classifiersbased on variants of Chou’spseudo amino acid compo-sition and on evolutionaryinformation. IEEE/ACMTransactions on Computa-tional Biology and Bioinfor-matics, 9(2):467–475, March2012. CODEN ITCBCY.ISSN 1545-5963 (print),1557-9964 (electronic).

Nguyen:2017:BAR

[NLHL17] Thao Thi Phuong Nguyen,Vinh Sy Le, Hai Bich Ho,and Quang Si Le. Build-ing ancestral recombinationgraphs for whole genomes.IEEE/ACM Transactions onComputational Biology andBioinformatics, 14(2):478–483, March 2017. CODENITCBCY. ISSN 1545-5963(print), 1557-9964 (elec-tronic).

Niu:2018:CSR

[NLW+18] Ben Niu, Jing Liu, TeresaWu, Xianghua Chu, ZhengxuWang, and Yanmin Liu.Coevolutionary structure-redesigned-based bacterialforaging optimization. IEEE/ACM Transactions on Com-putational Biology and Bioin-formatics, 15(6):1865–1876,November 2018. CODENITCBCY. ISSN 1545-5963(print), 1557-9964 (elec-tronic).

Nguyen:2019:NDL

[NLXS19] Son P. Nguyen, Zhaoyu Li,Dong Xu, and Yi Shang.New deep learning meth-ods for protein loop mod-eling. IEEE/ACM Trans-actions on ComputationalBiology and Bioinformatics,16(2):596–606, March 2019.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic). URL https://dl.acm.org/doi/abs/10.1109/TCBB.2017.2784434.

REFERENCES 258

Nounou:2012:FIB

[NNM+12a] Hazem N. Nounou, Mo-hamed N. Nounou, NaderMeskin, Aniruddha Datta,and Edward R. Dougherty.Fuzzy intervention in biolog-ical phenomena. IEEE/ACMTransactions on Computa-tional Biology and Bioin-formatics, 9(6):1819–1825,November 2012. CODENITCBCY. ISSN 1545-5963(print), 1557-9964 (elec-tronic).

Nounou:2012:MDB

[NNM+12b] M. N. Nounou, H. N.Nounou, N. Meskin, A. Datta,and E. R. Dougherty. Mul-tiscale denoising of bio-logical data: a compara-tive analysis. IEEE/ACMTransactions on Computa-tional Biology and Bioin-formatics, 9(5):1539–1545,September 2012. CODENITCBCY. ISSN 1545-5963(print), 1557-9964 (elec-tronic).

Nguyen:2007:RRN

[NNSZ07] C. Thach Nguyen, Nguyen BaoNguyen, Wing-Kin Sung,and Louxin Zhang. Recon-structing recombination net-work from sequence data:The small parsimony prob-lem. IEEE/ACM Trans-actions on ComputationalBiology and Bioinformat-ics, 4(3):394–402, July 2007.CODEN ITCBCY. ISSN


Niijima:2009:LLD

[NO09] Satoshi Niijima and YasushiOkuno. Laplacian linear dis-criminant analysis approachto unsupervised feature se-lection. IEEE/ACM Trans-actions on ComputationalBiology and Bioinformatics,6(4):605–614, October 2009.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Nguyen:2013:KBM

[NP13] Ken D. Nguyen and Yi Pan.A knowledge-based multiple-sequence alignment algo-rithm. IEEE/ACM Trans-actions on ComputationalBiology and Bioinformatics,10(4):884–896, July 2013.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Nguyen:2016:LDA

[NPBD16] An Nguyen, Adam Prugel-Bennett, and Srinandan Das-mahapatra. A low di-mensional approximation forcompetence in Bacillus Sub-tilis. IEEE/ACM Trans-actions on ComputationalBiology and Bioinformatics,13(2):272–280, March 2016.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

REFERENCES 259

Ni:2017:NCH

[NPD+17] Qingjian Ni, Qianqian Pan,Huimin Du, Cen Cao, andYuqing Zhai. A novel clus-ter head selection algorithmbased on fuzzy clusteringand particle swarm optimiza-tion. IEEE/ACM Trans-actions on ComputationalBiology and Bioinformatics,14(1):76–84, January 2017.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Ng:2007:NGW

[NPK+07] Lydia Ng, Sayan Pathak,Chihchau Kuan, Chris Lau,Hong wei Dong, AndrewSodt, Chinh Dang, BrianAvants, Paul Yushkevich,James Gee, David Haynor,Ed Lein, Allan Jones, andMike Hawrylycz. Neuroin-formatics for genome-wide3-D gene expression map-ping in the mouse brain.IEEE/ACM Transactions onComputational Biology andBioinformatics, 4(3):382–393, July 2007. CODENITCBCY. ISSN 1545-5963(print), 1557-9964 (elec-tronic).

Narasimhan:2009:SPG

[NRV09] Sridharakumar Narasimhan,Raghunathan Rengaswamy,and Rajanikanth Vadigepalli.Structural properties of generegulatory networks: Def-initions and connections.IEEE/ACM Transactions on

Computational Biology andBioinformatics, 6(1):158–170, January 2009. CODENITCBCY. ISSN 1545-5963(print), 1557-9964 (elec-tronic).

Nalbantoglu:2019:MAM

[NS19] O. Ufuk Nalbantoglu andKhalid Sayood. MIMOSA:Algorithms for microbialprofiling. IEEE/ACM Trans-actions on ComputationalBiology and Bioinformatics,16(6):2023–2034, November2019. CODEN ITCBCY.ISSN 1545-5963 (print),1557-9964 (electronic). URLhttps://dl.acm.org/doi/abs/10.1109/TCBB.2018.2830324.

Nishida:2019:EEP

[NSAH19] Shimpei Nishida, ShunSakuraba, Kiyoshi Asai, andMichiaki Hamada. Esti-mating energy parametersfor RNA secondary struc-ture predictions using bothexperimental and computa-tional data. IEEE/ACMTransactions on Computa-tional Biology and Bioin-formatics, 16(5):1645–1655,September 2019. CODENITCBCY. ISSN 1545-5963(print), 1557-9964 (elec-tronic).

Nawab:2017:IBA

[NSC17] Rao Muhammad AdeelNawab, Mark Stevenson,and Paul Clough. An

REFERENCES 260

IR-based approach utiliz-ing query expansion for pla-giarism detection in MED-LINE. IEEE/ACM Trans-actions on ComputationalBiology and Bioinformatics,14(4):796–804, July 2017.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Nizami:2019:EAS

[NSMH19] Bilal Nizami, Elham MousavinezhadSarasia, Mehbub I. K.Momin, and Bahareh Honarpar-var. Estrogenic active stil-bene derivatives as anti-cancer agents: a DFT andQSAR study. IEEE/ACMTransactions on Computa-tional Biology and Bioin-formatics, 16(2):560–568,March 2019. CODENITCBCY. ISSN 1545-5963(print), 1557-9964 (elec-tronic). URL https://dl.acm.org/doi/abs/10.1109/TCBB.2017.2779505.

Nishiyama:2019:RCN

[NSNA19] Yuhei Nishiyama, Alek-sandar Shurbevski, HiroshiNagamochi, and TatsuyaAkutsu. Resource cut, anew bounding procedure toalgorithms for enumeratingtree-like chemical graphs.IEEE/ACM Transactions onComputational Biology andBioinformatics, 16(1):77–90,January 2019. CODENITCBCY. ISSN 1545-5963(print), 1557-9964 (elec-tronic).

Noor:2012:IGR

[NSNN12] Amina Noor, Erchin Ser-pedin, Mohamed Nounou,and Hazem Nounou. In-ferring gene regulatory net-works via nonlinear state-space models and exploitingsparsity. IEEE/ACM Trans-actions on ComputationalBiology and Bioinformatics,9(4):1203–1211, July 2012.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Nguyen:2015:EAO

[NSZK15] Thuy-Diem Nguyen, BertilSchmidt, Zejun Zheng, andChee-Keong Kwoh. Effi-cient and accurate OTU clus-tering with GPU-based se-quence alignment and dy-namic dendrogram cutting.IEEE/ACM Transactionson Computational Biologyand Bioinformatics, 12(5):1060–1073, September 2015.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Neri:2007:AMA

[NTCO07] Ferrante Neri, Jari Toiva-nen, Giuseppe LeonardoCascella, and Yew-SoonOng. An adaptive multi-meme algorithm for design-ing HIV multidrug thera-pies. IEEE/ACM Trans-actions on ComputationalBiology and Bioinformatics,4(2):264–278, April 2007.CODEN ITCBCY. ISSN

REFERENCES 261


Nogueira:2016:BBW

[NTR16] David Nogueira, PedroTomas, and Nuno Roma.BowMapCL: Burrows–Wheelermapping on multiple hetero-geneous accelerators. IEEE/ACM Transactions on Com-putational Biology and Bioin-formatics, 13(5):926–938,September 2016. CODENITCBCY. ISSN 1545-5963(print), 1557-9964 (elec-tronic).

Nagarajan:2006:CSC

[NU06] Radhakrishnan Nagarajanand Meenakshi Upreti. Cor-relation statistics for cDNAmicroarray image analy-sis. IEEE/ACM Trans-actions on ComputationalBiology and Bioinformat-ics, 3(3):232–238, July 2006.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Nguyen:2018:HTN

[NVSH18] Nha Nguyen, An Vo, HaibinSun, and Heng Huang.Heavy-tailed noise suppres-sion and derivative waveletscalogram for detecting DNAcopy number aberrations.IEEE/ACM Transactionson Computational Biologyand Bioinformatics, 15(5):1625–1635, September 2018.CODEN ITCBCY. ISSN


Niu:2019:PPI

[NWW19] Yun Niu, Hongmei Wu,and Yuwei Wang. Protein-protein interaction identi-fication using a similarity-constrained graph model.IEEE/ACM Transactions onComputational Biology andBioinformatics, 16(2):607–616, March 2019. CODENITCBCY. ISSN 1545-5963(print), 1557-9964 (elec-tronic). URL https://dl.acm.org/doi/abs/10.1109/TCBB.2017.2777448.

Ni:2020:CDS

[NWZ+20] Peng Ni, Jianxin Wang, PingZhong, Yaohang Li, Fang-Xiang Wu, and Yi Pan. Con-structing disease similaritynetworks based on diseasemodule theory. IEEE/ACMTransactions on Computa-tional Biology and Bioinfor-matics, 17(3):906–915, May2020. CODEN ITCBCY.ISSN 1545-5963 (print),1557-9964 (electronic). URLhttps://dl.acm.org/doi/10.1109/TCBB.2018.2817624.

Nye:2014:ACP

[Nye14] Tom M. W. Nye. An algo-rithm for constructing prin-cipal geodesics in phyloge-netic treespace. IEEE/ACMTransactions on Computa-tional Biology and Bioin-formatics, 11(2):304–315,

REFERENCES 262

March 2014. CODENITCBCY. ISSN 1545-5963(print), 1557-9964 (elec-tronic).

Ng:2015:FAL

[NYOL15] Yen Kaow Ng, LinzhiYin, Hirotaka Ono, andShuai Cheng Li. Findingall longest common segmentsin protein structures effi-ciently. IEEE/ACM Trans-actions on ComputationalBiology and Bioinformatics,12(3):644–655, May 2015.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Nguyen:2011:TBU

[NZR11] Minh N. Nguyen, Jacek M.Zurada, and Jagath C. Ra-japakse. Toward betterunderstanding of proteinsecondary structure: Ex-tracting prediction rules.IEEE/ACM Transactionson Computational Biologyand Bioinformatics, 8(3):858–864, May/June 2011.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Ozsoy:2013:DCA

[OC13] Oyku Eren Ozsoy and TolgaCan. A divide and conquerapproach for constructionof large-scale signaling net-works from PPI and RNAidata using linear program-ming. IEEE/ACM Trans-actions on Computational

Biology and Bioinformatics,10(4):869–883, July 2013.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Ochs:2014:OAT

[OFC+14] Michael F. Ochs, Jason E.Farrar, Michael Considine,Yingying Wei, Soheil Mesh-inchi, and Robert J. Arceci.Outlier analysis and topscoring pair for integrateddata analysis and biomarkerdiscovery. IEEE/ACMTransactions on Computa-tional Biology and Bioinfor-matics, 11(3):520–532, May2014. CODEN ITCBCY.ISSN 1545-5963 (print),1557-9964 (electronic).

Oh:2011:FKD

[OG11] Jung Hun Oh and JeanGao. Fast kernel discrim-inant analysis for classifi-cation of liver cancer massspectra. IEEE/ACM Trans-actions on ComputationalBiology and Bioinformatics,8(6):1522–1534, November2011. CODEN ITCBCY.ISSN 1545-5963 (print),1557-9964 (electronic).

Ovaska:2013:GRO

[OLS+13] Kristian Ovaska, Lauri Lyly,Biswajyoti Sahu, Olli A.Janne, and Sampsa Hau-taniemi. Genomic region op-eration kit for flexible pro-cessing of deep sequencingdata. IEEE/ACM Transac-

REFERENCES 263

tions on Computational Bi-ology and Bioinformatics, 10(1):200–206, January 2013.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Oh:2011:ELA

[OLZ11] Sangyoon Oh, Min Su Lee,and Byoung-Tak Zhang. En-semble learning with activeexample selection for imbal-anced biomedical data classi-fication. IEEE/ACM Trans-actions on ComputationalBiology and Bioinformatics,8(2):316–325, March 2011.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Ogul:2007:SLP

[OM07] Hasan Ogul and Erkan U.Mumcuoglu. Subcellu-lar localization predictionwith new protein encodingschemes. IEEE/ACM Trans-actions on ComputationalBiology and Bioinformatics,4(2):227–232, April 2007.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Omony:2012:EDS

[OMAdG+12] Jimmy Omony, Astrid R.Mach-Aigner, Leo H. de Graaff,Gerrit van Straten, and An-ton J. B. van Boxtel. Evalu-ation of design strategies fortime course experiments ingenetic networks: Case studyof the XlnR regulon in As-

pergillus niger . IEEE/ACMTransactions on Computa-tional Biology and Bioin-formatics, 9(5):1316–1325,September 2012. CODENITCBCY. ISSN 1545-5963(print), 1557-9964 (elec-tronic).

Olman:2009:PCA

[OMWX09] Victor Olman, Fenglou Mao,Hongwei Wu, and Ying Xu.Parallel clustering algorithmfor large data sets with ap-plications in bioinformat-ics. IEEE/ACM Transac-tions on Computational Bi-ology and Bioinformatics,6(2):344–352, April 2009.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Owen:2011:FAC

[OP11] Megan Owen and J. ScottProvan. A fast algo-rithm for computing geodesicdistances in tree space.IEEE/ACM Transactions onComputational Biology andBioinformatics, 8(1):2–13,January 2011. CODENITCBCY. ISSN 1545-5963(print), 1557-9964 (elec-tronic).

Oakley:2013:PSO

[ORCJ13] Mark T. Oakley, Eliza-beth Grace Richardson, Har-riet Carr, and Roy L. John-ston. Protein structure opti-mization with a “Lamarck-ian” ant colony algorithm.

REFERENCES 264


Ogunleye:2020:XMC

[OW20] Adeola Ogunleye and Qing-Guo Wang. XGBoostmodel for chronic kidney dis-ease diagnosis. IEEE/ACMTransactions on Computa-tional Biology and Bioin-formatics, 17(6):2131–2140,November 2020. CODENITCBCY. ISSN 1545-5963(print), 1557-9964 (elec-tronic). URL https://dl.acm.org/doi/10.1109/TCBB.2019.2911071.

Ou-Yang:2015:DPC

[OYDZ15] Le Ou-Yang, Dao-QingDai, and Xiao-Fei Zhang.Detecting protein com-plexes from signed protein-protein interaction networks.IEEE/ACM Transactionson Computational Biologyand Bioinformatics, 12(6):1333–1344, November 2015.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Ozyurt:2012:AIC

[Ozy12] I. Burak Ozyurt. Au-tomatic identification andclassification of noun argu-ment structures in biomed-ical literature. IEEE/ACM

Transactions on Computa-tional Biology and Bioin-formatics, 9(6):1639–1648,November 2012. CODENITCBCY. ISSN 1545-5963(print), 1557-9964 (elec-tronic).

Ponzoni:2007:IAR

[PAAG07] Ignacio Ponzoni, FranciscoAzuaje, Juan Augusto, andDavid Glass. Inferring adap-tive regulation thresholdsand association rules fromgene expression data throughcombinatorial optimizationlearning. IEEE/ACM Trans-actions on ComputationalBiology and Bioinformatics,4(4):624–634, October 2007.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Palaniappan:2012:HFF

[PAL+12] Sucheendra K. Palaniap-pan, S. Akshay, Bing Liu,Blaise Genest, and P. S.Thiagarajan. A hybridfactored frontier algorithmfor dynamic Bayesian net-works with a biopathwaysapplication. IEEE/ACMTransactions on Computa-tional Biology and Bioin-formatics, 9(5):1352–1365,September 2012. CODENITCBCY. ISSN 1545-5963(print), 1557-9964 (elec-tronic).

Pattengale:2011:UHP

[PAS+11] Nicholas Pattengale, An-

REFERENCES 265

dre Aberer, Krister Swen-son, Alexandros Stamatakis,and Bernard Moret. Un-covering hidden phyloge-netic consensus in large datasets. IEEE/ACM Trans-actions on ComputationalBiology and Bioinformat-ics, 8(4):902–911, July 2011.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Pauleve:2018:RQM

[Pau18] Loic Pauleve. Reduc-tion of qualitative modelsof biological networks fortransient dynamics analy-sis. IEEE/ACM Transac-tions on Computational Bi-ology and Bioinformatics, 15(4):1167–1179, July 2018.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Pal:2012:TDR

[PB12a] Ranadip Pal and Sonal Bhat-tacharya. Transient dynam-ics of reduced-order mod-els of genetic regulatory net-works. IEEE/ACM Transac-tions on Computational Bi-ology and Bioinformatics, 9(4):1230–1244, July 2012.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Phipps:2012:OPN

[PB12b] Paul Phipps and SergeyBereg. Optimizing phyloge-netic networks for circular

split systems. IEEE/ACMTransactions on Computa-tional Biology and Bioinfor-matics, 9(2):535–547, March2012. CODEN ITCBCY.ISSN 1545-5963 (print),1557-9964 (electronic).

Paul:2019:IAI

[PB19] Sushmita Paul and Dhana-jit Brahma. An integratedapproach for identificationof functionally similar Mi-croRNAs in colorectal can-cer. IEEE/ACM Transac-tions on Computational Bi-ology and Bioinformatics, 16(1):183–192, January 2019.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Peters:2011:TSC

[PBhL+11] Tim Peters, David W. Bul-ger, To ha Loi, Jean Yee HwaYang, and David Ma. Two-step cross-entropy feature se-lection for microarrays —power through complemen-tarity. IEEE/ACM Transac-tions on Computational Bi-ology and Bioinformatics, 8(4):1148–1151, July 2011.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Pirola:2012:EAH

[PBJ12] Yuri Pirola, Paola Boniz-zoni, and Tao Jiang. An ef-ficient algorithm for haplo-type inference on pedigreeswith recombinations and mu-

REFERENCES 266

tations. IEEE/ACM Trans-actions on ComputationalBiology and Bioinformatics,9(1):12–25, January 2012.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Petti:2020:CSD

[PBV+20] Manuela Petti, Daniele Biz-zarri, Antonella Verrienti,Rosa Falcone, and LorenzoFarina. Connectivity signif-icance for disease gene pri-oritization in an expand-ing universe. IEEE/ACMTransactions on Computa-tional Biology and Bioin-formatics, 17(6):2155–2161,November 2020. CODENITCBCY. ISSN 1545-5963(print), 1557-9964 (elec-tronic). URL https://dl.acm.org/doi/10.1109/TCBB.2019.2938512.

Pirayre:2018:BCC

[PCDP18] Aurelie Pirayre, CamilleCouprie, Laurent Duval, andJean-Christophe Pesquet.BRANE clust: Cluster-assisted gene regulatory net-work inference refinement.IEEE/ACM Transactions onComputational Biology andBioinformatics, 15(3):850–860, May 2018. CODENITCBCY. ISSN 1545-5963(print), 1557-9964 (elec-tronic).

Pisanti:2005:BMG

[PCGS05] Nadia Pisanti, MaximeCrochemore, Roberto Grossi,

and Marie-France Sagot.Bases of motifs for generat-ing repeated patterns withwild cards. IEEE/ACMTransactions on Computa-tional Biology and Bioinfor-matics, 2(1):40–50, January2005. CODEN ITCBCY.ISSN 1545-5963 (print),1557-9964 (electronic).

Pesantez-Cabrera:2019:EDC

[PCK19] Paola Pesantez-Cabrera andAnanth Kalyanaraman. Ef-ficient detection of commu-nities in biological bipar-tite networks. IEEE/ACMTransactions on Computa-tional Biology and Bioin-formatics, 16(1):258–271,January 2019. CODENITCBCY. ISSN 1545-5963(print), 1557-9964 (elec-tronic).

Peng:2019:CMC

[PCY+19] Shaoliang Peng, Yingbo Cui,Shunyun Yang, Wenhe Su,Xiaoyu Zhang, TenglilangZhang, Weiguo Liu, andXing-Ming Zhao. A CPU–MIC collaborated parallelframework for GROMACSon Tianhe-2 supercomputer.IEEE/ACM Transactions onComputational Biology andBioinformatics, 16(2):425–433, March 2019. CODENITCBCY. ISSN 1545-5963(print), 1557-9964 (elec-tronic). URL https://dl.acm.org/doi/abs/10.1109/TCBB.2017.2713362.

REFERENCES 267

pour:2020:OBF

[pD20] Ali Foroughi pour andLori A. Dalton. Opti-mal Bayesian filtering forbiomarker discovery: Per-formance and robustness.IEEE/ACM Transactions onComputational Biology andBioinformatics, 17(1):250–263, January 2020. CO-DEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic). URL https://dl.acm.org/doi/abs/10.1109/TCBB.2018.2858814.

Pan:2019:KFP

[PFJ+19] Tony Pan, Patrick Flick,Chirag Jain, YongchaoLiu, and Srinivas Aluru.Kmerind: a flexible paral-lel library for K-mer index-ing of biological sequenceson distributed memory sys-tems. IEEE/ACM Transac-tions on Computational Bi-ology and Bioinformatics, 16(4):1117–1131, July 2019.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Pirinen:2006:FCG

[PG06] Matti Pirinen and DarioGasbarra. Finding consistentgene transmission patternson large and complex pedi-grees. IEEE/ACM Trans-actions on ComputationalBiology and Bioinformat-ics, 3(3):252–262, July 2006.CODEN ITCBCY. ISSN


Papadakis:2012:SSD

[PG12] George Papadakis and Elec-tra Gizeli. In silico search ofDNA drugs targeting onco-genes. IEEE/ACM Trans-actions on ComputationalBiology and Bioinformatics,9(6):1826–1830, November2012. CODEN ITCBCY.ISSN 1545-5963 (print),1557-9964 (electronic).

Paszek:2018:EAG

[PG18] Jaroslaw Paszek and PawelGorecki. Efficient algo-rithms for genomic duplica-tion models. IEEE/ACMTransactions on Computa-tional Biology and Bioin-formatics, 15(5):1515–1524,September 2018. CODENITCBCY. ISSN 1545-5963(print), 1557-9964 (elec-tronic).

Poirier:2018:DAB

[PGF18] Carl Poirier, Benoit Gos-selin, and Paul Fortier. DNAassembly with de Bruijngraphs using an FPGA plat-form. IEEE/ACM Transac-tions on Computational Bi-ology and Bioinformatics, 15(3):1003–1009, May 2018.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

REFERENCES 268

Pang:2012:GSU

[PGHT12] Herbert Pang, Stephen L.George, Ken Hui, and TiejunTong. Gene selection us-ing iterative feature elimina-tion random forests for sur-vival outcomes. IEEE/ACMTransactions on Computa-tional Biology and Bioin-formatics, 9(5):1422–1431,September 2012. CODENITCBCY. ISSN 1545-5963(print), 1557-9964 (elec-tronic).

Pelikan:2010:EPL

[PH10a] Richard Pelikan and Mi-los Hauskrecht. Effi-cient peak-labeling algo-rithms for whole-samplemass spectrometry pro-teomics. IEEE/ACM Trans-actions on ComputationalBiology and Bioinformatics,7(1):126–137, January 2010.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Perkins:2010:TBS

[PH10b] Theodore J. Perkins andMichael T. Hallett. A trade-off between sample complex-ity and computational com-plexity in learning Booleannetworks from time-seriesdata. IEEE/ACM Transac-tions on Computational Bi-ology and Bioinformatics, 7(1):118–125, January 2010.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Parker:2008:SPT

[PHX+08] Douglass Stott Parker, Ruey-Lung Hsiao, Yi Xing,Alissa M. Resch, and Christo-pher J. Lee. Solving theproblem of trans-genomicquery with alignment ta-bles. IEEE/ACM Trans-actions on ComputationalBiology and Bioinformat-ics, 5(3):432–447, July 2008.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Paul:2009:PCC

[PI09] Topon Kumar Paul and Hi-toshi Iba. Prediction ofcancer class with major-ity voting genetic program-ming classifier using gene ex-pression data. IEEE/ACMTransactions on Computa-tional Biology and Bioinfor-matics, 6(2):353–367, April2009. CODEN ITCBCY.ISSN 1545-5963 (print),1557-9964 (electronic).

Patra:2018:RAP

[PIPC18] Pranjal Patra, Tatsuo Izawa,and Lourdes Pena-Castillo.REPA: Applying pathwayanalysis to genome-widetranscription factor bindingdata. IEEE/ACM Transac-tions on Computational Bi-ology and Bioinformatics, 15(4):1270–1283, July 2018.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

REFERENCES 269

Patton:2014:HPI

[PJN+14] Kristopher L. Patton, David J.John, James L. Norris,Daniel R. Lewis, and Glo-ria K. Muday. Hierar-chical probabilistic interac-tion modeling for multi-ple gene expression repli-cates. IEEE/ACM Trans-actions on ComputationalBiology and Bioinformatics,11(2):336–346, March 2014.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Piovesan:2013:SFP

[PK13] Teresa Piovesan and StevenKelk. A simple fixed pa-rameter tractable algorithmfor computing the hybridiza-tion number of two (notnecessarily binary) trees.IEEE/ACM Transactions onComputational Biology andBioinformatics, 10(1):18–25,January 2013. CODENITCBCY. ISSN 1545-5963(print), 1557-9964 (elec-tronic).

Pyne:2020:RRT

[PKA20] Saptarshi Pyne, Alok Ran-jan Kumar, and AshishAnand. Rapid recon-struction of time-varyinggene regulatory networks.IEEE/ACM Transactions onComputational Biology andBioinformatics, 17(1):278–291, January 2020. CO-DEN ITCBCY. ISSN1545-5963 (print), 1557-9964


Popescu:2006:FMG

[PKM06] Mihail Popescu, James M.Keller, and Joyce A. Mitchell.Fuzzy measures on the geneontology for gene prod-uct similarity. IEEE/ACMTransactions on Computa-tional Biology and Bioinfor-matics, 3(3):263–274, July2006. CODEN ITCBCY.ISSN 1545-5963 (print),1557-9964 (electronic).

Paoletti:2012:INC

[PKRD12] David R. Paoletti, Dan E.Krane, Michael L. Raymer,and Travis E. Doom. In-ferring the number of con-tributors to mixed DNA pro-files. IEEE/ACM Transac-tions on Computational Bi-ology and Bioinformatics, 9(1):113–122, January 2012.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Peng:2017:HNB

[PL17] Chen Peng and Ao Li.A heterogeneous networkbased method for identify-ing GBM-related genes by in-tegrating multi-dimensionaldata. IEEE/ACM Trans-actions on ComputationalBiology and Bioinformatics,14(3):713–720, May 2017.CODEN ITCBCY. ISSN

REFERENCES 270


Paoletti:2020:DDR

[PLC+20] Nicola Paoletti, Kin SumLiu, Hongkai Chen, Scott A.Smolka, and Shan Lin.Data-driven robust con-trol for a closed-loop artifi-cial pancreas. IEEE/ACMTransactions on Computa-tional Biology and Bioin-formatics, 17(6):1981–1993,November 2020. CODENITCBCY. ISSN 1545-5963(print), 1557-9964 (elec-tronic). URL https://dl.acm.org/doi/10.1109/TCBB.2019.2912609.

Peng:2017:PPF

[PLCW17] Wei Peng, Min Li, Lu Chen,and Lusheng Wang. Pre-dicting protein functionsby using unbalanced ran-dom walk algorithm onthree biological networks.IEEE/ACM Transactions onComputational Biology andBioinformatics, 14(2):360–369, March 2017. CODENITCBCY. ISSN 1545-5963(print), 1557-9964 (elec-tronic).

Passerini:2012:PMB

[PLF12] Andrea Passerini, MarcoLippi, and Paolo Fras-coni. Predicting metal-binding sites from protein se-quence. IEEE/ACM Trans-actions on ComputationalBiology and Bioinformatics,


Paoletti:2012:MCM

[PLMV12] Nicola Paoletti, Pietro Lio,Emanuela Merelli, andMarco Viceconti. Multilevelcomputational modeling andquantitative analysis of boneremodeling. IEEE/ACMTransactions on Computa-tional Biology and Bioin-formatics, 9(5):1366–1378,September 2012. CODENITCBCY. ISSN 1545-5963(print), 1557-9964 (elec-tronic).

Paul:2020:IRS

[PM20] Sushmita Paul and Madhu-mita. RFCM3: Compu-tational method for identi-fication of miRNA–mRNAregulatory modules in cer-vical cancer. IEEE/ACMTransactions on Computa-tional Biology and Bioin-formatics, 17(5):1729–1740,September 2020. CODENITCBCY. ISSN 1545-5963(print), 1557-9964 (elec-tronic). URL https://dl.acm.org/doi/10.1109/TCBB.2019.2910851.

Pouyan:2017:ICP

[PN17] Maziyar Baran Pouyan andMehrdad Nourani. Iden-tifying cell populations inflow cytometry data us-ing phenotypic signatures.

REFERENCES 271


Pan:2020:FBG

[PNA20] Tony Pan, Rahul Nihalani,and Srinivas Aluru. Fast deBruijn graph compaction indistributed memory environ-ments. IEEE/ACM Transac-tions on Computational Bi-ology and Bioinformatics, 17(1):136–148, January 2020.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic). URL https://dl.acm.org/doi/abs/10.1109/TCBB.2018.2858797.

Pesonen:2018:CPN

[PNP+18] Maiju Pesonen, JaakkoNevalainen, Steven Potter,Somnath Datta, and SusmitaDatta. A combined PLS andnegative binomial regressionmodel for inferring associ-ation networks from next-generation sequencing countdata. IEEE/ACM Trans-actions on ComputationalBiology and Bioinformatics,15(3):760–773, May 2018.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Poleksic:2011:OWU

[Pol11] Aleksandar Poleksic. Opti-mizing a widely used protein

structure alignment measurein expected polynomial time.IEEE/ACM Transactionson Computational Biologyand Bioinformatics, 8(6):1716–1720, November 2011.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Poleksic:2012:CPS

[Pol12] Aleksandar Poleksic. Oncomplexity of protein struc-ture alignment problemunder distance constraint.IEEE/ACM Transactions onComputational Biology andBioinformatics, 9(2):511–516, March 2012. CODENITCBCY. ISSN 1545-5963(print), 1557-9964 (elec-tronic).

Poleksic:2013:IAM

[Pol13] Aleksandar Poleksic. Im-proved algorithms for match-ing r-separated sets with ap-plications to protein struc-ture alignment. IEEE/ACMTransactions on Computa-tional Biology and Bioin-formatics, 10(1):226–229,January 2013. CODENITCBCY. ISSN 1545-5963(print), 1557-9964 (elec-tronic).

Pizzi:2018:EAS

[POS+18] Cinzia Pizzi, Mattia Or-namenti, Simone Spangaro,Simona E. Rombo, andLaxmi Parida. Efficient al-gorithms for sequence anal-

REFERENCES 272

ysis with entropic profiles.IEEE/ACM Transactions onComputational Biology andBioinformatics, 15(1):117–128, January 2018. CODENITCBCY. ISSN 1545-5963(print), 1557-9964 (elec-tronic).

Pichene:2020:MVP

[PPFG20] Matthieu Pichene, Sucheen-dra K. Palaniappan, EricFabre, and Blaise Genest.Modeling variability in pop-ulations of cells using ap-proximated multivariate dis-tributions. IEEE/ACMTransactions on Computa-tional Biology and Bioin-formatics, 17(5):1691–1702,September 2020. CODENITCBCY. ISSN 1545-5963(print), 1557-9964 (elec-tronic). URL https://dl.acm.org/doi/10.1109/TCBB.2019.2904276.

Panja:2013:CLC

[PPM+13] Surajit Panja, Sourav Patra,Anirban Mukherjee, Mad-humita Basu, SanghamitraSengupta, and Pranab K.Dutta. A closed-loop con-trol scheme for steeringsteady states of glycoly-sis and glycogenolysis path-way. IEEE/ACM Transac-tions on Computational Bi-ology and Bioinformatics,10(4):858–868, July 2013.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Piraveenan:2012:AMD

[PPZ12] Mahendra Piraveenan, MikhailProkopenko, and AlbertZomaya. Assortative mix-ing in directed biological net-works. IEEE/ACM Trans-actions on ComputationalBiology and Bioinformatics,9(1):66–78, January 2012.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Pizzuti:2012:CAM

[PR12] Clara Pizzuti and Simona E.Rombo. A coclusteringapproach for mining largeprotein-protein interactionnetworks. IEEE/ACMTransactions on Computa-tional Biology and Bioinfor-matics, 9(3):717–730, May2012. CODEN ITCBCY.ISSN 1545-5963 (print),1557-9964 (electronic).

Pandey:2014:GES

[PR14] Gaurav Pandey and HuzefaRangwala. Guest edito-rial for special section onBIOKDD2013. IEEE/ACMTransactions on Computa-tional Biology and Bioin-formatics, 11(5):773–774,September 2014. CODENITCBCY. ISSN 1545-5963(print), 1557-9964 (elec-tronic).

Pease:2018:EDU

[PR18] James B. Pease and Ben-jamin K. Rosenzweig. En-coding data using biological

REFERENCES 273

principles: The multisamplevariant format for phyloge-nomics and population ge-nomics. IEEE/ACM Trans-actions on ComputationalBiology and Bioinformatics,15(4):1231–1238, July 2018.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Preparata:2004:SHR

[Pre04] Franco P. Preparata. Sequencing-by-hybridization revisited:The analog-spectrum pro-posal. IEEE/ACM Trans-actions on ComputationalBiology and Bioinformatics,1(1):46–52, January 2004.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Pizzi:2011:FSM

[PRU11] Cinzia Pizzi, Pasi Rastas,and Esko Ukkonen. Findingsignificant matches of posi-tion weight matrices in lin-ear time. IEEE/ACM Trans-actions on ComputationalBiology and Bioinformatics,8(1):69–79, January 2011.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Prabhakaran:2014:HHI

[PRZ+14] Sandhya Prabhakaran, MelanieRey, Osvaldo Zagordi, NikoBeerenwinkel, and VolkerRoth. HIV haplotype in-ference using a propagat-ing Dirichlet process mixture

model. IEEE/ACM Transac-tions on Computational Bi-ology and Bioinformatics, 11(1):182–191, January 2014.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Peng:2011:MSA

[PS11] Qian Peng and Andrew D.Smith. Multiple sequence as-sembly from reads alignableto a common referencegenome. IEEE/ACM Trans-actions on ComputationalBiology and Bioinformatics,8(5):1283–1295, September2011. CODEN ITCBCY.ISSN 1545-5963 (print),1557-9964 (electronic).

Priyadarshana:2015:MBP

[PS15] W. J. R. M. Priyadarshanaand Georgy Sofronov. Mul-tiple break-points detectionin array CGH data viathe cross-entropy method.IEEE/ACM Transactions onComputational Biology andBioinformatics, 12(2):487–498, March 2015. CODENITCBCY. ISSN 1545-5963(print), 1557-9964 (elec-tronic).

Paul:2019:IDE

[PS19] Amit Paul and Jaya Sil.Identification of differentiallyexpressed genes to estab-lish new biomarker for can-cer prediction. IEEE/ACMTransactions on Computa-tional Biology and Bioin-

REFERENCES 274

formatics, 16(6):1970–1985,November 2019. CODENITCBCY. ISSN 1545-5963(print), 1557-9964 (elec-tronic). URL https://dl.acm.org/doi/abs/10.1109/TCBB.2018.2837095.

Pons:2020:GLL

[PSC20] Joan Carles Pons, CelineScornavacca, and GabrielCardona. Generation oflevel-k k LGT networks.IEEE/ACM Transactions onComputational Biology andBioinformatics, 17(1):158–164, January 2020. CO-DEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic). URL https://dl.acm.org/doi/abs/10.1109/TCBB.2019.2895344.

Park:2017:NAP

[PSIM17] Heewon Park, Yuichi Shi-raishi, Seiya Imoto, andSatoru Miyano. A noveladaptive penalized logisticregression for uncoveringbiomarker associated withanti-cancer drug sensitiv-ity. IEEE/ACM Transac-tions on Computational Bi-ology and Bioinformatics,14(4):771–782, July 2017.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Pang:2015:IAS

[PSK+15] Bin Pang, David Schless-man, Xingyan Kuang, NanZhao, Daniel Shyu, Dmitry

Korkin, and Chi-Ren Shyu.An integrated approach tosequence-independent localalignment of protein bind-ing sites. IEEE/ACM Trans-actions on ComputationalBiology and Bioinformatics,12(2):298–308, March 2015.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Pavelka:2016:CAA

[PSK+16] Antonin Pavelka, Eva Sebestova,Barbora Kozlikova, Jan Bre-zovsky, Jiri Sochor, and JiriDamborsky. CAVER: al-gorithms for analyzing dy-namics of tunnels in macro-molecules. IEEE/ACMTransactions on Computa-tional Biology and Bioinfor-matics, 13(3):505–517, May2016. CODEN ITCBCY.ISSN 1545-5963 (print),1557-9964 (electronic).

Pradeep:2015:NSB

[PSN+15] Prachi Pradeep, Craig Stru-ble, Terrence Neumann,Daniel S. Sem, and Stephen J.Merrill. A novel scor-ing based distributed pro-tein docking applicationto improve enrichment.IEEE/ACM Transactionson Computational Biologyand Bioinformatics, 12(6):1464–1469, November 2015.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

REFERENCES 275

Paul:2020:EAT

[PSPM20] Soumya Paul, Cui Su, JunPang, and Andrzej Mizera.An efficient approach to-wards the source-target con-trol of Boolean networks.IEEE/ACM Transactionson Computational Biologyand Bioinformatics, 17(6):1932–1945, November 2020.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic). URL https://dl.acm.org/doi/10.1109/TCBB.2019.2915081.

Park:2009:NBI

[PSS09] Yongjin Park, Stanley Shack-ney, and Russell Schwartz.Network-based inference ofcancer progression from mi-croarray data. IEEE/ACMTransactions on Computa-tional Biology and Bioinfor-matics, 6(2):200–212, April2009. CODEN ITCBCY.ISSN 1545-5963 (print),1557-9964 (electronic).

Prakash:2009:ADM

[PT09] Amol Prakash and MartinTompa. Assessing the discor-dance of multiple sequencealignments. IEEE/ACMTransactions on Computa-tional Biology and Bioinfor-matics, 6(4):542–551, Octo-ber 2009. CODEN ITCBCY.ISSN 1545-5963 (print),1557-9964 (electronic).

Peng:2018:JTL

[PTH+18] Xin Peng, Yang Tang, Wan-

gli He, Wenli Du, and FengQian. A just-in-time learn-ing based monitoring andclassification method for hy-per/hypocalcemia diagno-sis. IEEE/ACM Transac-tions on Computational Bi-ology and Bioinformatics,15(3):788–801, May 2018.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Patoary:2019:PSD

[PTM+19] Mohammad Nazrul Ish-lam Patoary, Carl Trop-per, Robert A. McDou-gal, Zhongwei Lin, andWilliam W. Lytton. Par-allel stochastic discreteevent simulation of cal-cium dynamics in neuron.IEEE/ACM Transactions onComputational Biology andBioinformatics, 16(3):1007–1019, May 2019. CODENITCBCY. ISSN 1545-5963(print), 1557-9964 (elec-tronic).

Puljiz:2016:DGV

[PV16] Zrinka Puljiz and HarisVikalo. Decoding geneticvariations: communications-inspired haplotype assem-bly. IEEE/ACM Transac-tions on Computational Bi-ology and Bioinformatics,13(3):518–530, May 2016.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

REFERENCES 276

Pirola:2012:FPA

[PVB+12] Yuri Pirola, Gianluca DellaVedova, Stefano Biffani,Alessandra Stella, and PaolaBonizzoni. A fast and prac-tical approach to genotypephasing and imputation ona pedigree with erroneousand incomplete information.IEEE/ACM Transactionson Computational Biologyand Bioinformatics, 9(6):1582–1594, November 2012.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Pathak:2020:PSR

[PvRV+20] Shreyasi Pathak, Jorit vanRossen, Onno Vijlbrief,Jeroen Geerdink, ChristinSeifert, and Maurice vanKeulen. Post-structuring ra-diology reports of breast can-cer patients for clinical qual-ity assurance. IEEE/ACMTransactions on Computa-tional Biology and Bioin-formatics, 17(6):1883–1894,November 2020. CODENITCBCY. ISSN 1545-5963(print), 1557-9964 (elec-tronic). URL https://dl.acm.org/doi/10.1109/TCBB.2019.2914678.

Peng:2015:UAI

[PWC+15] Wei Peng, Jianxin Wang,Yingjiao Cheng, Yu Lu,Fangxiang Wu, and Yi Pan.UDoNC: an algorithm foridentifying essential proteinsbased on protein domains

and protein–protein interac-tion networks. IEEE/ACMTransactions on Computa-tional Biology and Bioin-formatics, 12(2):276–288,March 2015. CODENITCBCY. ISSN 1545-5963(print), 1557-9964 (elec-tronic).

Pehkonen:2010:HBS

[PWT10] Petri Pehkonen, GarryWong, and Petri Toronen.Heuristic Bayesian segmen-tation for discovery of coex-pressed genes within genomicregions. IEEE/ACM Trans-actions on ComputationalBiology and Bioinformatics,7(1):37–49, January 2010.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Peng:2015:IPC

[PWZW15] Wei Peng, Jianxin Wang,Bihai Zhao, and LushengWang. Identification ofprotein complexes usingweighted PageRank–Nibblealgorithm and core-attachmentstructure. IEEE/ACMTransactions on Computa-tional Biology and Bioin-formatics, 12(1):179–192,January 2015. CODENITCBCY. ISSN 1545-5963(print), 1557-9964 (elec-tronic).

Peng:2020:CNB

[PZH20] Chen Peng, Yang Zheng, andDe-Shuang Huang. Cap-

REFERENCES 277

sule network based model-ing of multi-omics data fordiscovery of breast cancer-related genes. IEEE/ACMTransactions on Computa-tional Biology and Bioin-formatics, 17(5):1605–1612,September 2020. CODENITCBCY. ISSN 1545-5963(print), 1557-9964 (elec-tronic). URL https://dl.acm.org/doi/10.1109/TCBB.2019.2909905.

Peng:2020:HSC

[PZS+20] Shaoliang Peng, XiaoyuZhang, Wenhe Su, DongDong, Yutong Lu, XiangkeLiao, Kai Lu, CanqunYang, Jie Liu, Weiliang Zhu,and Dongqing Wei. High-scalable collaborated paral-lel framework for large-scalemolecular dynamic simula-tion on Tianhe-2 supercom-puter. IEEE/ACM Trans-actions on ComputationalBiology and Bioinformatics,17(3):804–816, May 2020.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic). URL https://dl.acm.org/doi/10.1109/TCBB.2018.2805709.

Peng:2020:MRA

[PZWC20] Jiajie Peng, Linjiao Zhu,Yadong Wang, and JinChen. Mining relation-ships among multiple enti-ties in biological networks.IEEE/ACM Transactions onComputational Biology andBioinformatics, 17(3):769–

776, May 2020. CODENITCBCY. ISSN 1545-5963(print), 1557-9964 (elec-tronic). URL https://dl.acm.org/doi/10.1109/TCBB.2019.2904965.

Quevedo:2012:DLP

[QBPEL12] Jose R. Quevedo, AntonioBahamonde, Miguel Perez-Enciso, and Oscar Luaces.Disease liability predictionfrom large scale genotypingdata using classifiers with areject option. IEEE/ACMTransactions on Computa-tional Biology and Bioinfor-matics, 9(1):88–97, January2012. CODEN ITCBCY.ISSN 1545-5963 (print),1557-9964 (electronic).

Qian:2012:IGR

[QD12] Xiaoning Qian and Ed-ward R. Dougherty. Inter-vention in gene regulatorynetworks via phenotypicallyconstrained control policiesbased on long-run behav-ior. IEEE/ACM Transac-tions on Computational Bi-ology and Bioinformatics, 9(1):123–136, January 2012.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Qiu:2014:UHD

[Qiu14] Peng Qiu. Unfold high-dimensional clouds for ex-haustive gating of flow cy-tometry data. IEEE/ACMTransactions on Computa-

REFERENCES 278


Qiao:2018:QDA

[QKO18] Shi Qiao, Mehmet Koyuturk,and Meral Z. Ozsoyoglu.Querying of disparate as-sociation and interactiondata in biomedical applica-tions. IEEE/ACM Transac-tions on Computational Bi-ology and Bioinformatics, 15(4):1052–1065, July 2018.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Qiu:2009:FMK

[QL09] Shibin Qiu and Terran Lane.A framework for multiplekernel support vector re-gression and its applicationsto siRNA efficacy predic-tion. IEEE/ACM Trans-actions on ComputationalBiology and Bioinformatics,6(2):190–199, April 2009.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Qi:2016:PEP

[QL16] Yi Qi and Jiawei Luo. Pre-diction of essential pro-teins based on local inter-action density. IEEE/ACMTransactions on Computa-tional Biology and Bioin-formatics, 13(6):1170–1182,

November 2016. CODENITCBCY. ISSN 1545-5963(print), 1557-9964 (elec-tronic).

Qi:2010:SGR

[QLLX10] Xingqin Qi, Guojun Li,Shuguang Li, and Ying Xu.Sorting genomes by recipro-cal translocations, insertions,and deletions. IEEE/ACMTransactions on Computa-tional Biology and Bioinfor-matics, 7(2):365–374, April2010. CODEN ITCBCY.ISSN 1545-5963 (print),1557-9964 (electronic).

Qin:2016:IDA

[QLZ16] Gui-Min Qin, Rui-Yi Li, andXing-Ming Zhao. Identifyingdisease associated miRNAsbased on protein domains.IEEE/ACM Transactionson Computational Biologyand Bioinformatics, 13(6):1027–1035, November 2016.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Qingge:2020:AOS

[QSJ+20] Letu Qingge, Killian Smith,Sean Jungst, Baihui Wang,Qing Yang, and Binhai Zhu.Approaching the one-sidedexemplar adjacency num-ber problem. IEEE/ACMTransactions on Computa-tional Biology and Bioin-formatics, 17(6):1946–1954,November 2020. CODENITCBCY. ISSN 1545-5963

REFERENCES 279


Qiu:2015:IMA

[QTZ15] Yu-Qing Qiu, Xue Tian, andShihua Zhang. Infer metage-nomic abundance and re-veal homologous genomesbased on the structure oftaxonomy tree. IEEE/ACMTransactions on Computa-tional Biology and Bioin-formatics, 12(5):1112–1122,September 2015. CODENITCBCY. ISSN 1545-5963(print), 1557-9964 (elec-tronic).

Qi:2017:SCM

[QV17] Zhen Qi and Eberhard O.Voit. Strategies for compar-ing metabolic profiles: Im-plications for the inferenceof biochemical mechanismsfrom metabolomics data.IEEE/ACM Transactionson Computational Biologyand Bioinformatics, 14(6):1434–1445, November 2017.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Qu:2016:PSL

[QWC+16] Xumi Qu, Dong Wang, Yue-hui Chen, Shanping Qiao,and Qing Zhao. Predict-ing the subcellular localiza-tion of proteins with multi-ple sites based on multiplefeatures fusion. IEEE/ACM

Transactions on Computa-tional Biology and Bioinfor-matics, 13(1):36–42, January2016. CODEN ITCBCY.ISSN 1545-5963 (print),1557-9964 (electronic).

Roy:2016:DMB

[RA16] Indranil Roy and SrinivasAluru. Discovering motifsin biological sequences usingthe Micron automata proces-sor. IEEE/ACM Transac-tions on Computational Bi-ology and Bioinformatics, 13(1):99–111, January 2016.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Rajasekaran:2010:IAP

[RAA10] Sanguthevar Rajasekaran,Sahar Al Seesi, and Reda A.Ammar. Improved algo-rithms for parsing ESLT-AGs: a grammatical modelsuitable for RNA pseudo-knots. IEEE/ACM Transac-tions on Computational Bi-ology and Bioinformatics, 7(4):619–627, October 2010.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Raza:2020:SPF

[RAA20] Saad Raza, Ghulam Abbas,and Syed Sikander Azam.Screening pipeline for fla-vivirus based inhibitors forZika virus NS1. IEEE/ACMTransactions on Computa-tional Biology and Bioin-

REFERENCES 280

formatics, 17(5):1751–1761,September 2020. CODENITCBCY. ISSN 1545-5963(print), 1557-9964 (elec-tronic). URL https://dl.acm.org/doi/10.1109/TCBB.2019.2911081.

Ritz:2017:PAS

[RAM17] Anna Ritz, Brendan Avent,and T. M. Murali. Path-way analysis with signalinghypergraphs. IEEE/ACMTransactions on Computa-tional Biology and Bioin-formatics, 14(5):1042–1055,September 2017. CODENITCBCY. ISSN 1545-5963(print), 1557-9964 (elec-tronic).

Rizvi:2014:DRO

[RB14] Ahsan Z. Rizvi and C. Bhat-tacharya. Detection of repli-cation origin sites in her-pesvirus genomes by clus-tering and scoring of palin-dromes with quadratic en-tropy measures. IEEE/ACMTransactions on Computa-tional Biology and Bioin-formatics, 11(6):1108–1118,November 2014. CODENITCBCY. ISSN 1545-5963(print), 1557-9964 (elec-tronic).

Ray:2016:DCS

[RB16] Sumanta Ray and Sanghami-tra Bandyopadhyay. Discov-ering condition specific topo-logical pattern changes in co-expression network: an ap-

plication to HIV-1 progres-sion. IEEE/ACM Trans-actions on ComputationalBiology and Bioinformatics,13(6):1086–1099, November2016. CODEN ITCBCY.ISSN 1545-5963 (print),1557-9964 (electronic).

Rampogu:2019:INS

[RBB+19] Shailima Rampogu, AyoungBaek, Rohit Bavi, MinkySon, Guang Ping Cao, RajKumar, Chanin Park, AmirZeb, Rabia Mukthar Rana,Seok Ju Park, and Keun WooLee. Identification of novelscaffolds with dual role asantiepileptic and anti-breastcancer. IEEE/ACM Trans-actions on ComputationalBiology and Bioinformatics,16(5):1663–1674, September2019. CODEN ITCBCY.ISSN 1545-5963 (print),1557-9964 (electronic).

Ropers:2011:MRU

[RBdJ11] Delphine Ropers, ValentinaBaldazzi, and Hidde de Jong.Model reduction using piecewise-linear approximations pre-serves dynamic propertiesof the carbon starvation re-sponse in Escherichia coli .IEEE/ACM Transactions onComputational Biology andBioinformatics, 8(1):166–181, January 2011. CODENITCBCY. ISSN 1545-5963(print), 1557-9964 (elec-tronic).

REFERENCES 281

Rivera-Borroto:2016:RAM

[RBdlVMPG16] Oscar Miguel Rivera-Borroto,Jose Manuel Garcia de laVega, Yovani Marrero-Ponce,and Ricardo Grau. Rela-tional agreement measuresfor similarity searching ofcheminformatic data sets.IEEE/ACM Transactions onComputational Biology andBioinformatics, 13(1):158–167, January 2016. CODENITCBCY. ISSN 1545-5963(print), 1557-9964 (elec-tronic).

Ram:2011:MBB

[RC11] Ramesh Ram and MadhuChetty. A Markov-Blanket-based model for gene reg-ulatory network inference.IEEE/ACM Transactions onComputational Biology andBioinformatics, 8(2):353–367, March 2011. CODENITCBCY. ISSN 1545-5963(print), 1557-9964 (elec-tronic).

Rasheed:2019:SFU

[RCBB19] Muhibur Rasheed, NathanClement, Abhishek Bhowmick,and Chandrajit L. Bajaj.Statistical framework foruncertainty quantificationin computational molecu-lar modeling. IEEE/ACMTransactions on Computa-tional Biology and Bioin-formatics, 16(4):1154–1167,July 2019. CODEN ITCBCY.ISSN 1545-5963 (print),1557-9964 (electronic).

Rizzi:2019:HCA

[RCM+19] Romeo Rizzi, MassimoCairo, Veli Makinen, Alexan-dru I. Tomescu, and DanielValenzuela. Hardness of cov-ering alignment: Phase tran-sition in post-sequence ge-nomics. IEEE/ACM Trans-actions on ComputationalBiology and Bioinformatics,16(1):23–30, January 2019.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Raisaro:2018:PPS

[RCP+18] Jean Louis Raisaro, Gwang-bae Choi, Sylvain Prader-vand, Raphael Colsenet,Nathalie Jacquemont, Nico-las Rosat, Vincent Mooser,and Jean-Pierre Hubaux.Protecting privacy and secu-rity of genomic data in i2b2with homomorphic encryp-tion and differential privacy.IEEE/ACM Transactionson Computational Biologyand Bioinformatics, 15(5):1413–1426, September 2018.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Rasmussen:2009:MVU

[RdlCGW09] Carl Rasmussen, Bernardde la Cruz, Zoubin Ghahra-mani, and David Wild. Mod-eling and visualizing uncer-tainty in gene expressionclusters using Dirichlet pro-cess mixtures. IEEE/ACM

REFERENCES 282

Transactions on Computa-tional Biology and Bioinfor-matics, 6(4):615–628, Octo-ber 2009. CODEN ITCBCY.ISSN 1545-5963 (print),1557-9964 (electronic).

Requeno:2013:TLP

[RdMCBC13] Jose Ignacio Requeno, Gre-gorio de Miguel Casado,Roberto Blanco, and Jose ManuelColom. Temporal log-ics for phylogenetic anal-ysis via model checking.IEEE/ACM Transactions onComputational Biology andBioinformatics, 10(4):1058–1070, July 2013. CODENITCBCY. ISSN 1545-5963(print), 1557-9964 (elec-tronic).

Riesen:2020:AGE

[RFB20] Kaspar Riesen, Miquel Fer-rer, and Horst Bunke. Ap-proximate graph edit dis-tance in quadratic time.IEEE/ACM Transactions onComputational Biology andBioinformatics, 17(2):483–494, March 2020. CODENITCBCY. ISSN 1545-5963(print), 1557-9964 (elec-tronic). URL https://dl.acm.org/doi/abs/10.1109/TCBB.2015.2478463.

Ranjan:2020:DRF

[RFFB+20] Ashish Ranjan, Md ShahFahad, David Fernandez-Baca, Akshay Deepak, andSudhakar Tripathi. Deeprobust framework for pro-

tein function prediction us-ing variable-length proteinsequences. IEEE/ACMTransactions on Computa-tional Biology and Bioin-formatics, 17(5):1648–1659,September 2020. CODENITCBCY. ISSN 1545-5963(print), 1557-9964 (elec-tronic). URL https://dl.acm.org/doi/10.1109/TCBB.2019.2911609.

Raposo:2016:CAM

[RG16] Adriano N. Raposo and AbelJ. P. Gomes. Computational3D assembling methods forDNA: a survey. IEEE/ACMTransactions on Computa-tional Biology and Bioin-formatics, 13(6):1068–1085,November 2016. CODENITCBCY. ISSN 1545-5963(print), 1557-9964 (elec-tronic).

Rogers:2005:LPD

[RGCB05] Simon Rogers, Mark Giro-lami, Colin Campbell, andRainer Breitling. The la-tent process decompositionof cDNA microarray datasets. IEEE/ACM Transac-tions on Computational Bi-ology and Bioinformatics,2(2):143–156, April 2005.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Rajabli:2013:ADS

[RGI13] Farid Rajabli, Unal Goktas,and Gul Inan. Application

REFERENCES 283

of dempster-schafer methodin family-based associationstudies. IEEE/ACM Trans-actions on ComputationalBiology and Bioinformatics,10(4):1071–1075, July 2013.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Roytberg:2009:SSP

[RGN+09] Mikhail Roytberg, AnnaGambin, Laurent Noe, Sla-womir Lasota, EugeniaFurletova, Ewa Szczurek,and Gregory Kucherov. Onsubset seeds for proteinalignment. IEEE/ACMTransactions on Computa-tional Biology and Bioinfor-matics, 6(3):483–494, July2009. CODEN ITCBCY.ISSN 1545-5963 (print),1557-9964 (electronic).

Rajapakse:2005:MED

[RH05] Jagath C. Rajapakse andLoi Sy Ho. Markov en-coding for detecting sig-nals in genomic sequences.IEEE/ACM Transactions onComputational Biology andBioinformatics, 2(2):131–142, April 2005. CODENITCBCY. ISSN 1545-5963(print), 1557-9964 (elec-tronic).

Rathore:2013:RSC

[RHAK13] Saima Rathore, MutawarraHussain, Ahmad Ali, andAsifullah Khan. A recentsurvey on colon cancer detec-

tion techniques. IEEE/ACMTransactions on Computa-tional Biology and Bioinfor-matics, 10(3):545–563, May2013. CODEN ITCBCY.ISSN 1545-5963 (print),1557-9964 (electronic).

Ren:2016:FRA

[RHH16] Hai-Peng Ren, Xiao-NaHuang, and Jia-Xuan Hao.Finding robust adaptationgene regulatory networks us-ing multi-objective geneticalgorithm. IEEE/ACMTransactions on Computa-tional Biology and Bioinfor-matics, 13(3):571–577, May2016. CODEN ITCBCY.ISSN 1545-5963 (print),1557-9964 (electronic).

Rathore:2014:GGE

[RHK14] Saima Rathore, MutawarraHussain, and Asifullah Khan.GECC: gene expressionbased ensemble classifi-cation of colon samples.IEEE/ACM Transactionson Computational Biologyand Bioinformatics, 11(6):1131–1145, November 2014.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Rhodes:2020:TMT

[Rho20] John A. Rhodes. Topolog-ical metrizations of trees,and new quartet methods oftree inference. IEEE/ACMTransactions on Computa-tional Biology and Bioin-

REFERENCES 284

formatics, 17(6):2107–2118,November 2020. CODENITCBCY. ISSN 1545-5963(print), 1557-9964 (elec-tronic). URL https://dl.acm.org/doi/10.1109/TCBB.2019.2917204.

Rydzewski:2018:CSB

[RJNN18] Jakub Rydzewski, RafalJakubowski, Giuseppe Nicosia,and Wieslaw Nowak. Con-formational sampling of abiomolecular rugged energylandscape. IEEE/ACMTransactions on Computa-tional Biology and Bioinfor-matics, 15(3):732–739, May2018. CODEN ITCBCY.ISSN 1545-5963 (print),1557-9964 (electronic).

Raiford:2010:AIT

[RKDR10] Douglas W. Raiford, Dan E.Krane, Travis E. Doom, andMichael L. Raymer. Au-tomated isolation of trans-lational efficiency bias thatresists the confounding ef-fect of GC(AT)-content.IEEE/ACM Transactions onComputational Biology andBioinformatics, 7(2):238–250, April 2010. CODENITCBCY. ISSN 1545-5963(print), 1557-9964 (elec-tronic).

Raiford:2011:GOA

[RKDR11] Douglas W. Raiford, Dan E.Krane, Travis E. Doom, andMichael L. Raymer. A ge-netic optimization approach

for isolating translational ef-ficiency bias. IEEE/ACMTransactions on Computa-tional Biology and Bioinfor-matics, 8(2):342–352, March2011. CODEN ITCBCY.ISSN 1545-5963 (print),1557-9964 (electronic).

Ray:2016:IAC

[RKZ16] Meredith Ray, Jian Kang,and Hongmei Zhang. Iden-tifying activation centerswith spatial Cox point pro-cesses using fMRI data.IEEE/ACM Transactionson Computational Biologyand Bioinformatics, 13(6):1130–1141, November 2016.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Rahman:2020:PPM

[RLR20] Mohammad Arifur Rah-man, Nathan LaPierre, andHuzefa Rangwala. Pheno-type prediction from metage-nomic data using clusteringand assembly with multipleinstance learning (CAMIL).IEEE/ACM Transactions onComputational Biology andBioinformatics, 17(3):828–840, May 2020. CODENITCBCY. ISSN 1545-5963(print), 1557-9964 (elec-tronic). URL https://dl.acm.org/doi/10.1109/TCBB.2017.2758782.

Ramalho:2018:PEF

[RLRH18] Rodrigo F. Ramalho, Su-jun Li, Predrag Radi-

REFERENCES 285

vojac, and Matthew W.Hahn. Proteomic evidencefor in-frame and out-of-frame alternatively splicedisoforms in human andmouse. IEEE/ACM Trans-actions on ComputationalBiology and Bioinformatics,15(4):1284–1289, July 2018.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Raphael:2004:UPM

[RLV04] Benjamin Raphael, Lung-Tien Liu, and George Vargh-ese. A uniform projec-tion method for motif dis-covery in DNA sequences.IEEE/ACM Transactionson Computational Biologyand Bioinformatics, 1(2):91–94, April 2004. CODENITCBCY. ISSN 1545-5963(print), 1557-9964 (elec-tronic).

Rajapakse:2013:MGS

[RM13] Jagath C. Rajapakse andPiyushkumar A. Mundra.Multiclass gene selection us-ing Pareto-fronts. IEEE/ACM Transactions on Com-putational Biology and Bioin-formatics, 10(1):87–97, Jan-uary 2013. CODEN ITCBCY.ISSN 1545-5963 (print),1557-9964 (electronic).

Ray:2018:DPM

[RM18] Sumanta Ray and UjjwalMaulik. Discovering pertur-bation of modular structure

in HIV progression by inte-grating multiple data sourcesthrough non-negative matrixfactorization. IEEE/ACMTransactions on Computa-tional Biology and Bioinfor-matics, 15(3):869–877, May2018. CODEN ITCBCY.ISSN 1545-5963 (print),1557-9964 (electronic).

Rubiolo:2015:MGR

[RMS15] Mariano Rubiolo, Diego H.Milone, and Georgina Stegmayer.Mining gene regulatory net-works by neural modelingof expression time-series.IEEE/ACM Transactionson Computational Biologyand Bioinformatics, 12(6):1365–1373, November 2015.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Re:2012:FRA

[RMV12] Matteo Re, Marco Mesiti,and Giorgio Valentini. Afast ranking algorithm forpredicting gene functionsin biomolecular networks.IEEE/ACM Transactionson Computational Biologyand Bioinformatics, 9(6):1812–1818, November 2012.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Roch:2006:SPP

[Roc06] Sebastien Roch. A shortproof that phylogenetic treereconstruction by maxi-

REFERENCES 286

mum likelihood is hard.IEEE/ACM Transactions onComputational Biology andBioinformatics, 3(1):92–94,January 2006. CODENITCBCY. ISSN 1545-5963(print), 1557-9964 (elec-tronic).

Rocha:2011:GCL

[Roc11] J. Rocha. Graph com-parison by log-odds scorematrices with applicationto protein topology analy-sis. IEEE/ACM Transac-tions on Computational Bi-ology and Bioinformatics, 8(2):564–569, March 2011.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Rosenberg:2013:CHC

[Ros13] Noah A. Rosenberg. Coales-cent histories for caterpillar-like families. IEEE/ACMTransactions on Computa-tional Biology and Bioin-formatics, 10(5):1253–1262,September 2013. CODENITCBCY. ISSN 1545-5963(print), 1557-9964 (elec-tronic).

Ray:2013:RSS

[RP13] Shubhra Sankar Ray andSankar K. Pal. RNA sec-ondary structure predic-tion using soft comput-ing. IEEE/ACM Transac-tions on Computational Bi-ology and Bioinformatics,10(1):2–17, January 2013.


Rahman:2013:REM

[RPB+13] Ahsanur Rahman, Christo-pher L. Poirel, David J. Bad-ger, Craig Estep, and T. M.Murali. Reverse engineer-ing molecular hypergraphs.IEEE/ACM Transactionson Computational Biologyand Bioinformatics, 10(5):1113–1124, September 2013.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Russo:2018:CPN

[RPBP18] Giulia Russo, Marzio Pen-nisi, Roberta Boscarino, andFrancesco Pappalardo. Con-tinuous Petri nets and mi-croRNA analysis in melanoma.IEEE/ACM Transactionson Computational Biologyand Bioinformatics, 15(5):1492–1499, September 2018.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Rottger:2012:HLD

[RRTB12] Richard Rottger, UlrichRuckert, Jan Taubert, andJan Baumbach. How lit-tle do we actually know?On the size of gene regula-tory networks. IEEE/ACMTransactions on Computa-tional Biology and Bioin-formatics, 9(5):1293–1300,September 2012. CODEN

REFERENCES 287


Ren:2018:IAS

[RSCX18] Shuai Ren, Yan Shi, MaolinCai, and Weiqing Xu. In-fluence of airway secretionon airflow dynamics of me-chanical ventilated respira-tory system. IEEE/ACMTransactions on Computa-tional Biology and Bioin-formatics, 15(5):1660–1668,September 2018. CODENITCBCY. ISSN 1545-5963(print), 1557-9964 (elec-tronic).

Roth:2018:TES

[RSG18] Adam Roth, Sandeep Sub-ramanian, and Madhavi K.Ganapathiraju. Towardsextracting supporting in-formation about predictedprotein-protein interactions.IEEE/ACM Transactions onComputational Biology andBioinformatics, 15(4):1239–1246, July 2018. CODENITCBCY. ISSN 1545-5963(print), 1557-9964 (elec-tronic).

Rud:2013:RFL

[RSJK13] Ali Gholami Rud, SaeedShahrivari, Saeed Jalili, andZahra Razaghi MoghadamKashani. RANGI: a fastlist-colored graph motif find-ing algorithm. IEEE/ACMTransactions on Computa-tional Biology and Bioin-

formatics, 10(2):504–513,March 2013. CODENITCBCY. ISSN 1545-5963(print), 1557-9964 (elec-tronic).

Rinaldi:2010:OBI

[RSK+10] Fabio Rinaldi, Gerold Schnei-der, Kaarel Kaljurand, Si-mon Clematide, Therese Va-chon, and Martin Romacker.OntoGene in BioCreativeII.5. IEEE/ACM Trans-actions on ComputationalBiology and Bioinformat-ics, 7(3):472–480, July 2010.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Rother:2008:SCP

[RSP08] Diego Rother, GuillermoSapiro, and Vijay Pande.Statistical characterizationof protein ensembles. IEEE/ACM Transactions on Com-putational Biology and Bioin-formatics, 5(1):42–55, Jan-uary 2008. CODEN ITCBCY.ISSN 1545-5963 (print),1557-9964 (electronic).

Randhawa:2010:MCM

[RST10] Ranjit Randhawa, Cliff Shaf-fer, and John Tyson. Modelcomposition for macromolec-ular regulatory networks.IEEE/ACM Transactions onComputational Biology andBioinformatics, 7(2):278–287, April 2010. CODENITCBCY. ISSN 1545-5963

REFERENCES 288


Ranganarayanan:2016:IGB

[RTA+16] Preethi Ranganarayanan,Narmadha Thanigesan, VivekAnanth, Valadi K. Jayara-man, and Vigneshwar Ra-makrishnan. Identificationof glucose-binding pockets inhuman serum albumin usingsupport vector machine andmolecular dynamics simula-tions. IEEE/ACM Transac-tions on Computational Bi-ology and Bioinformatics, 13(1):148–157, January 2016.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Raisaro:2019:MES

[RTPM+19] Jean Louis Raisaro, Juan Ra-mon Troncoso-Pastoriza,Mickael Misbach, Joao SaSousa, Sylvain Pradervand,Edoardo Missiaglia, OlivierMichielin, Bryan Ford,and Jean-Pierre Hubaux.MedCo: Enabling secureand privacy-preserving ex-ploration of distributed clin-ical and genomic data.IEEE/ACM Transactions onComputational Biology andBioinformatics, 16(4):1328–1341, July 2019. CODENITCBCY. ISSN 1545-5963(print), 1557-9964 (elec-tronic).

Ranjbar:2015:BNM

[RTWR15] Mohammad R. Nezami Ran-

jbar, Mahlet G. Tadesse,Yue Wang, and Habtom W.Ressom. Bayesian normal-ization model for label-freequantitative analysis by LC–MS. IEEE/ACM Transac-tions on Computational Bi-ology and Bioinformatics,12(4):914–927, July 2015.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Rueda:2006:HCA

[RV06] Luis Rueda and VidyaVidyadharan. A hill-climbing approach for au-tomatic gridding of cDNAmicroarray images. IEEE/ACM Transactions on Com-putational Biology and Bioin-formatics, 3(1):72–83, Jan-uary 2006. CODEN ITCBCY.ISSN 1545-5963 (print),1557-9964 (electronic).

Re:2013:NBD

[RV13] Matteo Re and GiorgioValentini. Network-baseddrug ranking and reposition-ing with respect to Drug-Bank therapeutic categories.IEEE/ACM Transactionson Computational Biologyand Bioinformatics, 10(6):1359–1371, November 2013.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Reinert:2007:LLE

[RW07] Gesine Reinert and Michael S.Waterman. On the length

REFERENCES 289

of the longest exact posi-tion match in a random se-quence. IEEE/ACM Trans-actions on ComputationalBiology and Bioinformatics,4(1):153–156, January 2007.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Rubel:2010:IDC

[RWH+10] Oliver Rubel, Gunther H.Weber, Min-Yu Huang,E. Wes Bethel, Mark D. Big-gin, Charless C. Fowlkes,Cris L. Luengo Hendriks,Soile V. E. Keranen, Michael B.Eisen, David W. Knowles, Ji-tendra Malik, Hans Hagen,and Bernd Hamann. Inte-grating data clustering andvisualization for the anal-ysis of 3D gene expressiondata. IEEE/ACM Trans-actions on ComputationalBiology and Bioinformatics,7(1):64–79, January 2010.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Rhee:2019:ILC

[RYK+19] Je-Keun Rhee, Jinseon Yoo,Kyu Ryung Kim, JeeyoonKim, Yong-Jae Lee, By-oung Chul Cho, and Tae-MinKim. Identification of localclusters of mutation hotspotsin cancer-related genes andtheir biological relevance.IEEE/ACM Transactionson Computational Biologyand Bioinformatics, 16(5):


Rajapakse:2007:GEI

[RZF07] Jagath C. Rajapakse, Yan-Qing Zhang, and Gary B. Fo-gel. Guest Editors’ introduc-tion to the Special Section:Computational IntelligenceApproaches in Computa-tional Biology and Bioinfor-matics. IEEE/ACM Trans-actions on ComputationalBiology and Bioinformatics,4(2):161–162, April 2007.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Rajaraman:2017:ACR

[RZMC17] Ashok Rajaraman, JoaoPaulo Pereira Zanetti, JanManuch, and Cedric Chauve.Algorithms and complex-ity results for genome map-ping problems. IEEE/ACMTransactions on Computa-tional Biology and Bioin-formatics, 14(2):418–430,March 2017. CODENITCBCY. ISSN 1545-5963(print), 1557-9964 (elec-tronic).

Raveh:2015:RFM

[RZMT15] Alon Raveh, Yoram Zarai,Michael Margaliot, andTamir Tuller. Ribosome flowmodel on a ring. IEEE/ACMTransactions on Computa-tional Biology and Bioin-

REFERENCES 290

formatics, 12(6):1429–1439,November 2015. CODENITCBCY. ISSN 1545-5963(print), 1557-9964 (elec-tronic).

Setubal:2015:TSS

[SA15] Joao C. Setubal and NalvoAlmeida. TCBB special sec-tion on the Brazilian Sym-posium on Bioinformatics2013. IEEE/ACM Trans-actions on ComputationalBiology and Bioinformat-ics, 12(3):499, May 2015.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Sarkar:2020:EAI

[SAE+20] Aisharjya Sarkar, YilmazAtay, Alana Lorraine Er-ickson, Ivan Arisi, CesareSaltini, and Tamer Kahveci.An efficient algorithm foridentifying mutated subnet-works associated with sur-vival in cancer. IEEE/ACMTransactions on Computa-tional Biology and Bioin-formatics, 17(5):1582–1594,September 2020. CODENITCBCY. ISSN 1545-5963(print), 1557-9964 (elec-tronic). URL https://dl.acm.org/doi/10.1109/TCBB.2019.2911069.

Sagot:2009:EE

[Sag09a] Marie-France Sagot. EIC ed-itorial. IEEE/ACM Trans-actions on ComputationalBiology and Bioinformat-ics, 6(2):177, April 2009.


Sagot:2009:EEI

[Sag09b] Marie-France Sagot. EIC ed-itorial: Introducing new As-sociate Editors. IEEE/ACMTransactions on Computa-tional Biology and Bioinfor-matics, 6(3):369, July 2009.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Sagot:2009:NEE

[Sag09c] Marie-France Sagot. NewEIC editorial. IEEE/ACMTransactions on Computa-tional Biology and Bioinfor-matics, 6(1):3, January 2009.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Sagot:2010:EE

[Sag10] Marie-France Sagot. EIC ed-itorial. IEEE/ACM Trans-actions on ComputationalBiology and Bioinformatics,7(2):193–194, April 2010.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Sagot:2011:EEa

[Sag11a] Marie-France Sagot. EIC ed-itorial. IEEE/ACM Trans-actions on ComputationalBiology and Bioinformat-ics, 8(1):1, January 2011.CODEN ITCBCY. ISSN

REFERENCES 291


Sagot:2011:EEb

[Sag11b] Marie-France Sagot. EIC ed-itorial. IEEE/ACM Trans-actions on ComputationalBiology and Bioinformatics,8(2):289–291, March 2011.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Sagot:2012:EE

[Sag12] Marie-France Sagot. EIC ed-itorial. IEEE/ACM Trans-actions on ComputationalBiology and Bioinformatics,9(6):1553–1557, November2012. CODEN ITCBCY.ISSN 1545-5963 (print),1557-9964 (electronic).

Sadat:2019:SSG

[SAM+19] Md Nazmus Sadat, Md MominAl Aziz, Noman Mohammed,Feng Chen, Xiaoqian Jiang,and Shuang Wang. SAFETY:Secure gwAs in FederatedEnvironment through a hY-brid Solution. IEEE/ACMTransactions on Computa-tional Biology and Bioinfor-matics, 16(1):93–102, Jan-uary 2019. CODEN ITCBCY.ISSN 1545-5963 (print),1557-9964 (electronic).

Sun:2009:DPP

[SB09] Yanni Sun and Jeremy Buh-ler. Designing patternsand profiles for faster HMM

search. IEEE/ACM Trans-actions on ComputationalBiology and Bioinformatics,6(2):232–243, April 2009.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Sengupta:2012:NDP

[SB12] Soumi Sengupta and Sang-hamitra Bandyopadhyay.De novo design of poten-tial RecA inhibitors us-ing MultiObjective optimiza-tion. IEEE/ACM Transac-tions on Computational Bi-ology and Bioinformatics, 9(4):1139–1154, July 2012.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Stamoulis:2016:OSD

[SB16] Catherine Stamoulis and Re-becca A. Betensky. Opti-mization of signal decom-position matched filtering(SDMF) for improved detec-tion of copy-number varia-tions. IEEE/ACM Trans-actions on ComputationalBiology and Bioinformatics,13(3):584–591, May 2016.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Sriwastava:2015:PPP

[SBM15] Brijesh K. Sriwastava, Sub-hadip Basu, and UjjwalMaulik. Predicting protein-protein interaction siteswith a novel membership

REFERENCES 292

based fuzzy SVM classifier.IEEE/ACM Transactionson Computational Biologyand Bioinformatics, 12(6):1394–1404, November 2015.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Song:2011:MSS

[SBRK11] Bin Song, I Esra Buyuktahtakin,Sanjay Ranka, and TamerKahveci. Manipulating thesteady state of metabolicpathways. IEEE/ACMTransactions on Computa-tional Biology and Bioinfor-matics, 8(3):732–747, May/June 2011. CODENITCBCY. ISSN 1545-5963(print), 1557-9964 (elec-tronic).

Sengupta:2015:CAU

[SBW15] T. Sengupta, M. Bhushan,and P. P. Wangikar. Acomputational approach us-ing ratio statistics for iden-tifying housekeeping genesfrom cDNA microarray data.IEEE/ACM Transactionson Computational Biologyand Bioinformatics, 12(6):1457–1463, November 2015.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Sun:2012:DFF

[SBY12] Yanni Sun, Jeremy Buhler,and Cheng Yuan. Designingfilters for fast-known NcRNAidentification. IEEE/ACM

Transactions on Computa-tional Biology and Bioinfor-matics, 9(3):774–787, May2012. CODEN ITCBCY.ISSN 1545-5963 (print),1557-9964 (electronic).

Shah:2011:GFA

[SC11] Mohak Shah and JacquesCorbeil. A general frame-work for analyzing data fromtwo short time-series mi-croarray experiments. IEEE/ACM Transactions on Com-putational Biology and Bioin-formatics, 8(1):14–26, Jan-uary 2011. CODEN ITCBCY.ISSN 1545-5963 (print),1557-9964 (electronic).

Song:2015:PBM

[SCC+15] Dandan Song, Jiaxing Chen,Guang Chen, Ning Li, JinLi, Jun Fan, Dongbo Bu,and Shuai Cheng Li. Pa-rameterized BLOSUM ma-trices for protein alignment.IEEE/ACM Transactions onComputational Biology andBioinformatics, 12(3):686–694, May 2015. CODENITCBCY. ISSN 1545-5963(print), 1557-9964 (elec-tronic).

Sotiropoulos:2009:MRM

[SCCDK09] Vassilios Sotiropoulos, Marrie-Nathalie Contou-Carrere,Prodromos Daoutidis, andYiannis N. Kaznessis. Modelreduction of multiscale chem-ical Langevin equations:a numerical case study.

REFERENCES 293


Stella:2019:DDB

[SCM19] Sabrina Stella, RobertoChignola, and EdoardoMilotti. Dynamical detec-tion of boundaries and cav-ities in biophysical cell-basedsimulations of growing tu-mor tissues. IEEE/ACMTransactions on Computa-tional Biology and Bioin-formatics, 16(6):1901–1911,November 2019. CODENITCBCY. ISSN 1545-5963(print), 1557-9964 (elec-tronic). URL https://dl.acm.org/doi/abs/10.1109/TCBB.2018.2827374.

Swenson:2012:KMA

[SCPS12] Krister M. Swenson, EricChen, Nicholas D. Patten-gale, and David Sankoff. Thekernel of maximum agree-ment subtrees. IEEE/ACMTransactions on Computa-tional Biology and Bioinfor-matics, 9(4):1023–1031, July2012. CODEN ITCBCY.ISSN 1545-5963 (print),1557-9964 (electronic).

Schliep:2005:AGE

[SCSS05] Alexander Schliep, Ivan G.Costa, Christine Steinhoff,and Alexander Schonhuth.

Analyzing gene expressiontime-courses. IEEE/ACMTransactions on Computa-tional Biology and Bioinfor-matics, 2(3):179–193, July2005. CODEN ITCBCY.ISSN 1545-5963 (print),1557-9964 (electronic).

Sebastian:2006:STA

[SDA+06] Rafael Sebastian, Maria-Elena Diaz, Guillermo Ay-ala, Kresimir Letinic, JoseMoncho-Bogani, and DerekToomre. Spatio-temporalanalysis of constitutive ex-ocytosis in epithelial cells.IEEE/ACM Transactions onComputational Biology andBioinformatics, 3(1):17–32,January 2006. CODENITCBCY. ISSN 1545-5963(print), 1557-9964 (elec-tronic).

Seetan:2014:RRH

[SDAA+14] Raed I. Seetan, Anne M.Denton, Omar Al-Azzam,Ajay Kumar, M. Javed Iqbal,and Shahryar F. Kianian.Reliable radiation hybridmaps: an efficient scalableclustering-based approach.IEEE/ACM Transactionson Computational Biologyand Bioinformatics, 11(5):788–800, September 2014.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Sridhar:2007:AEN

[SDB+07] Srinath Sridhar, Kedar

REFERENCES 294

Dhamdhere, Guy Blelloch,Eran Halperin, R. Ravi,and Russell Schwartz. Al-gorithms for efficient near-perfect phylogenetic tree re-construction in theory andpractice. IEEE/ACM Trans-actions on ComputationalBiology and Bioinformatics,4(4):561–571, October 2007.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Sheng:2011:IAG

[SDCW11] Jinhua Sheng, Hong-WenDeng, Vince Calhoun, andYu-Ping Wang. Integratedanalysis of gene expressionand copy number data ongene shaving using indepen-dent component analysis.IEEE/ACM Transactionson Computational Biologyand Bioinformatics, 8(6):1568–1579, November 2011.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Shen:2020:CNP

[SDH20a] Zhen Shen, Su-Ping Deng,and De-Shuang Huang. Cap-sule network for predictingRNA–protein binding prefer-ences using hybrid feature.IEEE/ACM Transactionson Computational Biologyand Bioinformatics, 17(5):1483–1492, September 2020.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic). URL https://


Shen:2020:RPB

[SDH20b] Zhen Shen, Su-Ping Deng,and De-Shuang Huang.RNA-Protein binding sitesprediction via multi scaleconvolutional gated recur-rent unit networks. IEEE/ACM Transactions on Com-putational Biology and Bioin-formatics, 17(5):1741–1750,September 2020. CODENITCBCY. ISSN 1545-5963(print), 1557-9964 (elec-tronic). URL https://dl.acm.org/doi/10.1109/TCBB.2019.2910513.

Sehgal:2011:IRD

[SDN+11] Aditya Kumar Sehgal, San-may Das, Keith Noto, Mil-ton H. Saier, Jr., and CharlesElkan. Identifying rele-vant data for a biologicaldatabase: Handcrafted rulesversus machine learning.IEEE/ACM Transactionson Computational Biologyand Bioinformatics, 8(3):851–857, May/June 2011.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Sambo:2012:MMO

[SdOD+12] Francesco Sambo, MarcoA. Montes de Oca, Bar-bara Di Camillo, Gianna Tof-folo, and Thomas Stutzle.MORE: Mixed optimizationfor reverse engineering — an

REFERENCES 295

application to modeling bi-ological networks responsevia sparse systems of non-linear differential equations.IEEE/ACM Transactionson Computational Biologyand Bioinformatics, 9(5):1459–1471, September 2012.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Sapin:2018:OME

[SDS18] Emmanuel Sapin, Ken-neth A. De Jong, andAmarda Shehu. From op-timization to mapping: anevolutionary algorithm forprotein energy landscapes.IEEE/ACM Transactions onComputational Biology andBioinformatics, 15(3):719–731, May 2018. CODENITCBCY. ISSN 1545-5963(print), 1557-9964 (elec-tronic).

Sun:2019:EMM

[SDTK19] Mengmeng Sun, Tao Ding,Xu-Qing Tang, and Yu Kem-ing. An efficient mixed-model for screening differ-entially expressed genes ofbreast cancer based on LR–RF. IEEE/ACM Transac-tions on Computational Bi-ology and Bioinformatics, 16(1):124–130, January 2019.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Spencer:2015:DLN

[SEC15] Matt Spencer, Jesse Eick-holt, and Jianlin Cheng. Adeep learning network ap-proach to ab initio proteinsecondary structure predic-tion. IEEE/ACM Transac-tions on Computational Bi-ology and Bioinformatics, 12(1):103–112, January 2015.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Senf:2019:EES

[Sen19] Alexander Senf. End-to-end security for local andremote human genetic dataapplications at the EGA.IEEE/ACM Transactions onComputational Biology andBioinformatics, 16(4):1324–1327, July 2019. CODENITCBCY. ISSN 1545-5963(print), 1557-9964 (elec-tronic).

Sadot:2008:TVB

[SFB+08] Avital Sadot, Jasmin Fisher,Dan Barak, Yishai Admanit,Michael J. Stern, E. Jane Al-bert Hubbard, and DavidHarel. Toward verified bio-logical models. IEEE/ACMTransactions on Computa-tional Biology and Bioinfor-matics, 5(2):223–234, April2008. CODEN ITCBCY.ISSN 1545-5963 (print),1557-9964 (electronic).

REFERENCES 296

Stock:2014:IFR

[SFH+14] Michiel Stock, ThomasFober, Eyke Hullermeier,Serghei Glinca, GerhardKlebe, Tapio Pahikkala,Antti Airola, Bernard DeBaets, and Willem Waege-man. Identification of func-tionally related enzymes bylearning-to-rank methods.IEEE/ACM Transactionson Computational Biologyand Bioinformatics, 11(6):1157–1169, November 2014.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Sedaghat:2018:CSU

[SFMS18] Nafiseh Sedaghat, MahmoodFathy, Mohammad HosseinModarressi, and Ali Sho-jaie. Combining supervisedand unsupervised learningfor improved miRNA tar-get prediction. IEEE/ACMTransactions on Computa-tional Biology and Bioin-formatics, 15(5):1594–1604,September 2018. CODENITCBCY. ISSN 1545-5963(print), 1557-9964 (elec-tronic).

Schneider:2007:SDM

[SGC07] Adrian Schneider, GastonGonnet, and Gina Can-narozzi. SynPAM—A dis-tance measure based on syn-onymous codon substitu-tions. IEEE/ACM Transac-tions on Computational Bi-ology and Bioinformatics, 4

(4):553–560, October 2007.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Sun:2012:PEU

[SGH12] Jianyong Sun, Jonathan M.Garibaldi, and Charlie Hodg-man. Parameter esti-mation using metaheuris-tics in systems biology:a comprehensive review.IEEE/ACM Transactions onComputational Biology andBioinformatics, 9(1):185–202, January 2012. CODENITCBCY. ISSN 1545-5963(print), 1557-9964 (elec-tronic).

Sun:2012:RBC

[SGK12] Jianyong Sun, Jonathan M.Garibaldi, and Kim Kenobi.Robust Bayesian cluster-ing for replicated gene ex-pression data. IEEE/ACMTransactions on Computa-tional Biology and Bioin-formatics, 9(5):1504–1514,September 2012. CODENITCBCY. ISSN 1545-5963(print), 1557-9964 (elec-tronic).

Sokolovsky:2020:DLA

[SGP+20] Michael Sokolovsky, Fran-cisco Guerrero, Sarun Pais-arnsrisomsuk, Carolina Ruiz,and Sergio A. Alvarez. Deeplearning for automated fea-ture discovery and clas-sification of sleep stages.IEEE/ACM Transactions

REFERENCES 297

on Computational Biologyand Bioinformatics, 17(6):1835–1845, November 2020.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic). URL https://dl.acm.org/doi/10.1109/TCBB.2019.2912955.

Stojanovic:2017:MHQ

[SGR+17] Jelena Stojanovic, DjordjeGligorijevic, Vladan Ra-dosavljevic, Nemanja Djuric,Mihajlo Grbovic, and Zo-ran Obradovic. Model-ing healthcare quality viacompact representations ofelectronic health records.IEEE/ACM Transactions onComputational Biology andBioinformatics, 14(3):545–554, May 2017. CODENITCBCY. ISSN 1545-5963(print), 1557-9964 (elec-tronic).

Sabnis:2011:CTD

[SH11a] Amit Sabnis and Robert W.Harrison. A continuous-time, discrete-state methodfor simulating the dynam-ics of biochemical systems.IEEE/ACM Transactions onComputational Biology andBioinformatics, 8(2):335–341, March 2011. CODENITCBCY. ISSN 1545-5963(print), 1557-9964 (elec-tronic).

Shibberu:2011:SAP

[SH11b] Yosi Shibberu and AllenHolder. A spectral approach

to protein structure align-ment. IEEE/ACM Trans-actions on ComputationalBiology and Bioinformat-ics, 8(4):867–875, July 2011.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Sharan:2006:ITP

[SHI06] Roded Sharan, Bjarni V.Halldorsson, and Sorin Is-trail. Islands of tractabil-ity for parsimony haplotyp-ing. IEEE/ACM Trans-actions on ComputationalBiology and Bioinformat-ics, 3(3):303–311, July 2006.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Shibuya:2010:FHD

[Shi10] Tetsuo Shibuya. Fasthinge detection algorithmsfor flexible protein struc-tures. IEEE/ACM Trans-actions on ComputationalBiology and Bioinformatics,7(2):333–341, April 2010.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Smalter:2010:GGP

[SHJL10] Aaron Smalter, Jun Huan,Yi Jia, and Gerald Lushing-ton. GPD: a graph patterndiffusion kernel for accurategraph classification with ap-plications in cheminformat-ics. IEEE/ACM Transac-tions on Computational Bi-

REFERENCES 298

ology and Bioinformatics,7(2):197–207, April 2010.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Saeed:2014:CRC

[SHK14] Fahad Saeed, Jason D. Hof-fert, and Mark A. Knep-per. CAMS–RS: cluster-ing algorithm for large-scalemass spectrometry data us-ing restricted search spaceand intelligent random sam-pling. IEEE/ACM Transac-tions on Computational Bi-ology and Bioinformatics, 11(1):128–141, January 2014.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Siederdissen:2015:PGA

[SHS15] Christian Honer Zu Siederdis-sen, Ivo L. Hofacker, andPeter F. Stadler. Productgrammars for alignment andfolding. IEEE/ACM Trans-actions on ComputationalBiology and Bioinformatics,12(3):507–519, May 2015.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Siragusa:2019:LTA

[SHUP19] Enrico Siragusa, Niina Haimi-nen, Filippo Utro, andLaxmi Parida. Lineartime algorithms to con-struct populations fittingmultiple constraint distri-butions at genomic scales.


Som-In:2020:EPS

[SIK20] Sarawoot Som-In and WarangkhanaKimpan. Enhancing ofparticle swarm optimiza-tion based method for mul-tiple motifs detection inDNA sequences collections.IEEE/ACM Transactions onComputational Biology andBioinformatics, 17(3):990–998, May 2020. CODENITCBCY. ISSN 1545-5963(print), 1557-9964 (elec-tronic). URL https://dl.acm.org/doi/10.1109/TCBB.2018.2872978.

Sharma:2012:TRF

[SIM12] Alok Sharma, Seiya Imoto,and Satoru Miyano. Atop-r feature selection algo-rithm for microarray gene ex-pression data. IEEE/ACMTransactions on Computa-tional Biology and Bioinfor-matics, 9(3):754–764, May2012. CODEN ITCBCY.ISSN 1545-5963 (print),1557-9964 (electronic).

Sudo:2019:SWM

[SJNS19] Hiroki Sudo, MasanobuJimbo, Koji Nuida, andKana Shimizu. Securewavelet matrix: Alphabet-friendly privacy-preserving

REFERENCES 299

string search for bioinfor-matics. IEEE/ACM Trans-actions on ComputationalBiology and Bioinformatics,16(5):1675–1684, September2019. CODEN ITCBCY.ISSN 1545-5963 (print),1557-9964 (electronic).

Sharifi:2019:ARC

[SJS19] Maryam Sharifi, Arta A.Jamshidi, and Nazanin Na-mazi Sarvestani. An adap-tive robust control strat-egy in a cancer tumor-immune system under uncer-tainties. IEEE/ACM Trans-actions on ComputationalBiology and Bioinformatics,16(3):865–873, May 2019.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Shen:2019:MSS

[SJZ19] Bairong Shen, XiaoqianJiang, and Xingming Zhao.Modeling and simulationstudies of complex bio-logical systems for preci-sion medicine and health-care. IEEE/ACM Trans-actions on ComputationalBiology and Bioinformatics,16(1):91–92, January 2019.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Schliep:2008:EAC

[SK08] Alexander Schliep and RolandKrause. Efficient algorithmsfor the computational de-

sign of optimal tiling ar-rays. IEEE/ACM Transac-tions on Computational Bi-ology and Bioinformatics, 5(4):557–567, October 2008.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Steinbiss:2012:NED

[SK12] Sascha Steinbiss and StefanKurtz. A new efficient datastructure for storage andretrieval of multiple biose-quences. IEEE/ACM Trans-actions on ComputationalBiology and Bioinformatics,9(2):345–357, March 2012.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Shao:2019:THM

[SK19] Mingfu Shao and Carl Kings-ford. Theory and a heuris-tic for the minimum pathflow decomposition prob-lem. IEEE/ACM Transac-tions on Computational Bi-ology and Bioinformatics,16(2):658–670, March 2019.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic). URL https://dl.acm.org/doi/abs/10.1109/TCBB.2017.2779509.

Sjahputera:2007:RAC

[SKD+07] Ozy Sjahputera, James M.Keller, J. Wade Davis,Kristen H. Taylor, Farah-naz Rahmatpanah, HuidongShi, Derek T. Ander-

REFERENCES 300

son, Samuel N. Blisard,Robert H. Luke, MihailPopescu, Gerald C. Arthur,and Charles W. Caldwell.Relational analysis of CpGislands methylation and geneexpression in human lym-phomas using possibilistic C-means clustering and mod-ified cluster fuzzy density.IEEE/ACM Transactions onComputational Biology andBioinformatics, 4(2):176–189, April 2007. CODENITCBCY. ISSN 1545-5963(print), 1557-9964 (elec-tronic).

Saha:2019:DFM

[SKDA19] Tanay Kumar Saha, AtaurKatebi, Wajdi Dhifli, andMohammad Al Hasan. Dis-covery of functional motifsfrom the interface regionof oligomeric proteins usingfrequent subgraph mining.IEEE/ACM Transactionson Computational Biologyand Bioinformatics, 16(5):1537–1549, September 2019.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Suvorova:2014:SPC

[SKK14] Yulia M. Suvorova, Maria A.Korotkova, and Eugene V.Korotkov. Study of thepaired change points in bac-terial genes. IEEE/ACMTransactions on Computa-tional Biology and Bioin-formatics, 11(5):955–964,


Sergeev:2019:GWA

[SKS+19] Roman Sergeevich Sergeev,Ivan S. Kavaliou, Uladzis-lau V. Sataneuski, An-drei Gabrielian, Alex Rosen-thal, Michael Tartakovsky,and Alexander V. Tuzikov.Genome-wide analysis ofMDR and XDR tuberculo-sis from Belarus: Machine-learning approach. IEEE/ACM Transactions on Com-putational Biology and Bioin-formatics, 16(4):1398–1408,July 2019. CODEN ITCBCY.ISSN 1545-5963 (print),1557-9964 (electronic).

Sridhar:2008:MIL

[SLB+08] Srinath Sridhar, Fumei Lam,Guy E. Blelloch, R. Ravi,and Russell Schwartz. Mixedinteger linear programmingfor maximum-parsimony phy-logeny inference. IEEE/ACM Transactions on Com-putational Biology and Bioin-formatics, 5(3):323–331, July2008. CODEN ITCBCY.ISSN 1545-5963 (print),1557-9964 (electronic).

Savel:2017:PEL

[SLGK17] Daniel Savel, Thomas LaFram-boise, Ananth Grama, andMehmet Koyuturk. Pluribus— exploring the limits of er-ror correction using a suf-

REFERENCES 301

fix tree. IEEE/ACM Trans-actions on ComputationalBiology and Bioinformatics,14(6):1378–1388, November2017. CODEN ITCBCY.ISSN 1545-5963 (print),1557-9964 (electronic).

Song:2006:EPA

[SLH+06a] Yinglei Song, ChunmeiLiu, Xiuzhen Huang, Rus-sell L. Malmberg, YingXu, and Liming Cai. Ef-ficient parameterized al-gorithms for biopolymerstructure-sequence align-ment. IEEE/ACM Transac-tions on Computational Bi-ology and Bioinformatics, 3(4):423–432, October 2006.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Song:2006:CAP

[SLH06b] Yun S. Song, Rune Lyngso,and Jotun Hein. Count-ing all possible ancestralconfigurations of sample se-quences in population ge-netics. IEEE/ACM Trans-actions on ComputationalBiology and Bioinformat-ics, 3(3):239–251, July 2006.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Sun:2019:IAL

[SLL+19] Weiping Sun, Yi Liu,Gills A. Lajoie, Bin Ma,and Kaizhong Zhang. Animproved approach for N -

linked glycan structure iden-tification from HCD MS/MSspectra. IEEE/ACM Trans-actions on ComputationalBiology and Bioinformatics,16(2):388–395, March 2019.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic). URL https://dl.acm.org/doi/abs/10.1109/TCBB.2017.2701819.

Singh:2019:TSK

[SLRQ19] Ritambhara Singh, JackLanchantin, Gabriel Robins,and Yanjun Qi. Trans-fer string kernel for cross-context DNA–protein bind-ing prediction. IEEE/ACMTransactions on Computa-tional Biology and Bioin-formatics, 16(5):1524–1536,September 2019. CODENITCBCY. ISSN 1545-5963(print), 1557-9964 (elec-tronic).

Song:2014:MSS

[SLS+14] Xuebo Song, Lin Li, Pradip K.Srimani, Philip S. Yu, andJames Z. Wang. Mea-sure the semantic similar-ity of GO terms using ag-gregate information con-tent. IEEE/ACM Trans-actions on ComputationalBiology and Bioinformatics,11(3):468–476, May 2014.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

REFERENCES 302

Song:2015:MLA

[SLW15] Yinglei Song, Chunmei Liu,and Zhi Wang. A machinelearning approach for accu-rate annotation of noncodingRNAs. IEEE/ACM Trans-actions on ComputationalBiology and Bioinformatics,12(3):551–559, May 2015.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Shao:2018:OCG

[SLX+18] Wei Shao, Mingxia Liu,Ying-Ying Xu, Hong-BinShen, and Daoqiang Zhang.An organelle correlation-guided feature selection ap-proach for classifying multi-label subcellular bio-images.IEEE/ACM Transactions onComputational Biology andBioinformatics, 15(3):828–838, May 2018. CODENITCBCY. ISSN 1545-5963(print), 1557-9964 (elec-tronic).

Satya:2008:UIP

[SM08] Ravi Vijaya Satya and AmarMukherjee. The undirectedincomplete perfect phy-logeny problem. IEEE/ACMTransactions on Computa-tional Biology and Bioinfor-matics, 5(4):618–629, Octo-ber 2008. CODEN ITCBCY.ISSN 1545-5963 (print),1557-9964 (electronic).

Sengupta:2012:WMC

[SMB12] Debarka Sengupta, UjjwalMaulik, and SanghamitraBandyopadhyay. WeightedMarkov chain based aggre-gation of biomolecule order-ings. IEEE/ACM Trans-actions on ComputationalBiology and Bioinformat-ics, 9(3):924–933, May 2012.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Smith:2009:RSD

[Smi09] Jennifer A. Smith. RNAsearch with decision treesand partial covariance mod-els. IEEE/ACM Trans-actions on ComputationalBiology and Bioinformat-ics, 6(3):517–527, July 2009.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Stegmayer:2012:BIV

[SMK+12] Georgina Stegmayer, Diego H.Milone, Laura Kamenetzky,Mariana G. Lopez, and Fer-nando Carrari. A biologicallyinspired validity measurefor comparison of clusteringmethods over metabolic datasets. IEEE/ACM Trans-actions on ComputationalBiology and Bioinformat-ics, 9(3):706–716, May 2012.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

REFERENCES 303

Shahdoust:2020:NBC

[SMPS20] Maryam Shahdoust, HosseinMahjub, Hamid Pezeshk,and Mehdi Sadeghi. Anetwork-based comparisonbetween molecular apocrinebreast cancer tumor andbasal and luminal tumorsby joint graphical lasso.IEEE/ACM Transactionson Computational Biologyand Bioinformatics, 17(5):1555–1562, September 2020.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic). URL https://dl.acm.org/doi/10.1109/TCBB.2019.2911074.

Sehhati:2015:SGS

[SMRP15] Mohammadreza Sehhati,Alireza Mehridehnavi, Hos-sein Rabbani, and MerajPourhossein. Stable genesignature selection for pre-diction of breast cancer re-currence using joint mutualinformation. IEEE/ACMTransactions on Computa-tional Biology and Bioin-formatics, 12(6):1440–1448,November 2015. CODENITCBCY. ISSN 1545-5963(print), 1557-9964 (elec-tronic).

Stalidzans:2017:SMS

[SMSZ17] Egils Stalidzans, Ivars Mozga,Jurijs Sulins, and PeterisZikmanis. Search for a mini-mal set of parameters by as-sessing the total optimiza-tion potential for a dynamic

model of a biochemical net-work. IEEE/ACM Trans-actions on ComputationalBiology and Bioinformatics,14(4):978–985, July 2017.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Serang:2012:FMS

[SN12] Oliver Serang and William Strat-ford Noble. Faster massspectrometry-based proteininference: Junction treesare more efficient than sam-pling and marginalization byenumeration. IEEE/ACMTransactions on Computa-tional Biology and Bioinfor-matics, 9(3):809–817, May2012. CODEN ITCBCY.ISSN 1545-5963 (print),1557-9964 (electronic).

Shi:2016:OEM

[SNC+16] Yan Shi, Jinglong Niu,Zhixin Cao, Maolin Cai,Jian Zhu, and Weiqing Xu.Online estimation methodfor respiratory parametersbased on a pneumatic model.IEEE/ACM Transactionson Computational Biologyand Bioinformatics, 13(5):939–946, September 2016.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Spillner:2008:CPD

[SNM08] Andreas Spillner, Binh T.Nguyen, and Vincent Moul-ton. Computing phyloge-

REFERENCES 304

netic diversity for split sys-tems. IEEE/ACM Trans-actions on ComputationalBiology and Bioinformatics,5(2):235–244, April 2008.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Spillner:2012:CDR

[SNM12] Andreas Spillner, BinhNguyen, and Vincent Moul-ton. Constructing and draw-ing regular planar split net-works. IEEE/ACM Trans-actions on ComputationalBiology and Bioinformatics,9(2):395–407, March 2012.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Song:2006:CNS

[Son06] Yun S. Song. A concisenecessary and sufficient con-dition for the existence ofa galled-tree. IEEE/ACMTransactions on Computa-tional Biology and Bioinfor-matics, 3(2):186–191, April2006. CODEN ITCBCY.ISSN 1545-5963 (print),1557-9964 (electronic).

Sahu:2011:ELH

[SP11] Sitanshu Sekhar Sahu andGanapati Panda. Efficientlocalization of hot spots inproteins using a novel S-transform based filtering ap-proach. IEEE/ACM Trans-actions on ComputationalBiology and Bioinformatics,


Sirin:2017:BMT

[SPA17] Utku Sirin, Faruk Polat, andReda Alhajj. Batch modeTDλ for controlling par-tially observable gene regula-tory networks. IEEE/ACMTransactions on Computa-tional Biology and Bioin-formatics, 14(6):1214–1227,November 2017. CODENITCBCY. ISSN 1545-5963(print), 1557-9964 (elec-tronic).

Shehu:2019:GEA

[SPK19] Amarda Shehu, GiuseppePozzi, and Tamer Kahveci.Guest editorial for the ACMInternational Conference onBioinformatics, Computa-tional Biology, and HealthInformatics. IEEE/ACMTransactions on Computa-tional Biology and Bioinfor-matics, 16(5):1409, Septem-ber 2019. CODEN ITCBCY.ISSN 1545-5963 (print),1557-9964 (electronic).

Sengupta:2013:RKO

[SPMB13] Debarka Sengupta, Aroon-alok Pyne, Ujjwal Maulik,and Sanghamitra Bandy-opadhyay. Reformulated Ke-meny optimal aggregationwith application in consen-sus ranking of microRNAtargets. IEEE/ACM Trans-

REFERENCES 305

actions on ComputationalBiology and Bioinformatics,10(3):742–751, May 2013.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Song:2020:EBM

[SPW20] Junrong Song, Wei Peng,and Feng Wang. Anentropy-based method foridentifying mutual exclu-sive driver genes in can-cer. IEEE/ACM Transac-tions on Computational Bi-ology and Bioinformatics,17(3):758–768, May 2020.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic). URL https://dl.acm.org/doi/10.1109/TCBB.2019.2897931.

Sun:2014:MSA

[SPWF14] Jun Sun, Vasile Palade, Xi-aojun Wu, and Wei Fang.Multiple sequence alignmentwith hidden Markov mod-els learned by random driftparticle swarm optimiza-tion. IEEE/ACM Transac-tions on Computational Bi-ology and Bioinformatics, 11(1):243–257, January 2014.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Sajjadi:2014:NBM

[SQZA14] Seyed Javad Sajjadi, Xiaon-ing Qian, Bo Zeng, andAmin Ahmadi Adl. Network-based methods to identify

highly discriminating subsetsof biomarkers. IEEE/ACMTransactions on Computa-tional Biology and Bioin-formatics, 11(6):1029–1037,November 2014. CODENITCBCY. ISSN 1545-5963(print), 1557-9964 (elec-tronic).

Snir:2006:UMC

[SR06] Sagi Snir and Satish Rao.Using max cut to en-hance rooted trees consis-tency. IEEE/ACM Transac-tions on Computational Bi-ology and Bioinformatics, 3(4):323–333, October 2006.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Snir:2010:QMD

[SR10] Sagi Snir and Satish Rao.Quartets MaxCut: a divideand conquer quartets algo-rithm. IEEE/ACM Transac-tions on Computational Bi-ology and Bioinformatics, 7(4):704–718, October 2010.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Sarkar:2019:NAC

[SREK19] Aisharjya Sarkar, YuanfangRen, Rasha Elhesha, andTamer Kahveci. A new al-gorithm for counting inde-pendent motifs in probabilis-tic networks. IEEE/ACMTransactions on Computa-tional Biology and Bioin-

REFERENCES 306

formatics, 16(4):1049–1062,July 2019. CODEN ITCBCY.ISSN 1545-5963 (print),1557-9964 (electronic).

Srihari:2014:ECC

[SRLR14] Sriganesh Srihari, VenkateshRaman, Hon Wai Leong, andMark A. Ragan. Evolutionand controllability of can-cer networks: a Boolean per-spective. IEEE/ACM Trans-actions on ComputationalBiology and Bioinformatics,11(1):83–94, January 2014.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Shekhar:2018:STE

[SRM18] Shubhanshu Shekhar, Se-bastien Roch, and SiavashMirarab. Species tree es-timation using ASTRAL:How many genes are enough?IEEE/ACM Transactionson Computational Biologyand Bioinformatics, 15(5):1738–1747, September 2018.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Scheid:2004:SDS

[SS04] Stefanie Scheid and RainerSpang. A stochastic down-hill search algorithm for esti-mating the local false discov-ery rate. IEEE/ACM Trans-actions on ComputationalBiology and Bioinformat-ics, 1(3):98–108, July 2004.CODEN ITCBCY. ISSN


Sammeth:2006:CTR

[SS06a] Michael Sammeth and JensStoye. Comparing tandemrepeats with duplicationsand excisions of variable de-gree. IEEE/ACM Transac-tions on Computational Bi-ology and Bioinformatics, 3(4):395–407, October 2006.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Semple:2006:UNC

[SS06b] Charles Semple and MikeSteel. Unicyclic networks:Compatibility and enumer-ation. IEEE/ACM Trans-actions on ComputationalBiology and Bioinformatics,3(1):84–91, January 2006.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Sigdel:2016:FFS

[SSD+16] Madhu S. Sigdel, MadhavSigdel, Semih Dinc, ImrenDinc, Marc L. Pusey, andRamazan S. Aygun. Fo-cusALL: Focal stacking ofmicroscopic images usingmodified Harris corner re-sponse measure. IEEE/ACMTransactions on Computa-tional Biology and Bioin-formatics, 13(2):326–340,March 2016. CODENITCBCY. ISSN 1545-5963

REFERENCES 307


Samaddar:2019:MDP

[SSD19] Sandip Samaddar, Ritu-parna Sinha, and Rajat K.De. A model for distributedprocessing and analyses ofNGS data under map-reduceparadigm. IEEE/ACMTransactions on Computa-tional Biology and Bioinfor-matics, 16(3):827–840, May2019. CODEN ITCBCY.ISSN 1545-5963 (print),1557-9964 (electronic).

Sargsyan:2012:MSR

[SSDN12] Khachik Sargsyan, CosminSafta, Bert Debusschere,and Habib Najm. Multipa-rameter spectral representa-tion of noise-induced com-petence in Bacillus Subtilis.IEEE/ACM Transactionson Computational Biologyand Bioinformatics, 9(6):1709–1723, November 2012.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Suryanto:2018:SCC

[SSF18] Chendra Hadi Suryanto, Hi-roto Saigo, and KazuhiroFukui. Structural class clas-sification of 3D protein struc-ture based on multi-view 2Dimages. IEEE/ACM Trans-actions on ComputationalBiology and Bioinformat-ics, 15(1):286–299, January2018. CODEN ITCBCY.


Sun:2012:SSM

[SSFW12] Hong Sun, Ahmet Sacan,Hakan Ferhatosmanoglu,and Yusu Wang. Smolign: aspatial motifs-based proteinmultiple structural align-ment method. IEEE/ACMTransactions on Computa-tional Biology and Bioinfor-matics, 9(1):249–261, Jan-uary 2012. CODEN ITCBCY.ISSN 1545-5963 (print),1557-9964 (electronic).

Saribudak:2020:GEH

[SSK+20] Aydin Saribudak, Adar-sha A. Subick, Na HyunKim, Joshua A. Rutta, andM. Umit Uyar. Gene ex-pressions, hippocampal vol-ume loss, and MMSE scoresin computation of progres-sion and pharmacologic ther-apy effects for Alzheimer’sdisease. IEEE/ACM Trans-actions on ComputationalBiology and Bioinformatics,17(2):608–622, March 2020.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic). URL https://dl.acm.org/doi/abs/10.1109/TCBB.2018.2870363.

Seok:2015:ESA

[SSKH15] Ho-Sik Seok, Taemin Song,Sek Won Kong, and Kyu-Baek Hwang. An efficientsearch algorithm for find-ing genomic-range overlaps

REFERENCES 308

based on the maximum rangelength. IEEE/ACM Trans-actions on ComputationalBiology and Bioinformatics,12(4):778–784, July 2015.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Segar:2015:MTD

[SSML15] Matthew W. Segar, Cyn-thia J. Sakofsky, AnnaMalkova, and Yunlong Liu.MMBIRFinder: a toolto detect microhomology-mediated break-induced repli-cation. IEEE/ACM Trans-actions on ComputationalBiology and Bioinformatics,12(4):799–806, July 2015.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Sevilla:2005:CBG

[SSP+05] Jose L. Sevilla, Victor Se-gura, Adam Podhorski, Eliz-abeth Guruceaga, Jose M.Mato, Luis A. Martinez-Cruz, Fernando J. Corrales,and Angel Rubio. Corre-lation between gene expres-sion and GO semantic simi-larity. IEEE/ACM Transac-tions on Computational Bi-ology and Bioinformatics, 2(4):330–338, October 2005.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Sinha:2017:PDV

[SSP+17] Arvind Kumar Sinha, Pradeep

Singh, Anand Prakash,Dharm Pal, Anuradha Dube,and Awanish Kumar. Puta-tive drug and vaccine targetidentification in Leishmaniadonovani membrane proteinsusing naıve Bayes probabilis-tic classifier. IEEE/ACMTransactions on Computa-tional Biology and Bioin-formatics, 14(1):204–211,January 2017. CODENITCBCY. ISSN 1545-5963(print), 1557-9964 (elec-tronic).

Saraswathi:2011:IPE

[SSS+11] Saras Saraswathi, SureshSundaram, Narasimhan Sun-dararajan, Michael Zimmer-mann, and Marit Nilsen-Hamilton. ICGA-PSO-ELMapproach for accurate multi-class cancer classification re-sulting in reduced gene setsin which genes encoding se-creted proteins are highlyrepresented. IEEE/ACMTransactions on Computa-tional Biology and Bioinfor-matics, 8(2):452–463, March2011. CODEN ITCBCY.ISSN 1545-5963 (print),1557-9964 (electronic).

Shakya:2013:AWL

[SSS13a] Devendra K. Shakya, Ra-jiv Saxena, and Sanjeev N.Sharma. An adaptive win-dow length strategy for eu-karyotic CDS prediction.IEEE/ACM Transactionson Computational Biology

REFERENCES 309


Subramanian:2013:NMS

[SSS13b] Ayshwarya Subramanian,Stanley Shackney, and Rus-sell Schwartz. Novel multi-sample scheme for inferringphylogenetic markers fromwhole genome tumor profiles.IEEE/ACM Transactionson Computational Biologyand Bioinformatics, 10(6):1422–1431, November 2013.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Sung:2015:MLM

[SSS+15] Wing-Kin Sung, KunihikoSadakane, Tetsuo Shibuya,Abha Belorkar, and IanaPyrogova. An O(m logm)-time algorithm for detectingsuperbubbles. IEEE/ACMTransactions on Computa-tional Biology and Bioinfor-matics, 12(4):770–777, July2015. CODEN ITCBCY.ISSN 1545-5963 (print),1557-9964 (electronic).

Sharma:2020:ESL

[SSS20a] Nirmala Sharma, HarishSharma, and Ajay Sharma.An effective solution for largescale single machine totalweighted tardiness problemusing lunar cycle inspired ar-tificial bee colony algorithm.

IEEE/ACM Transactionson Computational Biologyand Bioinformatics, 17(5):1573–1581, September 2020.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic). URL https://dl.acm.org/doi/10.1109/TCBB.2019.2897302.

Sharma:2020:ISE

[SSS20b] Sunildatt Sharma, San-jeev Narayan Sharma, andRajiv Saxena. Identificationof short exons disunited bya short intron in eukaryoticDNA regions. IEEE/ACMTransactions on Computa-tional Biology and Bioin-formatics, 17(5):1660–1670,September 2020. CODENITCBCY. ISSN 1545-5963(print), 1557-9964 (elec-tronic). URL https://dl.acm.org/doi/10.1109/TCBB.2019.2900040.

Sevakula:2019:TLM

[SSV+19] Rahul K. Sevakula, VikasSingh, Nishchal K. Verma,Chandan Kumar, and YanCui. Transfer learningfor molecular cancer clas-sification using deep neu-ral networks. IEEE/ACMTransactions on Computa-tional Biology and Bioin-formatics, 16(6):2089–2100,November 2019. CODENITCBCY. ISSN 1545-5963(print), 1557-9964 (elec-tronic). URL https://dl.acm.org/doi/abs/10.1109/TCBB.2018.2822803.

REFERENCES 310

Shen:2005:DRB

[ST05] Li Shen and Eng ChongTan. Dimension reduction-based penalized logistic re-gression for cancer classi-fication using microarraydata. IEEE/ACM Trans-actions on ComputationalBiology and Bioinformatics,2(2):166–175, April 2005.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Salmela:2019:SFG

[ST19] Leena Salmela and Alexan-dru I. Tomescu. Safely fill-ing gaps with partial solu-tions common to all solu-tions. IEEE/ACM Trans-actions on ComputationalBiology and Bioinformatics,16(2):617–626, March 2019.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic). URL https://dl.acm.org/doi/abs/10.1109/TCBB.2017.2785831.

Singh:2019:EPG

[STB+19] Kumar Saurabh Singh, Bart-lomiej J. Troczka, Kather-ine Beadle, Linda M. Field,T. G. Emyr Davies, Mar-tin S. Williamson, RalfNauen, and Chris Bass. Ex-tension of partial gene tran-scripts by iterative map-ping of RNA-Seq raw reads.IEEE/ACM Transactions onComputational Biology andBioinformatics, 16(3):1036–1041, May 2019. CODEN


Shrestha:2020:SMD

[STB+20] Midusha Shrestha, Truong X.Tran, Bidhan Bhattarai,Marc L. Pusey, and Ra-mazan S. Aygun. Schemamatching and data integra-tion with consistent nam-ing on protein crystalliza-tion screens. IEEE/ACMTransactions on Computa-tional Biology and Bioin-formatics, 17(6):2074–2085,November 2020. CODENITCBCY. ISSN 1545-5963(print), 1557-9964 (elec-tronic). URL https://dl.acm.org/doi/10.1109/TCBB.2019.2913368.

Sen:2020:AAS

[STD20] Rishika Sen, Somnath Tagore,and Rajat K. De. ASAPP:Architectural similarity-basedautomated pathway predic-tion system and its applica-tion in host-pathogen inter-actions. IEEE/ACM Trans-actions on ComputationalBiology and Bioinformatics,17(2):506–515, March 2020.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic). URL https://dl.acm.org/doi/abs/10.1109/TCBB.2018.2872527.

Shibuya:2015:GEI

[STHA15] Tetsuo Shibuya, Chuan YiTang, Paul Horton, andKiyoshi Asai. Guest editorial

REFERENCES 311

for the 25th InternationalConference on Genome In-formatics (GIW/ISCB-Asia2014). IEEE/ACM Trans-actions on ComputationalBiology and Bioinformatics,12(4):761–762, July 2015.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Sevon:2006:TTP

[STO06] Petteri Sevon, Hannu Toivo-nen, and Vesa Ollikainen.TreeDT: Tree pattern min-ing for gene mapping.IEEE/ACM Transactions onComputational Biology andBioinformatics, 3(2):174–185, April 2006. CODENITCBCY. ISSN 1545-5963(print), 1557-9964 (elec-tronic).

Strutz:2011:SRL

[Str11] Tilo Strutz. 3D shape re-construction of loop objectsin X-ray protein crystallog-raphy. IEEE/ACM Trans-actions on ComputationalBiology and Bioinformat-ics, 8(3):797–807, May/June2011. CODEN ITCBCY.ISSN 1545-5963 (print),1557-9964 (electronic).

Shen:2014:LKS

[STT+14] Qingliang Shen, Hong Tian,Daoqi Tang, Wenbing Yao,and Xiangdong Gao. Ligand-K* sequence elimination: anovel algorithm for ensemble-based redesign of receptor-

ligand binding. IEEE/ACMTransactions on Computa-tional Biology and Bioinfor-matics, 11(3):573–578, May2014. CODEN ITCBCY.ISSN 1545-5963 (print),1557-9964 (electronic).

Singh:2016:BAI

[SV16] Nitin Singh and Mathuku-malli Vidyasagar. bLARS:an algorithm to infer generegulatory networks. IEEE/ACM Transactions on Com-putational Biology and Bioin-formatics, 13(2):301–314,March 2016. CODENITCBCY. ISSN 1545-5963(print), 1557-9964 (elec-tronic).

Sato:2018:CNM

[SVdSS+18] Joao Ricardo Sato, Ma-ciel Calebe Vidal, Suzanade Siqueira Santos, Katlin BrauerMassirer, and Andre Fujita.Complex network measuresin autism spectrum disor-ders. IEEE/ACM Trans-actions on ComputationalBiology and Bioinformatics,15(2):581–587, March 2018.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Siren:2014:IGP

[SVM14] Jouni Siren, Niko Valimaki,and Veli Makinen. Index-ing graphs for path querieswith applications in genomeresearch. IEEE/ACM Trans-actions on Computational

REFERENCES 312


Salicru:2009:ICA

[SVZ09] Miquel Salicru, Sergi Vives,and Tian Zheng. Infer-ential clustering approachfor microarray experimentswith replicated measure-ments. IEEE/ACM Transac-tions on Computational Bi-ology and Bioinformatics, 6(4):594–604, October 2009.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Stoye:2009:UAR

[SW09] Jens Stoye and Roland Wit-tler. A unified approach forreconstructing ancient geneclusters. IEEE/ACM Trans-actions on ComputationalBiology and Bioinformat-ics, 6(3):387–400, July 2009.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Shabash:2017:RVR

[SW17] Boris Shabash and Kay C.Wiese. RNA visualization:Relevance and the currentstate-of-the-art focusing onpseudoknots. IEEE/ACMTransactions on Computa-tional Biology and Bioinfor-matics, 14(3):696–712, May2017. CODEN ITCBCY.


Su:2012:INP

[SWH+12] Chien-Hao Su, Tse-Yi Wang,Ming-Tsung Hsu, FrancisCheng-Hsuan Weng, Cheng-Yan Kao, Daryi Wang, andHuai-Kuang Tsai. The im-pact of normalization andphylogenetic information onestimating the distance formetagenomes. IEEE/ACMTransactions on Computa-tional Biology and Bioinfor-matics, 9(2):619–628, March2012. CODEN ITCBCY.ISSN 1545-5963 (print),1557-9964 (electronic).

Sun:2019:MDN

[SWL19] Dongdong Sun, MinghuiWang, and Ao Li. A multi-modal deep neural networkfor human breast cancerprognosis prediction by in-tegrating multi-dimensionaldata. IEEE/ACM Trans-actions on ComputationalBiology and Bioinformatics,16(3):841–850, May 2019.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Su:2019:DMD

[SWX+19] Ran Su, Huichen Wu, Bo Xu,Xiaofeng Liu, and LeyiWei. Developing a multi-dose computational modelfor drug-induced hepato-toxicity prediction basedon toxicogenomics data.

REFERENCES 313


Su:2014:AMD

[SXL+14] Hai Su, Fuyong Xing,Jonah D. Lee, Charlotte A.Peterson, and Lin Yang. Au-tomatic myonuclear detec-tion in isolated single mus-cle fibers using robust ellipsefitting and sparse represen-tation. IEEE/ACM Trans-actions on ComputationalBiology and Bioinformatics,11(4):714–726, July 2014.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Shaik:2009:FAS

[SY09] Jahangheer Shaik and Mo-hammed Yeasin. Fuzzy-adaptive-subspace-iteration-based two-way clustering ofmicroarray data. IEEE/ACM Transactions on Com-putational Biology and Bioin-formatics, 6(2):244–259, April2009. CODEN ITCBCY.ISSN 1545-5963 (print),1557-9964 (electronic).

Stegmayer:2017:HCI

[SYKM17] Georgina Stegmayer, Cris-tian Yones, Laura Kamenet-zky, and Diego H. Milone.High class-imbalance in pre-miRNA prediction: a novel

approach based on deep-SOM. IEEE/ACM Trans-actions on ComputationalBiology and Bioinformatics,14(6):1316–1326, November2017. CODEN ITCBCY.ISSN 1545-5963 (print),1557-9964 (electronic).

Seniya:2015:SSS

[SYKS15] Chandrabhan Seniya, AjayYadav, G. J. Khan, andNand K. Sah. In-silico stud-ies show potent inhibition ofHIV-1 reverse transcriptaseactivity by a herbal drug.IEEE/ACM Transactionson Computational Biologyand Bioinformatics, 12(6):1355–1364, November 2015.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Song:2019:PGA

[SYL19] You Song, Siyu Yang, andJinzhi Lei. ParaCells: a GPUarchitecture for cell-centeredmodels in computational bi-ology. IEEE/ACM Trans-actions on ComputationalBiology and Bioinformatics,16(3):994–1006, May 2019.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Saetre:2010:EPI

[SYM+10] Rune Sætre, Kazuhiro Yoshida,Makoto Miwa, Takuya Mat-suzaki, Yoshinobu Kano,and Jun’ichi Tsujii. Ex-tracting protein interactions

REFERENCES 314

from text with the unifiedAkaneRE event extractionsystem. IEEE/ACM Trans-actions on ComputationalBiology and Bioinformat-ics, 7(3):442–453, July 2010.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Shiraishi:2014:EVA

[SYV14] Fumihide Shiraishi, ErikaYoshida, and Eberhard O.Voit. An efficient and veryaccurate method for cal-culating steady-state sensi-tivities in metabolic reac-tion systems. IEEE/ACMTransactions on Computa-tional Biology and Bioin-formatics, 11(6):1077–1086,November 2014. CODENITCBCY. ISSN 1545-5963(print), 1557-9964 (elec-tronic).

Shao:2013:UMB

[SYZ+13] Gui-Fang Shao, Fan Yang,Qian Zhang, Qi-Feng Zhou,and Lin-Kai Luo. Usingthe maximum between-classvariance for automatic grid-ding of cDNA microarray im-ages. IEEE/ACM Transac-tions on Computational Bi-ology and Bioinformatics, 10(1):181–192, January 2013.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Sadjad:2011:TRS

[SZ11] Bashir Sadjad and Zsolt

Zsoldos. Toward a ro-bust search method for theprotein–drug docking prob-lem. IEEE/ACM Transac-tions on Computational Bi-ology and Bioinformatics, 8(4):1120–1133, July 2011.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Shi:2019:CED

[SZCX19] Yan Shi, Bolun Zhang,Maolin Cai, and WeiqingXu. Coupling effect of dou-ble lungs on a VCV ven-tilator with automatic se-cretion clearance function.IEEE/ACM Transactions onComputational Biology andBioinformatics, 16(4):1280–1287, July 2019. CODENITCBCY. ISSN 1545-5963(print), 1557-9964 (elec-tronic).

Shi:2020:QDD

[SZL+20] Jifan Shi, Juan Zhao, Xi-aoping Liu, Luonan Chen,and Tiejun Li. Quanti-fying direct dependenciesin biological networks bymultiscale association anal-ysis. IEEE/ACM Transac-tions on Computational Bi-ology and Bioinformatics,17(2):449–458, March 2020.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic). URL https://dl.acm.org/doi/abs/10.1109/TCBB.2018.2846648.

REFERENCES 315

Sun:2011:CFS

[SZLL11] Bing-Yu Sun, Zhi-Hua Zhu,Jiuyong Li, and Bin Linghu.Combined feature selectionand cancer prognosis us-ing support vector machineregression. IEEE/ACMTransactions on Computa-tional Biology and Bioin-formatics, 8(6):1671–1677,November 2011. CODENITCBCY. ISSN 1545-5963(print), 1557-9964 (elec-tronic).

Sankoff:2019:MSD

[SZZ+19] David Sankoff, ChunfangZheng, Yue Zhang, JoaoMeidanis, Eric Lyons, andHaibao Tang. Models forsimilarity distributions ofsyntenic homologs and ap-plications to phylogenomics.IEEE/ACM Transactions onComputational Biology andBioinformatics, 16(3):727–737, May 2019. CODENITCBCY. ISSN 1545-5963(print), 1557-9964 (elec-tronic).

Tan:2011:IPK

[TAAP11] Mehmet Tan, MohammedAlshalalfa, Reda Alhajj,and Faruk Polat. Influ-ence of prior knowledgein constraint-based learn-ing of gene regulatory net-works. IEEE/ACM Transac-tions on Computational Bi-ology and Bioinformatics, 8(1):130–142, January 2011.CODEN ITCBCY. ISSN


Taha:2014:DSR

[Tah14] Kamal Taha. Determiningsemantically related signif-icant genes. IEEE/ACMTransactions on Computa-tional Biology and Bioin-formatics, 11(6):1119–1130,November 2014. CODENITCBCY. ISSN 1545-5963(print), 1557-9964 (elec-tronic).

Taha:2018:IFP

[Tah18] Kamal Taha. Inferring thefunctions of proteins fromthe interrelationships be-tween functional categories.IEEE/ACM Transactions onComputational Biology andBioinformatics, 15(1):157–167, January 2018. CODENITCBCY. ISSN 1545-5963(print), 1557-9964 (elec-tronic).

Tsompanas:2019:MMF

[TAI+19] Michail-Antisthenis Tsom-panas, Andrew Adamatzky,Ioannis Ieropoulos, Neil WilliamPhillips, Georgios Ch. Sir-akoulis, and John Green-man. Modelling microbialfuel cells using lattice Boltz-mann methods. IEEE/ACMTransactions on Computa-tional Biology and Bioin-formatics, 16(6):2035–2045,November 2019. CODENITCBCY. ISSN 1545-5963(print), 1557-9964 (elec-

REFERENCES 316

tronic). URL https://dl.acm.org/doi/abs/10.1109/TCBB.2018.2831223.

Torii:2015:RPG

[TAL+15] Manabu Torii, Cecilia N.Arighi, Gang Li, QinghuaWang, Cathy H. Wu, andK. Vijay-Shanker. RLIMS-P 2.0: a generalizable rule-based information extractionsystem for literature miningof protein phosphorylationinformation. IEEE/ACMTransactions on Computa-tional Biology and Bioinfor-matics, 12(1):17–29, January2015. CODEN ITCBCY.ISSN 1545-5963 (print),1557-9964 (electronic).

Tanaka:2014:IEE

[Tan14] Shunji Tanaka. Improved ex-act enumerative algorithmsfor the planted (l, d)-motifsearch problem. IEEE/ACMTransactions on Computa-tional Biology and Bioin-formatics, 11(2):361–374,March 2014. CODENITCBCY. ISSN 1545-5963(print), 1557-9964 (elec-tronic).

Tininini:2010:CHA

[TBGL10] Leonardo Tininini, PaolaBertolazzi, Alessandra Godi,and Giuseppe Lancia. Coll-Haps: a heuristic approachto haplotype inference byparsimony. IEEE/ACMTransactions on Computa-tional Biology and Bioinfor-


Turner:2005:BMS

[TBKH05] Heather L. Turner, Trevor C.Bailey, Wojtek J. Krzanowski,and Cheryl A. Heming-way. Biclustering modelsfor structured microarraydata. IEEE/ACM Transac-tions on Computational Bi-ology and Bioinformatics, 2(4):316–329, October 2005.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Tsai:2011:CTA

[TBRS11] Ming-Chi Tsai, Guy E. Blel-loch, R. Ravi, and Rus-sell Schwartz. A consen-sus tree approach for re-constructing human evo-lutionary history and de-tecting population substruc-ture. IEEE/ACM Trans-actions on ComputationalBiology and Bioinformat-ics, 8(4):918–928, July 2011.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Tsai:2013:CBM

[TBRS13] Ming-Chi Tsai, Guy E. Blel-loch, R. Ravi, and RussellSchwartz. Coalescent-basedmethod for learning param-eters of admixture eventsfrom large-scale genetic vari-ation data. IEEE/ACM

REFERENCES 317

Transactions on Computa-tional Biology and Bioin-formatics, 10(5):1137–1149,September 2013. CODENITCBCY. ISSN 1545-5963(print), 1557-9964 (elec-tronic).

Tu:2013:INR

[TC13] Chien-Ta Tu and Bor-SenChen. On the increase innetwork robustness and de-crease in network responseability during the agingprocess: a systems biol-ogy approach via microar-ray data. IEEE/ACM Trans-actions on ComputationalBiology and Bioinformatics,10(2):468–480, March 2013.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Tran:2016:AOP

[TC16] Ngoc Hieu Tran and XinChen. AMAS: Optimizingthe partition and filtration ofadaptive seeds to speed upread mapping. IEEE/ACMTransactions on Computa-tional Biology and Bioinfor-matics, 13(4):623–633, 2016.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Treangen:2009:NHL

[TDA+09] Todd J. Treangen, Aaron E.Darling, Guillaume Achaz,Mark A. Ragan, XavierMesseguer, and EduardoP. C. Rocha. A novel heuris-

tic for local multiple align-ment of interspersed DNArepeats. IEEE/ACM Trans-actions on ComputationalBiology and Bioinformatics,6(2):180–189, April 2009.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Thomas:2014:MLE

[TDD14] Minta Thomas, AnneleenDaemen, and Bart De Moor.Maximum likelihood esti-mation of GEVD: appli-cations in bioinformatics.IEEE/ACM Transactions onComputational Biology andBioinformatics, 11(4):673–680, July 2014. CODENITCBCY. ISSN 1545-5963(print), 1557-9964 (elec-tronic).

Todor:2013:CTP

[TDK13a] Andrei Todor, Alin Dobra,and Tamer Kahveci. Char-acterizing the topology ofprobabilistic biological net-works. IEEE/ACM Trans-actions on ComputationalBiology and Bioinformatics,10(4):970–983, July 2013.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Todor:2013:PBN

[TDK13b] Andrei Todor, Alin Do-bra, and Tamer Kahveci.Probabilistic biological net-work alignment. IEEE/ACMTransactions on Computa-

REFERENCES 318

tional Biology and Bioin-formatics, 10(1):109–121,January 2013. CODENITCBCY. ISSN 1545-5963(print), 1557-9964 (elec-tronic).

Tang:2018:SRS

[TDY+18] Qirong Tang, Lu Ding,Fangchao Yu, Yuan Zhang,Yinghao Li, and Haibo Tu.Swarm robots search for mul-tiple targets based on animproved grouping strategy.IEEE/ACM Transactionson Computational Biologyand Bioinformatics, 15(6):1943–1950, November 2018.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Tian:2019:REA

[TDZ+19] Bo Tian, Qiong Duan,Can Zhao, Ben Teng, andZengyou He. Reinforce: anensemble approach for in-ferring PPI network fromAP–MS data. IEEE/ACMTransactions on Computa-tional Biology and Bioin-formatics, 16(2):365–376,March 2019. CODENITCBCY. ISSN 1545-5963(print), 1557-9964 (elec-tronic). URL https://dl.acm.org/doi/abs/10.1109/TCBB.2017.2705060.

Torres:2012:UGE

[TED+12] Jose Salavert Torres, Igna-cio Blanquer Espert, An-dres Tomas Dominguez, Vi-

cente Hernendez, IgnacioMedina, Joaquin Terraga,and Joaquin Dopazo. Us-ing GPUs for the exactalignment of short-read ge-netic sequences by means ofthe Burrows–Wheeler trans-form. IEEE/ACM Transac-tions on Computational Bi-ology and Bioinformatics, 9(4):1245–1256, July 2012.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Tang:2016:RMC

[TGD+16] Yang Tang, Huijun Gao, WeiDu, Jianquan Lu, Athana-sios V. Vasilakos, and JurgenKurths. Robust multi-objective controllability ofcomplex neuronal networks.IEEE/ACM Transactionson Computational Biologyand Bioinformatics, 13(4):778–791, 2016. CODENITCBCY. ISSN 1545-5963(print), 1557-9964 (elec-tronic).

Tenenhaus:2010:GAN

[TGGF10] Arthur Tenenhaus, VincentGuillemot, Xavier Gidrol,and Vincent Frouin. Gene as-sociation networks from mi-croarray data using a regu-larized estimation of partialcorrelation based on PLS re-gression. IEEE/ACM Trans-actions on ComputationalBiology and Bioinformatics,7(2):251–262, April 2010.CODEN ITCBCY. ISSN

REFERENCES 319


Tang:2013:MIC

[TGK13] Yang Tang, Huijun Gao, andJurgen Kurths. Multiobjec-tive identification of control-ling areas in neuronal net-works. IEEE/ACM Trans-actions on ComputationalBiology and Bioinformatics,10(3):708–720, May 2013.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Taliun:2016:FSB

[TGLP16] Daniel Taliun, Johann Gam-per, Ulf Leser, and Cris-tian Pattaro. Fast sampling-based whole-genome hap-lotype block recognition.IEEE/ACM Transactions onComputational Biology andBioinformatics, 13(2):315–325, March 2016. CODENITCBCY. ISSN 1545-5963(print), 1557-9964 (elec-tronic).

Tomescu:2015:EWD

[TGP+15] Alexandru I. Tomescu, TravisGagie, Alexandru Popa,Romeo Rizzi, Anna Kuos-manen, and Veli Makinen.Explaining a weighted DAGwith few paths for solv-ing genome-guided multi-assembly. IEEE/ACMTransactions on Computa-tional Biology and Bioin-formatics, 12(6):1345–1354,November 2015. CODEN


Tian:2018:GES

[TH18] Tianhai Tian and Jing-shan Huang. Guest edito-rial for special section onBIBM 2015. IEEE/ACMTransactions on Computa-tional Biology and Bioin-formatics, 15(6):1752–1753,November 2018. CODENITCBCY. ISSN 1545-5963(print), 1557-9964 (elec-tronic).

Thiele:2019:DOE

[THH+19] Sven Thiele, Sandra Heise,Wiebke Hessenkemper, HannesBongartz, Melissa Fensky,Fred Schaper, and SteffenKlamt. Designing opti-mal experiments to discrimi-nate interaction graph mod-els. IEEE/ACM Transac-tions on Computational Bi-ology and Bioinformatics,16(3):925–935, May 2019.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Tofigh:2011:SID

[THL11] Ali Tofigh, Michael Hal-lett, and Jens Lagergren.Simultaneous identificationof duplications and lateralgene transfers. IEEE/ACMTransactions on Computa-tional Biology and Bioinfor-matics, 8(2):517–535, March2011. CODEN ITCBCY.

REFERENCES 320


Thorvaldsen:2016:MMF

[Tho16] Steinar Thorvaldsen. A mu-tation model from first prin-ciples of the genetic code.IEEE/ACM Transactionson Computational Biologyand Bioinformatics, 13(5):878–886, September 2016.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Tamada:2011:EGW

[TIA+11] Yoshinori Tamada, SeiyaImoto, Hiromitsu Araki,Masao Nagasaki, CristinPrint, D. Stephen Charnock-Jones, and Satoru Miyano.Estimating genome-widegene networks using non-parametric Bayesian networkmodels on massively paral-lel computers. IEEE/ACMTransactions on Computa-tional Biology and Bioinfor-matics, 8(3):683–697, May/June 2011. CODENITCBCY. ISSN 1545-5963(print), 1557-9964 (elec-tronic).

Title:2013:AI

[Tit13] Title. 2012 annual in-dex. IEEE/ACM Transac-tions on Computational Bi-ology and Bioinformatics, 10(1):244–270, January 2013.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Title:2016:IIA

[Tit16] Title. 2015 index IEEE/ACM Transactions on Com-putational Biology andBioinformatics vol. 12. IEEE/ACM Transactions on Com-putational Biology and Bioin-formatics, 13(1):172–195,January 2016. CODENITCBCY. ISSN 1545-5963(print), 1557-9964 (elec-tronic).

Tseng:2005:EMG

[TK05] Vincent S. Tseng and Ching-Pin Kao. Efficiently min-ing gene expression data viaa novel parameterless clus-tering method. IEEE/ACMTransactions on Computa-tional Biology and Bioinfor-matics, 2(4):355–365, Octo-ber 2005. CODEN ITCBCY.ISSN 1545-5963 (print),1557-9964 (electronic).

Tamura:2018:CMR

[TLSA18] Takeyuki Tamura, Wei Lu,Jiangning Song, and TatsuyaAkutsu. Computing mini-mum reaction modificationsin a Boolean metabolic net-work. IEEE/ACM Trans-actions on ComputationalBiology and Bioinformatics,15(6):1853–1862, November2018. CODEN ITCBCY.ISSN 1545-5963 (print),1557-9964 (electronic).

Tuller:2011:CEI

[TM11] Tamir Tuller and ElchananMossel. Co-evolution is in-

REFERENCES 321

compatible with the Markovassumption in phylogenetics.IEEE/ACM Transactionson Computational Biologyand Bioinformatics, 8(6):1667–1670, November 2011.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Timonen:2019:PFM

[TMLI19] Juho Timonen, Henrik Man-nerstrom, Harri Lahdesmaki,and Jukka Intosalmi. Aprobabilistic framework formolecular network structureinference by means of mecha-nistic modeling. IEEE/ACMTransactions on Computa-tional Biology and Bioin-formatics, 16(6):1843–1854,November 2019. CODENITCBCY. ISSN 1545-5963(print), 1557-9964 (elec-tronic). URL https://dl.acm.org/doi/abs/10.1109/TCBB.2018.2825327.

Tan:2008:NBP

[TNQ08] Tuan Zea Tan, Geok See Ng,and Chai Quek. A novelbiologically and psycholog-ically inspired fuzzy deci-sion support system: Hierar-chical complementary learn-ing. IEEE/ACM Transac-tions on Computational Bi-ology and Bioinformatics,5(1):67–79, January 2008.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Tu:2019:IGN

[TOYHZ19] Jia-Juan Tu, Le Ou-Yang,Xiaohua Hu, and Xiao-Fei Zhang. Inferringgene network rewiring bycombining gene expressionand gene mutation data.IEEE/ACM Transactions onComputational Biology andBioinformatics, 16(3):1042–1048, May 2019. CODENITCBCY. ISSN 1545-5963(print), 1557-9964 (elec-tronic).

Torshizi:2018:SPI

[TP18] Abolfazl Doostparast Tor-shizi and Linda Petzold.Sparse pathway-induced dy-namic network biomarkerdiscovery for early warningsignal detection in complexdiseases. IEEE/ACM Trans-actions on ComputationalBiology and Bioinformatics,15(3):1028–1034, May 2018.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Thireou:2007:BLS

[TR07] Trias Thireou and MartinReczko. Bidirectional longshort-term memory networksfor predicting the subcellu-lar localization of eukaryoticproteins. IEEE/ACM Trans-actions on ComputationalBiology and Bioinformat-ics, 4(3):441–446, July 2007.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

REFERENCES 322

Than:2013:MPD

[TR13] Cuong V. Than and Noah A.Rosenberg. Mathematicalproperties of the deep coa-lescence cost. IEEE/ACMTransactions on Computa-tional Biology and Bioinfor-matics, 10(1):61–72, January2013. CODEN ITCBCY.ISSN 1545-5963 (print),1557-9964 (electronic).

Thomas:2008:GMR

[TRBK08] John Thomas, Naren Ra-makrishnan, and ChrisBailey-Kellogg. Graphicalmodels of residue coupling inprotein families. IEEE/ACMTransactions on Computa-tional Biology and Bioinfor-matics, 5(2):183–197, April2008. CODEN ITCBCY.ISSN 1545-5963 (print),1557-9964 (electronic).

Thomas:2009:PDS

[TRBK09] John Thomas, Naren Ra-makrishnan, and ChrisBailey-Kellogg. Protein de-sign by sampling an undi-rected graphical model ofresidue constraints. IEEE/ACM Transactions on Com-putational Biology and Bioin-formatics, 6(3):506–516, July2009. CODEN ITCBCY.ISSN 1545-5963 (print),1557-9964 (electronic).

Tataw:2013:QAL

[TRKRC13] Oben M. Tataw, Gone-hal Venugopala Reddy, Ea-monn J. Keogh, and Amit K.

Roy-Chowdhury. Quanti-tative analysis of live-cellgrowth at the shoot apex ofArabidopsis thaliana : Algo-rithms for feature measure-ment and temporal align-ment. IEEE/ACM Trans-actions on ComputationalBiology and Bioinformatics,10(5):1150–1161, September2013. CODEN ITCBCY.ISSN 1545-5963 (print),1557-9964 (electronic).

Tan:2017:ESS

[TS17] Ying Tan and Yuhui Shi.Editorial: Special sectionon bio-inspired swarm com-puting and engineering.IEEE/ACM Transactions onComputational Biology andBioinformatics, 14(1):1–3,January 2017. CODENITCBCY. ISSN 1545-5963(print), 1557-9964 (elec-tronic).

Tan:2018:SSS

[TS18] Ying Tan and Yuhui Shi.Special section on swarm-based algorithms and ap-plications in computationalbiology and bioinformatics.IEEE/ACM Transactionson Computational Biologyand Bioinformatics, 15(6):1863–1864, November 2018.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Tsai:2012:IPP

[Tsa12] Richard Tzong-Han Tsai.

REFERENCES 323

Improving protein-proteininteraction pair ranking withan integrated global asso-ciation score. IEEE/ACMTransactions on Computa-tional Biology and Bioin-formatics, 9(6):1690–1695,November 2012. CODENITCBCY. ISSN 1545-5963(print), 1557-9964 (elec-tronic).

Tulpan:2014:TPP

[TSM14] Dan Tulpan, Derek H.Smith, and Roberto Mon-temanni. Thermodynamicpost-processing versus GC-content pre-processing forDNA codes satisfying theHamming distance andreverse-complement con-straints. IEEE/ACM Trans-actions on ComputationalBiology and Bioinformatics,11(2):441–452, March 2014.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Torres-Sanchez:2013:GFG

[TSMMG+13] Sergio Torres-Sanchez, NuriaMedina-Medina, Chris Gig-noux, Maria del Mar Abad-Grau, and Esteban Gonzalez-Burchard. GeneOnEarth:Fitting genetic PC plotson the globe. IEEE/ACMTransactions on Computa-tional Biology and Bioin-formatics, 10(4):1009–1016,July 2013. CODEN ITCBCY.ISSN 1545-5963 (print),1557-9964 (electronic).

Tsai:2013:PBL

[TTWR13] Tsung-Heng Tsai, Mahlet G.Tadesse, Yue Wang, andHabtom W. Ressom. Profile-based LC-MS data align-ment — a Bayesian ap-proach. IEEE/ACM Trans-actions on ComputationalBiology and Bioinformatics,10(2):494–503, March 2013.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Tenazinha:2011:SMM

[TV11] Nuno Tenazinha and SusanaVinga. A survey on meth-ods for modeling and analyz-ing integrated biological net-works. IEEE/ACM Trans-actions on ComputationalBiology and Bioinformat-ics, 8(4):943–958, July 2011.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Tsang:2010:SPA

[TW10] Herbert H. Tsang andKay C. Wiese. SARNA-Predict: Accuracy improve-ment of RNA secondarystructure prediction us-ing permutation-based simu-lated annealing. IEEE/ACMTransactions on Computa-tional Biology and Bioinfor-matics, 7(4):727–740, Octo-ber 2010. CODEN ITCBCY.ISSN 1545-5963 (print),1557-9964 (electronic).

REFERENCES 324

Tang:2012:CEC

[TWG+12] Yang Tang, Zidong Wang,Huijun Gao, Stephen Swift,and Jurgen Kurths. A con-strained evolutionary com-putation method for detect-ing controlling regions of cor-tical networks. IEEE/ACMTransactions on Computa-tional Biology and Bioin-formatics, 9(6):1569–1581,November 2012. CODENITCBCY. ISSN 1545-5963(print), 1557-9964 (elec-tronic).

Tan:2020:EEH

[TWW+20] Renjie Tan, Jixuan Wang,Xiaoliang Wu, Liran Juan,Tianjiao Zhang, Rui Ma,Qing Zhan, Tao Wang,Shuilin Jin, Qinghua Jiang,and Yadong Wang. ERDS-Exome: a hybrid ap-proach for copy number vari-ant detection from whole-exome sequencing data.IEEE/ACM Transactions onComputational Biology andBioinformatics, 17(3):796–803, May 2020. CODENITCBCY. ISSN 1545-5963(print), 1557-9964 (elec-tronic). URL https://dl.acm.org/doi/10.1109/TCBB.2017.2758779.

Tian:2014:INB

[TWZ+14] Ye Tian, Sean S. Wang, ZhenZhang, Olga C. Rodriguez,Emanuel Petricoin, Ie-MingShih, Daniel Chan, MariaAvantaggiati, Guoqiang Yu,

Shaozhen Ye, Robert Clarke,Chao Wang, Bai Zhang,Yue Wang, and Chris Al-banese. Integration of net-work biology and imagingto study cancer phenotypesand responses. IEEE/ACMTransactions on Computa-tional Biology and Bioin-formatics, 11(6):1009–1019,November 2014. CODENITCBCY. ISSN 1545-5963(print), 1557-9964 (elec-tronic).

Tang:2014:PEP

[TWZP14] Xiwei Tang, Jianxin Wang,Jiancheng Zhong, and Yi Pan.Predicting essential pro-teins based on weighted de-gree centrality. IEEE/ACMTransactions on Computa-tional Biology and Bioin-formatics, 11(2):407–418,March 2014. CODENITCBCY. ISSN 1545-5963(print), 1557-9964 (elec-tronic).

Tu:2016:UFC

[TWZW16] Xudong Tu, YuanliangWang, Maolan Zhang, andJinchuan Wu. Using for-mal concept analysis toidentify negative correla-tions in gene expressiondata. IEEE/ACM Trans-actions on ComputationalBiology and Bioinformatics,13(2):380–391, March 2016.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

REFERENCES 325

Taha:2015:ISI

[TYA15] Kamal Taha, Paul D. Yoo,and Mohammed Alzaabi.iPFPi: a system for improv-ing protein function predic-tion through cumulative it-erations. IEEE/ACM Trans-actions on ComputationalBiology and Bioinformatics,12(4):825–836, July 2015.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Teng:2016:EGP

[TYL+16] Ben Teng, Can Yang, Jim-ing Liu, Zhipeng Cai, andXiang Wan. Exploring thegenetic patterns of com-plex diseases via the in-tegrative genome-wide ap-proach. IEEE/ACM Trans-actions on ComputationalBiology and Bioinformatics,13(3):557–564, May 2016.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Tang:2016:NAF

[TZ16] Jian Tang and ShuigengZhou. A new approach forfeature selection from mi-croarray data based on mu-tual information. IEEE/ACM Transactions on Com-putational Biology and Bioin-formatics, 13(6):1004–1015,November 2016. CODENITCBCY. ISSN 1545-5963(print), 1557-9964 (elec-tronic).

Tang:2007:DTS

[TZH07] Yuchun Tang, Yan-QingZhang, and Zhen Huang.Development of two-stageSVM-RFE gene selectionstrategy for microarrayexpression data analysis.IEEE/ACM Transactions onComputational Biology andBioinformatics, 4(3):365–381, July 2007. CODENITCBCY. ISSN 1545-5963(print), 1557-9964 (elec-tronic).

Thanh:2017:ECT

[TZP17] Vo Hong Thanh, RobertoZunino, and Corrado Pri-ami. Efficient constant-time complexity algorithmfor stochastic simulationof large reaction networks.IEEE/ACM Transactions onComputational Biology andBioinformatics, 14(3):657–667, May 2017. CODENITCBCY. ISSN 1545-5963(print), 1557-9964 (elec-tronic).

Tino:2011:SCG

[TZY11] Peter Tino, Hongya Zhao,and Hong Yan. Search-ing for coexpressed genes inthree-color cDNA microar-ray data using a probabilisticmodel-based Hough Trans-form. IEEE/ACM Transac-tions on Computational Bi-ology and Bioinformatics, 8(4):1093–1107, July 2011.CODEN ITCBCY. ISSN

REFERENCES 326


Ullah:2016:GAC

[UAH16] Ehsan Ullah, Shuchin Aeron,and Soha Hassoun. gEFM:an algorithm for computingelementary flux modes usinggraph traversal. IEEE/ACMTransactions on Computa-tional Biology and Bioin-formatics, 13(1):122–134,January 2016. CODENITCBCY. ISSN 1545-5963(print), 1557-9964 (elec-tronic).

Urban:2019:DLD

[UBP+19] Gregor Urban, Kevin Bache,Duc T. T. Phan, Agua So-brino, Alexander K. Shmakov,Stephanie J. Hachey, Christo-pher C. W. Hughes, andPierre Baldi. Deep learningfor drug discovery and cancerresearch: Automated anal-ysis of vascularization im-ages. IEEE/ACM Transac-tions on Computational Bi-ology and Bioinformatics, 16(3):1029–1035, May 2019.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Unger:2010:LSG

[UC10] Giora Unger and BennyChor. Linear separabil-ity of gene expression datasets. IEEE/ACM Transac-tions on Computational Bi-ology and Bioinformatics,7(2):375–381, April 2010.


Uehara:2009:PDC

[UJ09] Hiroaki Uehara and MasakazuJimbo. A positive detect-ing code and its decod-ing algorithm for DNA li-brary screening. IEEE/ACMTransactions on Computa-tional Biology and Bioinfor-matics, 6(4):652–666, Octo-ber 2009. CODEN ITCBCY.ISSN 1545-5963 (print),1557-9964 (electronic).

Ushakov:2018:BLB

[UKV18] Anton V. Ushakov, Xe-nia Klimentova, and IgorVasilyev. Bi-level andbi-objective p-median typeproblems for integrative clus-tering: Application to analy-sis of cancer gene-expressionand drug-response data.IEEE/ACM Transactions onComputational Biology andBioinformatics, 15(1):46–59,January 2018. CODENITCBCY. ISSN 1545-5963(print), 1557-9964 (elec-tronic).

Urbini:2019:ERP

[USMS19] Laura Urbini, Blerina Sinaimeri,Catherine Matias, and Marie-France Sagot. Exploring therobustness of the parsimo-nious reconciliation methodin host-symbiont cophy-logeny. IEEE/ACM Trans-actions on Computational

REFERENCES 327


Ullah:2015:PUA

[UWLH15] Ehsan Ullah, Mark Walker,Kyongbum Lee, and SohaHassoun. PreProPath:an uncertainty-aware algo-rithm for identifying pre-dictable profitable pathwaysin biochemical networks.IEEE/ACM Transactionson Computational Biologyand Bioinformatics, 12(6):1405–1415, November 2015.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Valentini:2011:TPR

[Val11] Giorgio Valentini. Truepath rule hierarchical en-sembles for genome-widegene function prediction.IEEE/ACM Transactionson Computational Biologyand Bioinformatics, 8(3):832–847, May/June 2011.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Venkatachalam:2010:UTC

[VASG10] Balaji Venkatachalam, JimApple, Katherine St. John,and Daniel Gusfield. Un-tangling tanglegrams: Com-paring trees by their draw-ings. IEEE/ACM Transac-tions on Computational Bi-

ology and Bioinformatics, 7(4):588–597, October 2010.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Villaverde:2018:PTI

[VBB18] Alejandro F. Villaverde,Kolja Becker, and Julio R.Banga. PREMER: a toolto infer biological networks.IEEE/ACM Transactions onComputational Biology andBioinformatics, 15(4):1193–1202, July 2018. CODENITCBCY. ISSN 1545-5963(print), 1557-9964 (elec-tronic).

vanBerlo:2011:PMF

[vBdRD+11] Rogier J. P. van Berlo,Dick de Ridder, Jean-MarcDaran, Pascale A. S. Daran-Lapujade, Bas Teusink,and Marcel J. T. Rein-ders. Predicting metabolicfluxes using gene expres-sion differences as con-straints. IEEE/ACM Trans-actions on ComputationalBiology and Bioinformatics,8(1):206–216, January 2011.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Vyas:2018:AGP

[VBG+18] Renu Vyas, Sanket Ba-pat, Purva Goel, Muthuku-marasamy Karthikeyan, San-jeev S. Tambe, and Bhaskar D.Kulkarni. Application ofgenetic programming GP

REFERENCES 328

formalism for building dis-ease predictive models fromprotein–protein interactionsPPI data. IEEE/ACMTransactions on Computa-tional Biology and Bioinfor-matics, 15(1):27–37, January2018. CODEN ITCBCY.ISSN 1545-5963 (print),1557-9964 (electronic).

Vundavilli:2020:SDE

[VDS+20] Haswanth Vundavilli, Anirud-dha Datta, Chao Sima, Jian-ping Hua, Rosana Lopes,and Michael Bittner. In sil-ico design and experimen-tal validation of combinationtherapy for pancreatic can-cer. IEEE/ACM Transac-tions on Computational Bi-ology and Bioinformatics, 17(3):1010–1018, May 2020.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic). URL https://dl.acm.org/doi/10.1109/TCBB.2018.2872573.

VanDyck:2019:RSP

[VdTVV19] Michiel Van Dyck, Xavier Wootde Trixhe, An Vermeulen,and Wim Vanroose. A ro-bust simulator for physiolog-ically structured populationmodels. IEEE/ACM Trans-actions on ComputationalBiology and Bioinformatics,16(3):851–864, May 2019.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Vignes:2009:GCI

[VF09] Matthieu Vignes and Flo-rence Forbes. Gene cluster-ing via integrated Markovmodels combining individ-ual and pairwise features.IEEE/ACM Transactions onComputational Biology andBioinformatics, 6(2):260–270, April 2009. CODENITCBCY. ISSN 1545-5963(print), 1557-9964 (elec-tronic).

Verma:2019:POC

[VGBK19] Deeptak Verma, GevorgGrigoryan, and Chris Bailey-Kellogg. Pareto optimizationof combinatorial mutagenesislibraries. IEEE/ACM Trans-actions on ComputationalBiology and Bioinformatics,16(4):1143–1153, July 2019.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

vanIersel:2020:PTA

[vIJJ+20] Leo van Iersel, RemieJanssen, Mark Jones, Yuk-ihiro Murakami, and Nor-bert Zeh. Polynomial-timealgorithms for phylogeneticinference problems involv-ing duplication and reticu-lation. IEEE/ACM Trans-actions on ComputationalBiology and Bioinformatics,17(1):14–26, January 2020.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic). URL https:/

REFERENCES 329


vanIersel:2009:CLP

[vIKK+09] Leo van Iersel, Judith Kei-jsper, Steven Kelk, LeenStougie, Ferry Hagen, andTeun Boekhout. Con-structing level-2 phyloge-netic networks from triplets.IEEE/ACM Transactions onComputational Biology andBioinformatics, 6(4):667–681, October 2009. CODENITCBCY. ISSN 1545-5963(print), 1557-9964 (elec-tronic).

vanIersel:2008:SIT

[vIKKS08] Leo van Iersel, Judith Kei-jsper, Steven Kelk, andLeen Stougie. Shorelinesof islands of tractability:Algorithms for parsimonyand minimum perfect phy-logeny haplotyping prob-lems. IEEE/ACM Trans-actions on ComputationalBiology and Bioinformatics,5(2):301–312, April 2008.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Viswanath:2018:CET

[Vis18] Narayanan C. Viswanath.Calculating the expectedtime to eradicate HIV-1 using a Markov chain.IEEE/ACM Transactions onComputational Biology andBioinformatics, 15(1):60–67,January 2018. CODEN


Vashist:2007:OCM

[VKM07] Akshay Vashist, Casimir A.Kulikowski, and Ilya Much-nik. Ortholog clusteringon a multipartite graph.IEEE/ACM Transactions onComputational Biology andBioinformatics, 4(1):17–27,January 2007. CODENITCBCY. ISSN 1545-5963(print), 1557-9964 (elec-tronic).

Veltri:2017:IRA

[VKS17] Daniel Veltri, Uday Kamath,and Amarda Shehu. Im-proving recognition of an-timicrobial peptides and tar-get selectivity through ma-chine learning and geneticprogramming. IEEE/ACMTransactions on Computa-tional Biology and Bioin-formatics, 14(2):300–313,March 2017. CODENITCBCY. ISSN 1545-5963(print), 1557-9964 (elec-tronic).

Vijayan:2018:MNA

[VM18] Vipin Vijayan and TijanaMilenkovic. Multiple net-work alignment via Multi-MAGNA++. IEEE/ACMTransactions on Computa-tional Biology and Bioin-formatics, 15(5):1669–1682,September 2018. CODENITCBCY. ISSN 1545-5963

REFERENCES 330


Vassura:2008:RSP

[VMD+08] Marco Vassura, LucianoMargara, Pietro Di Lena,Filippo Medri, Piero Fariselli,and Rita Casadio. Re-construction of 3D struc-tures from protein contactmaps. IEEE/ACM Trans-actions on ComputationalBiology and Bioinformat-ics, 5(3):357–367, July 2008.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Vasylchenkova:2017:CMA

[VMZM17] Anastasiia Vasylchenkova,Miha Mraz, Nikolaj Zimic,and Miha Moskon. Classicalmechanics approach appliedto analysis of genetic oscil-lators. IEEE/ACM Trans-actions on ComputationalBiology and Bioinformatics,14(3):721–727, May 2017.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Vogt:2015:USD

[Vog15] Julia E. Vogt. Unsu-pervised structure detec-tion in biomedical data.IEEE/ACM Transactions onComputational Biology andBioinformatics, 12(4):753–760, July 2015. CODENITCBCY. ISSN 1545-5963(print), 1557-9964 (elec-tronic).

Varghese:2015:RLW

[VPB15] Blesson Varghese, Ishan Pa-tel, and Adam Barker. RBio-Cloud: a light-weight frame-work for bioconductor andR-based jobs on the cloud.IEEE/ACM Transactions onComputational Biology andBioinformatics, 12(4):871–878, July 2015. CODENITCBCY. ISSN 1545-5963(print), 1557-9964 (elec-tronic).

Verspoor:2010:ESB

[VRJ+10] Karin Verspoor, ChristopheRoeder, Helen L. John-son, Kevin Bretonnel Co-hen, William A. Baumgart-ner, Jr., and Lawrence E.Hunter. Exploring species-based strategies for genenormalization. IEEE/ACMTransactions on Computa-tional Biology and Bioinfor-matics, 7(3):462–471, July2010. CODEN ITCBCY.ISSN 1545-5963 (print),1557-9964 (electronic).

Vasic:2012:ITA

[VRK12] Bane Vasic, Vida Ravan-mehr, and Anantha Ra-man Krishnan. An infor-mation theoretic approach toconstructing robust Booleangene regulatory networks.IEEE/ACM Transactions onComputational Biology andBioinformatics, 9(1):52–65,January 2012. CODENITCBCY. ISSN 1545-5963

REFERENCES 331


Venkateswaran:2011:TTF

[VSKJ11] Jayendra Gnanaskandan Ven-kateswaran, Bin Song, TamerKahveci, and ChristopherJermaine. TRIAL: a toolfor finding distant structuralsimilarities. IEEE/ACMTransactions on Computa-tional Biology and Bioinfor-matics, 8(3):819–831, May/June 2011. CODENITCBCY. ISSN 1545-5963(print), 1557-9964 (elec-tronic).

Vass:2006:JMB

[VSR+06] Marc T. Vass, Clifford A.Shaffer, Naren Ramakrish-nan, Layne T. Watson, andJohn J. Tyson. The Jig-Cell model builder: a spread-sheet interface for creatingbiochemical reaction networkmodels. IEEE/ACM Trans-actions on ComputationalBiology and Bioinformatics,3(2):155–164, April 2006.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Vilor-Tejedor:2016:EPM

[VTGC16] Natalia Vilor-Tejedor, Juan R.Gonzalez, and M. LuzCalle. Efficient and power-ful method for combining P -values in genome-wide asso-ciation studies. IEEE/ACMTransactions on Computa-tional Biology and Bioin-

formatics, 13(6):1100–1106,November 2016. CODENITCBCY. ISSN 1545-5963(print), 1557-9964 (elec-tronic).

Weidman:2019:SIP

[WAG19] Jake Weidman, William Au-rite, and Jens Grossklags.On sharing intentions, andpersonal and interdependentprivacy considerations forgenetic data: a vignettestudy. IEEE/ACM Trans-actions on ComputationalBiology and Bioinformatics,16(4):1349–1361, July 2019.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Wohlers:2013:DOD

[WAK13] Inken Wohlers, Rumen An-donov, and Gunnar W. Klau.DALIX: Optimal DALI pro-tein structure alignment.IEEE/ACM Transactions onComputational Biology andBioinformatics, 10(1):26–36,January 2013. CODENITCBCY. ISSN 1545-5963(print), 1557-9964 (elec-tronic).

Wang:2012:OSA

[Wan12] Biing-Feng Wang. Output-sensitive algorithms for find-ing the nested common in-tervals of two general se-quences. IEEE/ACM Trans-actions on ComputationalBiology and Bioinformatics,9(2):548–559, March 2012.

REFERENCES 332


Wang:2016:NEA

[Wan16] Biing-Feng Wang. A newefficient algorithm for theall sorting reversals prob-lem with no bad compo-nents. IEEE/ACM Trans-actions on ComputationalBiology and Bioinformat-ics, 13(4):599–609, 2016.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Wong:2011:UKA

[WB11] William W. L. Wong andForbes J. Burkowski. Us-ing kernel alignment to se-lect features of molecular de-scriptors in a QSAR study.IEEE/ACM Transactionson Computational Biologyand Bioinformatics, 8(5):1373–1384, September 2011.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Wang:2017:BCO

[WB17] Xin Wang and Jinbo Bi.Bi-convex optimization tolearn classifiers from multi-ple biomedical annotations.IEEE/ACM Transactions onComputational Biology andBioinformatics, 14(3):564–575, May 2017. CODENITCBCY. ISSN 1545-5963(print), 1557-9964 (elec-tronic).

Wehe:2013:EAK

[WBE13] Andre Wehe, J. GordonBurleigh, and Oliver Eu-lenstein. Efficient al-gorithms for knowledge-enhanced supertree andsupermatrix phylogeneticproblems. IEEE/ACMTransactions on Computa-tional Biology and Bioin-formatics, 10(6):1432–1441,November 2013. CODENITCBCY. ISSN 1545-5963(print), 1557-9964 (elec-tronic).

Wang:2012:EMM

[WBP+12] Chong Wang, Peter Beyer-lein, Heike Pospisil, AntjeKrause, Chris Nugent, andWerner Dubitzky. An ef-ficient method for model-ing kinetic behavior of chan-nel proteins in cardiomy-ocytes. IEEE/ACM Trans-actions on ComputationalBiology and Bioinformatics,9(1):40–51, January 2012.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Wang:2019:MMV

[WCA+19] Aiguo Wang, Ye Chen, NingAn, Jing Yang, Lian Li,and Lili Jiang. Microarraymissing value imputation:a regularized local learningmethod. IEEE/ACM Trans-actions on ComputationalBiology and Bioinformatics,16(3):980–993, May 2019.CODEN ITCBCY. ISSN

REFERENCES 333


Wang:2018:PHR

[WCC+18] Haishuai Wang, ZhichengCui, Yixin Chen, MichaelAvidan, Arbi Ben Abdal-lah, and Alexander Kronzer.Predicting hospital read-mission via cost-sensitivedeep learning. IEEE/ACMTransactions on Computa-tional Biology and Bioin-formatics, 15(6):1968–1978,November 2018. CODENITCBCY. ISSN 1545-5963(print), 1557-9964 (elec-tronic).

Wu:2011:ACC

[WCL11] Yonghui Wu, Timothy J.Close, and Stefano Lonardi.Accurate construction ofconsensus genetic maps viainteger linear programming.IEEE/ACM Transactions onComputational Biology andBioinformatics, 8(2):381–394, March 2011. CODENITCBCY. ISSN 1545-5963(print), 1557-9964 (elec-tronic).

Wong:2012:MEA

[WCLY12] Thomas K. F. Wong, Y. S.Chiu, T. W. Lam, and S. M.Yiu. Memory efficient algo-rithms for structural align-ment of RNAs with pseudo-knots. IEEE/ACM Transac-tions on Computational Bi-ology and Bioinformatics, 9(1):161–168, January 2012.


Wang:2020:GDI

[WCLY20] Shunfang Wang, ZichengCao, Mingyuan Li, and Yaot-ing Yue. G-DipC: an im-proved feature representa-tion method for short se-quences to predict the typeof cargo in cell-penetratingpeptides. IEEE/ACMTransactions on Computa-tional Biology and Bioinfor-matics, 17(3):739–747, May2020. CODEN ITCBCY.ISSN 1545-5963 (print),1557-9964 (electronic). URLhttps://dl.acm.org/doi/10.1109/TCBB.2019.2930993.

Wingfield:2019:RMM

[WCMB19] Benjamin Wingfield, SonyaColeman, TM McGinnity,and AJ Bjourson. Ro-bust microbial markers fornon-invasive inflammatorybowel disease identification.IEEE/ACM Transactionson Computational Biologyand Bioinformatics, 16(6):2078–2088, November 2019.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic). URL https://dl.acm.org/doi/abs/10.1109/TCBB.2018.2831212.

Wang:2015:BMM

[WCMZ15] Beichen Wang, XiaodongChen, Hiroshi Mamitsuka,and Shanfeng Zhu. BMEx-pert: Mining MEDLINE for

REFERENCES 334

finding experts in biomedi-cal domains based on lan-guage model. IEEE/ACMTransactions on Computa-tional Biology and Bioin-formatics, 12(6):1286–1294,November 2015. CODENITCBCY. ISSN 1545-5963(print), 1557-9964 (elec-tronic).

Wang:2019:DDR

[WCQ+19] Yin-Ying Wang, ChunfengCui, Liqun Qi, Hong Yan,and Xing-Ming Zhao. Dr-POCS: Drug repositioningbased on projection ontoconvex sets. IEEE/ACMTransactions on Computa-tional Biology and Bioin-formatics, 16(1):154–162,January 2019. CODENITCBCY. ISSN 1545-5963(print), 1557-9964 (elec-tronic).

Wang:2007:ACC

[WCX07] Lipo Wang, Feng Chu, andWei Xie. Accurate can-cer classification using ex-pressions of very few genes.IEEE/ACM Transactions onComputational Biology andBioinformatics, 4(1):40–53,January 2007. CODENITCBCY. ISSN 1545-5963(print), 1557-9964 (elec-tronic).

Wu:2018:UDL

[WCXL18] Hongjie Wu, ChengyuanCao, Xiaoyan Xia, and QiangLu. Unified deep learning ar-

chitecture for modeling biol-ogy sequence. IEEE/ACMTransactions on Computa-tional Biology and Bioin-formatics, 15(5):1445–1452,September 2018. CODENITCBCY. ISSN 1545-5963(print), 1557-9964 (elec-tronic).

Wiese:2008:REA

[WDH08] Kay C. Wiese, Alain A.Deschenes, and Andrew G.Hendriks. RnaPredict—An evolutionary algorithmfor RNA secondary struc-ture prediction. IEEE/ACMTransactions on Computa-tional Biology and Bioinfor-matics, 5(1):25–41, January2008. CODEN ITCBCY.ISSN 1545-5963 (print),1557-9964 (electronic).

Wang:2017:SAL

[WDL+17] Chao Wang, Dong Dai,Xi Li, Aili Wang, and XuehaiZhou. SuperMIC: Analyz-ing large biological datasetsin bioinformatics with max-imal information coefficient.IEEE/ACM Transactions onComputational Biology andBioinformatics, 14(4):783–795, July 2017. CODENITCBCY. ISSN 1545-5963(print), 1557-9964 (elec-tronic).

Wu:2012:BIC

[WDS+12] Meng-Yun Wu, Dao-QingDai, Yu Shi, Hong Yan, andXiao-Fei Zhang. Biomarker

REFERENCES 335

identification and cancerclassification based on mi-croarray data using Laplacenaive Bayes model withmean shrinkage. IEEE/ACMTransactions on Computa-tional Biology and Bioin-formatics, 9(6):1649–1662,November 2012. CODENITCBCY. ISSN 1545-5963(print), 1557-9964 (elec-tronic).

Wang:2015:PDC

[WDX+15] Kun Wang, Avinash Das,Zheng-Mei Xiong, Kan Cao,and Sridhar Hannenhalli.Phenotype-dependent coex-pression gene clusters: ap-plication to normal and pre-mature ageing. IEEE/ACMTransactions on Computa-tional Biology and Bioinfor-matics, 12(1):30–39, January2015. CODEN ITCBCY.ISSN 1545-5963 (print),1557-9964 (electronic).

Wernicke:2006:EDN

[Wer06] Sebastian Wernicke. Efficientdetection of network mo-tifs. IEEE/ACM Transac-tions on Computational Bi-ology and Bioinformatics, 3(4):347–359, October 2006.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Wan:2015:PPL

[WFD15] Cen Wan, Alex A. Freitas,and Joao Pedro De Mag-alhaes. Predicting the pro-

longevity or anti-longevityeffect of model organismgenes with new hierarchi-cal feature selection meth-ods. IEEE/ACM Transac-tions on Computational Bi-ology and Bioinformatics,12(2):262–275, March 2015.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Wang:2019:NCA

[WFY+19] Yishu Wang, Huaying Fang,Dejie Yang, Hongyu Zhao,and Minghua Deng. Networkclustering analysis usingmixture exponential-familyrandom graph models andits application in genetic in-teraction data. IEEE/ACMTransactions on Computa-tional Biology and Bioin-formatics, 16(5):1743–1752,September 2019. CODENITCBCY. ISSN 1545-5963(print), 1557-9964 (elec-tronic).

Wu:2016:NBM

[WGK16] Hao Wu, Lin Gao, andNikola K. Kasabov. Network-based method for inferringcancer progression at thepathway level from cross-sectional mutation data.IEEE/ACM Transactionson Computational Biologyand Bioinformatics, 13(6):1036–1044, November 2016.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

REFERENCES 336

Wang:2011:IMG

[WGP11] Wenxue Wang, Bijoy K.Ghosh, and Himadri Pakrasi.Identification and model-ing of genes with diur-nal oscillations from mi-croarray time series data.IEEE/ACM Transactions onComputational Biology andBioinformatics, 8(1):108–121, January 2011. CODENITCBCY. ISSN 1545-5963(print), 1557-9964 (elec-tronic).

Wang:2017:HBH

[WGX+17] Pu Wang, Ruiquan Ge,Xuan Xiao, Manli Zhou,and Fengfeng Zhou. hMu-Lab: a biomedical hybridMUlti-LABel classifier basedon multiple linear regression.IEEE/ACM Transactionson Computational Biologyand Bioinformatics, 14(5):1173–1180, September 2017.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Wu:2011:GES

[WH11] Fang-Xiang Wu and JunHuan. Guest editorial:Special focus on bioinfor-matics and systems biol-ogy. IEEE/ACM Transac-tions on Computational Bi-ology and Bioinformatics, 8(2):292–293, March 2011.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Wieseke:2015:CRI

[WHBM15] Nicolas Wieseke, Tom Hart-mann, Matthias Bernt, andMartin Middendorf. Co-phylogenetic reconciliationwith ILP. IEEE/ACMTransactions on Computa-tional Biology and Bioin-formatics, 12(6):1227–1235,November 2015. CODENITCBCY. ISSN 1545-5963(print), 1557-9964 (elec-tronic).

Wang:2020:IIE

[WHF+20] Min Wang, Ting-Zhu Huang,Jian Fang, Vince D. Cal-houn, and Yu-Ping Wang.Integration of imaging (epi)genomicsdata for the study ofschizophrenia using groupsparse joint nonnegative ma-trix factorization. IEEE/ACM Transactions on Com-putational Biology and Bioin-formatics, 17(5):1671–1681,September 2020. CODENITCBCY. ISSN 1545-5963(print), 1557-9964 (elec-tronic). URL https://dl.acm.org/doi/10.1109/TCBB.2019.2899568.

Weskamp:2007:MGA

[WHKK07] Nils Weskamp, Eyke Huller-meier, Daniel Kuhn, andGerhard Klebe. Multi-ple graph alignment for thestructural analysis of pro-tein active sites. IEEE/ACMTransactions on Computa-tional Biology and Bioinfor-matics, 4(2):310–320, April

REFERENCES 337


Witwer:2004:PCR

[WHS04] Christina Witwer, Ivo L.Hofacker, and Peter F.Stadler. Prediction ofconsensus RNA secondarystructures including pseudo-knots. IEEE/ACM Trans-actions on ComputationalBiology and Bioinformat-ics, 1(2):66–77, April 2004.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Wang:2012:SCM

[WHWP12] Jianxin Wang, YuannanHuang, Fang-Xiang Wu, andYi Pan. Symmetry compres-sion method for discoveringnetwork motifs. IEEE/ACMTransactions on Computa-tional Biology and Bioin-formatics, 9(6):1776–1789,November 2012. CODENITCBCY. ISSN 1545-5963(print), 1557-9964 (elec-tronic).

Wang:2017:SLF

[WHXS17] Zhiyong Wang, Benika Hall,Jinbo Xu, and Xinghua Shi.A sparse learning frame-work for joint effect analy-sis of copy number variants.IEEE/ACM Transactionson Computational Biologyand Bioinformatics, 14(5):1013–1027, September 2017.CODEN ITCBCY. ISSN


Wu:2014:GWP

[WHZ14] Jian-Sheng Wu, Sheng-Jun Huang, and Zhi-HuaZhou. Genome-wide proteinfunction prediction throughmulti-instance multi-labellearning. IEEE/ACM Trans-actions on ComputationalBiology and Bioinformat-ics, 11(5):891–902, Septem-ber 2014. CODEN ITCBCY.ISSN 1545-5963 (print),1557-9964 (electronic).

Wigren:2015:MOI

[Wig15] Torbjorn Wigren. Modelorder and identifiability ofnon-linear biological sys-tems in stable oscillation.IEEE/ACM Transactionson Computational Biologyand Bioinformatics, 12(6):1479–1484, November 2015.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Williams:2004:INA

[Wil04a] Michael R. Williams. In-troduction of new AssociateEditors. IEEE/ACM Trans-actions on ComputationalBiology and Bioinformat-ics, 1(1):4–12, January 2004.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

REFERENCES 338

Williams:2004:WM

[Wil04b] Michael R. Williams. Wel-come message. IEEE/ACMTransactions on Computa-tional Biology and Bioinfor-matics, 1(1):1, January 2004.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Willson:2009:RTS

[Wil09] Stephen J. Willson. Ro-bustness of topological su-pertree methods for rec-onciling dense incompatibledata. IEEE/ACM Trans-actions on ComputationalBiology and Bioinformatics,6(1):62–75, January 2009.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Willson:2011:RNC

[Wil11] Stephen J. Willson. Regu-lar networks can be uniquelyconstructed from their trees.IEEE/ACM Transactionson Computational Biologyand Bioinformatics, 8(3):785–796, May/June 2011.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Willson:2012:CHB

[Wil12] Stephen Willson. CSD ho-momorphisms between phy-logenetic networks. IEEE/ACM Transactions on Com-putational Biology and Bioin-formatics, 9(4):1128–1138,


Wiedenhoeft:2011:PMI

[WKE11] John Wiedenhoeft, RolandKrause, and Oliver Eulen-stein. The plexus modelfor the inference of an-cestral multidomain pro-teins. IEEE/ACM Trans-actions on ComputationalBiology and Bioinformat-ics, 8(4):890–901, July 2011.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Wang:2012:NEA

[WKLL12] Biing-Feng Wang, Chung-Chin Kuo, Shang-Ju Liu,and Chien-Hsin Lin. A newefficient algorithm for thegene-team problem on gen-eral sequences. IEEE/ACMTransactions on Computa-tional Biology and Bioinfor-matics, 9(2):330–344, March2012. CODEN ITCBCY.ISSN 1545-5963 (print),1557-9964 (electronic).

Wan:2007:CCN

[WL07] Xiang Wan and GuohuiLin. CISA: CombinedNMR resonance connectiv-ity information determina-tion and sequential assign-ment. IEEE/ACM Trans-actions on ComputationalBiology and Bioinformat-ics, 4(3):336–348, July 2007.CODEN ITCBCY. ISSN

REFERENCES 339


Wang:2011:IAF

[WL11] Biing-Feng Wang and Chien-Hsin Lin. Improved al-gorithms for finding geneteams and constructing geneteam trees. IEEE/ACMTransactions on Computa-tional Biology and Bioin-formatics, 8(5):1258–1272,September 2011. CODENITCBCY. ISSN 1545-5963(print), 1557-9964 (elec-tronic).

Wandelt:2013:FRC

[WL13a] Sebastian Wandelt and UlfLeser. FRESCO: Referentialcompression of highly simi-lar sequences. IEEE/ACMTransactions on Computa-tional Biology and Bioin-formatics, 10(5):1275–1288,September 2013. CODENITCBCY. ISSN 1545-5963(print), 1557-9964 (elec-tronic).

Wang:2013:MLR

[WL13b] Xiao Wang and Guo-ZhengLi. Multilabel learningvia random label selec-tion for protein subcellu-lar multilocations predic-tion. IEEE/ACM Trans-actions on ComputationalBiology and Bioinformatics,10(2):436–446, March 2013.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Wong:2014:ACP

[WL14] Andrew K. C. Wong and En-Shiun Annie Lee. Aligningand clustering patterns to re-veal the protein functional-ity of sequences. IEEE/ACMTransactions on Computa-tional Biology and Bioinfor-matics, 11(3):548–560, May2014. CODEN ITCBCY.ISSN 1545-5963 (print),1557-9964 (electronic).

Wang:2019:FAC

[WL19] Biing-Feng Wang and Chih-Yu Li. Fast algorithms forcomputing path-differencedistances. IEEE/ACMTransactions on Computa-tional Biology and Bioin-formatics, 16(2):569–582,March 2019. CODENITCBCY. ISSN 1545-5963(print), 1557-9964 (elec-tronic). URL https://dl.acm.org/doi/abs/10.1109/TCBB.2018.2790957.

Wu:2013:ROC

[WLA+13] Xia Wu, Juan Li, Napatka-mon Ayutyanont, HillaryProtas, William Jagust,Adam Fleisher, Eric Reiman,Li Yao, and Kewei Chen.The receiver operationalcharacteristic for binaryclassification with multi-ple indices and its appli-cation to the neuroimagingstudy of Alzheimer’s dis-ease. IEEE/ACM Transac-tions on Computational Bi-ology and Bioinformatics, 10

REFERENCES 340

(1):173–180, January 2013.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Wong:2011:EAE

[WLC11] Samuel S. Y. Wong, WeiminLuo, and Keith C. C. Chan.EvoMD: An algorithm forevolutionary molecular de-sign. IEEE/ACM Trans-actions on ComputationalBiology and Bioinformatics,8(4):987–1003, July 2011.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Wang:2015:HCF

[WLC+15] Chao Wang, Xi Li, PengChen, Aili Wang, XuehaiZhou, and Hong Yu. Het-erogeneous cloud frameworkfor big data genome sequenc-ing. IEEE/ACM Transac-tions on Computational Bi-ology and Bioinformatics, 12(1):166–178, January 2015.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Wang:2018:GEA

[WLC18] Lusheng Wang, Shuai ChengLi, and Yi-Ping PhoebeChen. Guest editorialfor the 15th Asia PacificBioinformatics Conference.IEEE/ACM Transactionson Computational Biologyand Bioinformatics, 15(5):1513–1514, September 2018.CODEN ITCBCY. ISSN


Wang:2011:FHC

[WLCP11] Jianxin Wang, Min Li,Jianer Chen, and Yi Pan.A fast hierarchical cluster-ing algorithm for functionalmodules discovery in pro-tein interaction networks.IEEE/ACM Transactionson Computational Biologyand Bioinformatics, 8(3):607–620, May/June 2011.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Wang:2018:AMR

[WLCX18] Annie Wang, Hansaim Lim,Shu-Yuan Cheng, and LeiXie. ANTENNA, a multi-rank, multi-layered recom-mender system for inferringreliable drug-gene-disease as-sociations: Repurposing di-azoxide as a targeted anti-cancer therapy. IEEE/ACMTransactions on Computa-tional Biology and Bioin-formatics, 15(6):1960–1967,November 2018. CODENITCBCY. ISSN 1545-5963(print), 1557-9964 (elec-tronic).

Wei:2014:IPI

[WLG+14] Leyi Wei, Minghong Liao,Yue Gao, Rongrong Ji,Zengyou He, and QuanZou. Improved and promis-ing identification of humanMicroRNAs by incorporat-

REFERENCES 341

ing a high-quality negativeset. IEEE/ACM Transac-tions on Computational Bi-ology and Bioinformatics, 11(1):192–201, January 2014.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Wang:2016:CGS

[WLG+16] Dong Wang, Jin-Xing Liu,Ying-Lian Gao, Chun-HouZheng, and Yong Xu. Char-acteristic gene selectionbased on robust graph reg-ularized non-negative matrixfactorization. IEEE/ACMTransactions on Computa-tional Biology and Bioin-formatics, 13(6):1059–1067,November 2016. CODENITCBCY. ISSN 1545-5963(print), 1557-9964 (elec-tronic).

Wang:2019:LSF

[WLHY19] Yanbo Wang, Quan Liu,Shan Huang, and Bo Yuan.Learning a structural andfunctional representation forgene expressions: To system-atically dissect complex can-cer phenotypes. IEEE/ACMTransactions on Computa-tional Biology and Bioin-formatics, 16(5):1729–1742,September 2019. CODENITCBCY. ISSN 1545-5963(print), 1557-9964 (elec-tronic).

Wang:2009:EKF

[WLL+09] Zidong Wang, Xiaohui Liu,

Yurong Liu, Jinling Liang,and Veronica Vinciotti. Anextended Kalman filteringapproach to modeling non-linear dynamic gene regu-latory networks via shortgene expression time se-ries. IEEE/ACM Trans-actions on ComputationalBiology and Bioinformat-ics, 6(3):410–419, July 2009.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Wong:2013:PPL

[WLL13] Ginny Y. Wong, Frank H. F.Leung, and Sai-Ho Ling. Pre-dicting protein-ligand bind-ing site using support vec-tor machine with proteinproperties. IEEE/ACMTransactions on Computa-tional Biology and Bioin-formatics, 10(6):1517–1529,November 2013. CODENITCBCY. ISSN 1545-5963(print), 1557-9964 (elec-tronic).

Wu:2020:MME

[WLL+20] Binbin Wu, Min Li, XingyuLiao, Junwei Luo, Fang-Xiang Wu, Yi Pan, andJianxin Wang. MEC: Mis-assembly error correction incontigs based on distribu-tion of paired-end reads andstatistics of GC-contents.IEEE/ACM Transactions onComputational Biology andBioinformatics, 17(3):847–857, May 2020. CODEN

REFERENCES 342

ITCBCY. ISSN 1545-5963(print), 1557-9964 (elec-tronic). URL https://dl.acm.org/doi/10.1109/TCBB.2018.2876855.

Wang:2011:IMP

[WLMW+11] Li-San Wang, Jim Leebens-Mack, P. Kerr Wall, KevinBeckmann, Claude W. de-Pamphilis, and Tandy Warnow.The impact of multipleprotein sequence alignmenton phylogenetic estimation.IEEE/ACM Transactions onComputational Biology andBioinformatics, 8(4):1108–1119, July 2011. CODENITCBCY. ISSN 1545-5963(print), 1557-9964 (elec-tronic).

Wong:2016:CSD

[WLPW16] Ka-Chun Wong, Yue Li,Chengbin Peng, and Hau-San Wong. A comparisonstudy for DNA motif mod-eling on protein binding mi-croarray. IEEE/ACM Trans-actions on ComputationalBiology and Bioinformatics,13(2):261–271, March 2016.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Wang:2017:GES

[WLWN17] Fei Wang, Xiao-Li Li, Ja-son T. L. Wang, and See-Kiong Ng. Guest edito-rial: Special section on bi-ological data mining andits applications in health-

care. IEEE/ACM Trans-actions on ComputationalBiology and Bioinformatics,14(3):501–502, May 2017.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Wang:2012:IEP

[WLWP12] Jianxin Wang, Min Li, HuanWang, and Yi Pan. Identi-fication of essential proteinsbased on edge clustering co-efficient. IEEE/ACM Trans-actions on ComputationalBiology and Bioinformatics,9(4):1070–1080, July 2012.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Wang:2014:CGT

[WLY14] Biing-Feng Wang, Chien-Hsin Lin, and I-Tse Yang.Constructing a gene teamtree in almost O(n lg n)time. IEEE/ACM Transac-tions on Computational Bi-ology and Bioinformatics, 11(1):142–153, January 2014.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Wang:2015:CNI

[WLY15] Pei Wang, Jinhu Lu, andXinghuo Yu. Colored noiseinduced bistable switch inthe genetic toggle switch sys-tems. IEEE/ACM Trans-actions on ComputationalBiology and Bioinformatics,12(3):579–589, May 2015.

REFERENCES 343


Wang:2009:EPS

[WLYZ+09] Yong Wang, Wu Ling-Yun, Ji-Hong Zhang, Zhong-Wei Zhan, Zhang Xiang-Sun, and Chen Luonan.Evaluating protein simi-larity from coarse struc-tures. IEEE/ACM Transac-tions on Computational Bi-ology and Bioinformatics, 6(4):583–593, October 2009.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Wang:2019:MNL

[WLZ+19] Juan Wang, Jin-Xing Liu,Chun-Hou Zheng, Ya-XuanWang, Xiang-Zhen Kong,and Chang-Gang Wen. Amixed-norm Laplacian regu-larized low-rank representa-tion method for tumor sam-ples clustering. IEEE/ACMTransactions on Computa-tional Biology and Bioin-formatics, 16(1):172–182,January 2019. CODENITCBCY. ISSN 1545-5963(print), 1557-9964 (elec-tronic).

Wang:2019:AIR

[WM19a] Tiancong Wang and BinMa. Adjacent Y-ion ratiodistributions and its appli-cation in peptide sequenc-ing. IEEE/ACM Transac-tions on Computational Bi-

ology and Bioinformatics,16(1):43–51, January 2019.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Whidden:2019:CUS

[WM19b] Chris Whidden and Fred-erick A. Matsen. Calcu-lating the unrooted sub-tree prune-and-regraft dis-tance. IEEE/ACM Trans-actions on ComputationalBiology and Bioinformatics,16(3):898–911, May 2019.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Wan:2016:MMP

[WMK16] Shibiao Wan, Man-Wai Mak,and Sun-Yuan Kung. Mem-mEN: Predicting multi-functional types of mem-brane proteins by inter-pretable elastic nets. IEEE/ACM Transactions on Com-putational Biology and Bioin-formatics, 13(4):706–718,2016. CODEN ITCBCY.ISSN 1545-5963 (print),1557-9964 (electronic).

Wan:2017:TLM

[WMK17] Shibiao Wan, Man-Wai Mak,and Sun-Yuan Kung. Trans-ductive learning for multi-label protein subchloro-plast localization predic-tion. IEEE/ACM Transac-tions on Computational Bi-ology and Bioinformatics, 14(1):212–224, January 2017.

REFERENCES 344


Wu:2009:RPT

[WMS09] Taoyang Wu, Vincent Moul-ton, and Mike Steel. Refin-ing phylogenetic trees givenadditional data: An al-gorithm based on parsi-mony. IEEE/ACM Transac-tions on Computational Bi-ology and Bioinformatics, 6(1):118–125, January 2009.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Wang:2012:EGS

[WMWA12] Daifeng Wang, Mia K.Markey, Claus O. Wilke, andAri Arapostathis. Eigen-genomic system dynamic-pattern analysis (ESDA):Modeling mRNA degra-dation and self-regulation.IEEE/ACM Transactions onComputational Biology andBioinformatics, 9(2):430–437, March 2012. CODENITCBCY. ISSN 1545-5963(print), 1557-9964 (elec-tronic).

Walker:2017:ATS

[WNT+17] Peter B. Walker, Jacob N.Norris, Anna E. Tschif-fely, Melissa L. Mehalick,Craig A. Cunningham, andIan N. Davidson. Applica-tions of transductive spec-tral clustering methods ina military medical concus-

sion database. IEEE/ACMTransactions on Computa-tional Biology and Bioinfor-matics, 14(3):534–544, May2017. CODEN ITCBCY.ISSN 1545-5963 (print),1557-9964 (electronic).

Wu:2017:PCD

[WOYL17] Min Wu, Le Ou-Yang, andXiao-Li Li. Protein com-plex detection via effectiveintegration of base cluster-ing solutions and co-complexaffinity scores. IEEE/ACMTransactions on Computa-tional Biology and Bioinfor-matics, 14(3):733–739, May2017. CODEN ITCBCY.ISSN 1545-5963 (print),1557-9964 (electronic).

Wei:2008:IGF

[WP08] Peng Wei and Wei Pan.Incorporating gene func-tions into regression anal-ysis of DNA-protein bind-ing data and gene expressiondata to construct transcrip-tional networks. IEEE/ACMTransactions on Computa-tional Biology and Bioinfor-matics, 5(3):401–415, July2008. CODEN ITCBCY.ISSN 1545-5963 (print),1557-9964 (electronic).

Wong:2015:PIM

[WPL15] Ka-Chun Wong, Cheng-bin Peng, and Yue Li.Probabilistic inference onmultiple normalized signalprofiles from next genera-

REFERENCES 345

tion sequencing: Transcrip-tion factor binding sites.IEEE/ACM Transactionson Computational Biologyand Bioinformatics, 12(6):1416–1428, November 2015.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Wei:2016:MDD

[WQL+16] Guanyun Wei, Sheng Qin,Wenjuan Li, Liming Chen,and Fei Ma. MDTE DB: adatabase for MicroRNAs de-rived from transposable el-ement. IEEE/ACM Trans-actions on ComputationalBiology and Bioinformatics,13(6):1155–1160, November2016. CODEN ITCBCY.ISSN 1545-5963 (print),1557-9964 (electronic).

Wang:2018:GMS

[WQY18] Yanbo Wang, Weikang Qian,and Bo Yuan. A graphicalmodel of smoking-inducedglobal instability in lung can-cer. IEEE/ACM Transac-tions on Computational Bi-ology and Bioinformatics,15(1):1–14, January 2018.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Weber:2009:VET

[WRH+09] Gunther H. Weber, OliverRubel, Min-Yu Huang, An-gela H. DePace, Charless C.Fowlkes, Soile V. E. Kera-nen, Cris L. Luengo Hen-

driks, Hans Hagen, David W.Knowles, Jitendra Malik,Mark D. Biggin, and BerndHamann. Visual explo-ration of three-dimensionalgene expression using physi-cal views and linked abstractviews. IEEE/ACM Trans-actions on ComputationalBiology and Bioinformatics,6(2):296–309, April 2009.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Wang:2008:DCO

[WS08] Xueyi Wang and JackSnoeyink. Defining andcomputing optimum RMSDfor gapped and weightedmultiple-structure alignment.IEEE/ACM Transactions onComputational Biology andBioinformatics, 5(4):525–533, October 2008. CODENITCBCY. ISSN 1545-5963(print), 1557-9964 (elec-tronic).

Wan:2012:CAD

[WS12] Lin Wan and Fengzhu Sun.CEDER: Accurate detec-tion of differentially ex-pressed genes by combin-ing significance of exons us-ing RNA-Seq. IEEE/ACMTransactions on Computa-tional Biology and Bioin-formatics, 9(5):1281–1292,September 2012. CODENITCBCY. ISSN 1545-5963(print), 1557-9964 (elec-tronic).

REFERENCES 346

Wong:2015:DBC

[WSTL+15] Man-Hon Wong, Ho-Yin Sze-To, Leung-Yau Lo, Tak-MingChan, and Kwong-Sak Le-ung. Discovering bindingcores in Protein–DNA bind-ing using association rulemining with statistical mea-sures. IEEE/ACM Transac-tions on Computational Bi-ology and Bioinformatics, 12(1):142–154, January 2015.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Wang:2011:ICA

[WSX11] Qingguo Wang, Yi Shang,and Dong Xu. Improvinga consensus approach forprotein structure selectionby removing redundancy.IEEE/ACM Transactionson Computational Biologyand Bioinformatics, 8(6):1708–1715, November 2011.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

weiTan:2020:DLP

[wTCAK+20] Jing wei Tan, Siow-WeeChang, Sameem Abdul-Kareem, Hwa Jen Yap, andKien-Thai Yong. Deep learn-ing for plant species clas-sification using leaf veinmorphometric. IEEE/ACMTransactions on Computa-tional Biology and Bioinfor-matics, 17(1):82–90, January2020. CODEN ITCBCY.ISSN 1545-5963 (print),

1557-9964 (electronic). URLhttps://dl.acm.org/doi/abs/10.1109/TCBB.2018.2848653.

Wu:2010:ECC

[Wu10] Yufeng Wu. Exact com-putation of coalescent like-lihood for panmictic andsubdivided populations un-der the infinite sites model.IEEE/ACM Transactions onComputational Biology andBioinformatics, 7(4):611–618, October 2010. CODENITCBCY. ISSN 1545-5963(print), 1557-9964 (elec-tronic).

Wu:2011:NMI

[Wu11] Yufeng Wu. New methodsfor inference of local treetopologies with recombinantSNP sequences in popula-tions. IEEE/ACM Transac-tions on Computational Bi-ology and Bioinformatics, 8(1):182–193, January 2011.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Wu:2019:CDM

[WW19] Peng Wu and Dong Wang.Classification of a DNA mi-croarray for diagnosing can-cer using a complex networkbased method. IEEE/ACMTransactions on Computa-tional Biology and Bioinfor-matics, 16(3):801–808, May2019. CODEN ITCBCY.ISSN 1545-5963 (print),1557-9964 (electronic).

REFERENCES 347

Wassan:2019:CSP

[WWBZ19] Jyotsna Talreja Wassan,Haiying Wang, Fiona Browne,and Huiru Zheng. A com-prehensive study on pre-dicting functional role ofmetagenomes using ma-chine learning methods.IEEE/ACM Transactions onComputational Biology andBioinformatics, 16(3):751–763, May 2019. CODENITCBCY. ISSN 1545-5963(print), 1557-9964 (elec-tronic).

Wu:2018:NCG

[WWC18] Ho-Chun Wu, Xi-GuangWei, and Shing-Chow Chan.Novel consensus gene selec-tion criteria for distributedGPU partial least squares-based gene microarray anal-ysis in diffused Large B CellLymphoma DLBCL and re-lated findings. IEEE/ACMTransactions on Computa-tional Biology and Bioin-formatics, 15(6):2039–2052,November 2018. CODENITCBCY. ISSN 1545-5963(print), 1557-9964 (elec-tronic).

Wu:2017:DCR

[WWL+17] Hongjie Wu, Kun Wang,Liyao Lu, Yu Xue, QiangLyu, and Min Jiang. Deepconditional random field ap-proach to transmembranetopology prediction and ap-plication to GPCR three-dimensional structure mod-

eling. IEEE/ACM Trans-actions on ComputationalBiology and Bioinformatics,14(5):1106–1114, September2017. CODEN ITCBCY.ISSN 1545-5963 (print),1557-9964 (electronic).

Wang:2019:CAG

[WWL19] Pei Wang, Daojie Wang, andJinhu Lu. Controllabilityanalysis of a gene network forArabidopsis thaliana revealscharacteristics of functionalgene families. IEEE/ACMTransactions on Computa-tional Biology and Bioinfor-matics, 16(3):912–924, May2019. CODEN ITCBCY.ISSN 1545-5963 (print),1557-9964 (electronic).

Wang:2016:KBP

[WWLL16] Hong Wang, Xicheng Wang,Zheng Li, and Keqiu Li.Kriging-based parameterestimation algorithm formetabolic networks com-bined with single-dimensionaloptimization and dynamiccoordinate perturbation.IEEE/ACM Transactionson Computational Biologyand Bioinformatics, 13(6):1142–1154, November 2016.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Wu:2020:PNC

[WWT+20] Sijia Wu, Xiaoming Wu, JieTian, Xiaobo Zhou, and LiyuHuang. PredictFP2: a new

REFERENCES 348

computational model to pre-dict fusion peptide domain inall retroviruses. IEEE/ACMTransactions on Computa-tional Biology and Bioin-formatics, 17(5):1714–1720,September 2020. CODENITCBCY. ISSN 1545-5963(print), 1557-9964 (elec-tronic). URL https://dl.acm.org/doi/10.1109/TCBB.2019.2898943.

Wei:2019:FPP

[WXS+19] Leyi Wei, Pengwei Xing,Gaotao Shi, Zhiliang Ji,and Quan Zou. Fast pre-diction of protein methyla-tion sites using a sequence-based feature selection tech-nique. IEEE/ACM Transac-tions on Computational Bi-ology and Bioinformatics, 16(4):1264–1273, July 2019.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Wang:2020:DLS

[WXWL20] Hang Wang, Jianing Xi,Minghui Wang, and Ao Li.Dual-layer strengthened col-laborative topic regressionmodeling for predicting drugsensitivity. IEEE/ACMTransactions on Computa-tional Biology and Bioin-formatics, 17(2):587–598,March 2020. CODENITCBCY. ISSN 1545-5963(print), 1557-9964 (elec-tronic). URL https://dl.acm.org/doi/abs/10.1109/TCBB.2018.2864739.

Weyenberg:2017:NKB

[WYH17] Grady Weyenberg, RurikoYoshida, and Daniel Howe.Normalizing kernels in theBillera–Holmes–Vogtmanntreespace. IEEE/ACMTransactions on Computa-tional Biology and Bioin-formatics, 14(6):1359–1365,November 2017. CODENITCBCY. ISSN 1545-5963(print), 1557-9964 (elec-tronic).

Wang:2017:PSP

[WYHD17] Hua Wang, Lin Yan, HengHuang, and Chris Ding.From protein sequence toprotein function via multi-label linear discriminantanalysis. IEEE/ACM Trans-actions on ComputationalBiology and Bioinformatics,14(3):503–513, May 2017.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Wang:2020:CHS

[WYHZ20] Lei Wang, Zhu-Hong You,De-Shuang Huang, andFengfeng Zhou. Combin-ing high speed ELM learn-ing with a deep convolu-tional neural network fea-ture encoding for predict-ing Protein-RNA interac-tions. IEEE/ACM Trans-actions on ComputationalBiology and Bioinformatics,17(3):972–980, May 2020.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964

REFERENCES 349

(electronic). URL https://dl.acm.org/doi/10.1109/TCBB.2018.2874267.

Wu:2007:QBP

[WYL07] Gang Wu, Jia-Huai You, andGuohui Lin. Quartet-basedphylogeny reconstructionwith answer set program-ming. IEEE/ACM Transac-tions on Computational Bi-ology and Bioinformatics, 4(1):139–152, January 2007.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Wang:2016:GES

[WYWX16] Chao Wang, Hong Yu, AiliWang, and Kai Xia. Guesteditorial for special sectionon big data computing andprocessing in computationalbiology and bioinformatics.IEEE/ACM Transactionson Computational Biologyand Bioinformatics, 13(5):810–811, September 2016.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Wan:2013:HFA

[WYY+13] Xiang Wan, Can Yang,Qiang Yang, Hongyu Zhao,and Weichuan Yu. Hap-Boost: a fast approach toboosting haplotype associ-ation analyses in genome-wide association studies.IEEE/ACM Transactions onComputational Biology andBioinformatics, 10(1):207–212, January 2013. CODEN


Wu:2013:SBP

[WZ13a] Jian-Sheng Wu and Zhi-Hua Zhou. Sequence-basedprediction of microRNA-binding residues in proteinsusing cost-sensitive Lapla-cian support vector ma-chines. IEEE/ACM Trans-actions on ComputationalBiology and Bioinformatics,10(3):752–759, May 2013.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Wylie:2013:PCP

[WZ13b] Tim Wylie and BinhaiZhu. Protein chain pairsimplification under thediscrete Frechet distance.IEEE/ACM Transactionson Computational Biologyand Bioinformatics, 10(6):1372–1383, November 2013.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Wang:2014:OMI

[WZ14] Haiying Wang and HuiruZheng. Organized modu-larity in the interactome:evidence from the analysisof dynamic organization inthe cell cycle. IEEE/ACMTransactions on Computa-tional Biology and Bioin-formatics, 11(6):1264–1270,November 2014. CODEN

REFERENCES 350


Wang:2007:PBS

[WZA07] Haiying Wang, Huiru Zheng,and Francisco Azuaje. Poisson-based self-organizing fea-ture maps and hierarchicalclustering for serial analy-sis of gene expression data.IEEE/ACM Transactions onComputational Biology andBioinformatics, 4(2):163–175, April 2007. CODENITCBCY. ISSN 1545-5963(print), 1557-9964 (elec-tronic).

Wang:2015:CCA

[WZC+15] Jianxin Wang, JianchengZhong, Gang Chen, MinLi, Fang xiang Wu, andYi Pan. ClusterViz: acytoscape APP for clusteranalysis of biological net-work. IEEE/ACM Trans-actions on ComputationalBiology and Bioinformatics,12(4):815–822, July 2015.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Wang:2012:RCM

[WZJH12] Shu-Lin Wang, Yi-Hai Zhu,Wei Jia, and De-ShuangHuang. Robust classifica-tion method of tumor sub-type by using correlation fil-ters. IEEE/ACM Transac-tions on Computational Bi-ology and Bioinformatics, 9


Wang:2018:CDB

[WZZ+18] Bin Wang, Xuedong Zheng,Shihua Zhou, ChangjunZhou, Xiaopeng Wei, QiangZhang, and Ziqi Wei. Con-structing DNA barcode setsbased on particle swarmoptimization. IEEE/ACMTransactions on Computa-tional Biology and Bioinfor-matics, 15(3):999–1002, May2018. CODEN ITCBCY.ISSN 1545-5963 (print),1557-9964 (electronic).

Xu:2007:MCC

[XAW07] Rui Xu, Georgios C. Anag-nostopoulos, and Donald C.Wunsch. Multiclass cancerclassification using semisu-pervised ellipsoid ARTMAPand particle swarm optimiza-tion with gene expressiondata. IEEE/ACM Trans-actions on ComputationalBiology and Bioinformatics,4(1):65–77, January 2007.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Xu:2014:FIN

[XG14] Bin Xu and Jihong Guan.From function to interac-tion: a new paradigm foraccurately predicting proteincomplexes based on protein-to-protein interaction net-

REFERENCES 351

works. IEEE/ACM Trans-actions on ComputationalBiology and Bioinformatics,11(4):616–627, July 2014.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Xu:2019:EPD

[XGWW19] Bin Xu, Jihong Guan, YangWang, and Zewei Wang. Es-sential protein detection byrandom walk on weightedprotein–protein interactionnetworks. IEEE/ACMTransactions on Computa-tional Biology and Bioin-formatics, 16(2):377–387,March 2019. CODENITCBCY. ISSN 1545-5963(print), 1557-9964 (elec-tronic). URL https://dl.acm.org/doi/abs/10.1109/TCBB.2017.2701824.

Xia:2018:STS

[XHQ+18] Chun-Qiu Xia, Ke Han,Yong Qi, Yang Zhang, andDong-Jun Yu. A self-trainingsubspace clustering algo-rithm under low-rank rep-resentation for cancer clas-sification on gene expressiondata. IEEE/ACM Transac-tions on Computational Bi-ology and Bioinformatics, 15(4):1315–1324, July 2018.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Xu:2015:GEI

[XHS15] Dong Xu, Kun Huang, and

Jeanette Schmidt. Guesteditors introduction to thespecial section on softwareand databases. IEEE/ACMTransactions on Computa-tional Biology and Bioinfor-matics, 12(4):793–794, July2015. CODEN ITCBCY.ISSN 1545-5963 (print),1557-9964 (electronic).

Xie:2018:AGS

[XHY+18] Qian Xie, Xiaoyan He,Fangji Yang, Xuling Liu,Ying Li, Yujing Liu, Zheng-Meng Yang, Jianhai Yu, BaoZhang, and Wei Zhao. Anal-ysis of the genome sequenceand prediction of B-cell epi-topes of the envelope pro-tein of Middle East respira-tory syndrome-coronavirus.IEEE/ACM Transactions onComputational Biology andBioinformatics, 15(4):1344–1350, July 2018. CODENITCBCY. ISSN 1545-5963(print), 1557-9964 (elec-tronic).

Xi:2016:DRC

[XL16] Jianing Xi and Ao Li. Dis-covering recurrent copy num-ber aberrations in complexpatterns via non-negativesparse singular value de-composition. IEEE/ACMTransactions on Computa-tional Biology and Bioinfor-matics, 13(4):656–668, 2016.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

REFERENCES 352

Xiang:2015:RAA

[XLC+15] Yan-Ping Xiang, Ke Liu,Xian-Ying Cheng, ChengCheng, Fang Gong, Jian-BoPan, and Zhi-Liang Ji. Rapidassessment of adverse drugreactions by statistical solu-tion of gene association net-work. IEEE/ACM Trans-actions on ComputationalBiology and Bioinformatics,12(4):844–850, July 2015.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Xu:2018:IBI

[XLL+18] Bo Xu, Hongfei Lin, YuanLin, Yunlong Ma, LiangYang, Jian Wang, and Zhi-hao Yang. Improve biomed-ical information retrieval us-ing modified learning torank methods. IEEE/ACMTransactions on Computa-tional Biology and Bioin-formatics, 15(6):1797–1809,November 2018. CODENITCBCY. ISSN 1545-5963(print), 1557-9964 (elec-tronic).

Xu:2019:LRE

[XLL19] Bo Xu, Hongfei Lin, andYuan Lin. Learning torefine expansion terms forbiomedical information re-trieval using semantic re-sources. IEEE/ACM Trans-actions on ComputationalBiology and Bioinformatics,16(3):954–966, May 2019.CODEN ITCBCY. ISSN


Xiao:2020:ILM

[XLL+20] Qiu Xiao, Jiawei Luo, ChengLiang, Guanghui Li, Jie Cai,Pingjian Ding, and YingLiu. Identifying lncRNA andmRNA co-expression mod-ules from matched expres-sion data in ovarian can-cer. IEEE/ACM Transac-tions on Computational Bi-ology and Bioinformatics,17(2):623–634, March 2020.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic). URL https://dl.acm.org/doi/abs/10.1109/TCBB.2018.2864129.

Xi:2020:HNM

[XLW20] Jianing Xi, Ao Li, andMinghui Wang. HetRCNA:a novel method to identifyrecurrent copy number alter-nations from heterogeneoustumor samples based on ma-trix decomposition frame-work. IEEE/ACM Trans-actions on ComputationalBiology and Bioinformatics,17(2):422–434, March 2020.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic). URL https://dl.acm.org/doi/abs/10.1109/TCBB.2018.2846599.

Xia:2015:IGA

[XLWL15] Hong Xia, Yuanning Liu,Minghui Wang, and Ao Li.Identification of genomic

REFERENCES 353

aberrations in cancer sub-clones from heterogeneoustumor samples. IEEE/ACMTransactions on Computa-tional Biology and Bioinfor-matics, 12(3):679–685, May2015. CODEN ITCBCY.ISSN 1545-5963 (print),1557-9964 (electronic).

Xin:2015:ASI

[XLZ+15] Yao Xin, Will X. Y. Li,Zhaorui Zhang, Ray C. C.Cheung, Dong Song, andTheodore W. Berger. Anapplication specific instruc-tion set processor (ASIP)for adaptive filters in neu-ral prosthetics. IEEE/ACMTransactions on Computa-tional Biology and Bioin-formatics, 12(5):1034–1047,September 2015. CODENITCBCY. ISSN 1545-5963(print), 1557-9964 (elec-tronic).

Xu:2018:IGN

[XOYHZ18] Ting Xu, Le Ou-Yang, Xi-aohua Hu, and Xiao-FeiZhang. Identifying gene net-work rewiring by integrat-ing gene expression and genenetwork data. IEEE/ACMTransactions on Computa-tional Biology and Bioin-formatics, 15(6):2079–2085,November 2018. CODENITCBCY. ISSN 1545-5963(print), 1557-9964 (elec-tronic).

Xiang:2012:TDT

[XPH12] Yang Xiang, Philip R. O.Payne, and Kun Huang.Transactional database trans-formation and its applicationin prioritizing human diseasegenes. IEEE/ACM Transac-tions on Computational Bi-ology and Bioinformatics, 9(1):294–304, January 2012.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Xu:2020:CCP

[XPH20] Hongming Xu, Sunho Park,and Tae Hyun Hwang.Computerized classificationof prostate cancer Glea-son scores from wholeslide images. IEEE/ACMTransactions on Computa-tional Biology and Bioin-formatics, 17(6):1871–1882,November 2020. CODENITCBCY. ISSN 1545-5963(print), 1557-9964 (elec-tronic). URL https://dl.acm.org/doi/10.1109/TCBB.2019.2941195.

Xu:2011:MLP

[XPXY11] Qian Xu, Sinno Jialin Pan,Hannah Hong Xue, andQiang Yang. Multitasklearning for protein sub-cellular location prediction.IEEE/ACM Transactionson Computational Biologyand Bioinformatics, 8(3):748–759, May/June 2011.CODEN ITCBCY. ISSN

REFERENCES 354


Xie:2017:DFO

[XSS17] Lu Xie, Gregory R. Smith,and Russell Schwartz. Derivative-free optimization of rate pa-rameters of capsid assemblymodels from bulk in vitrodata. IEEE/ACM Trans-actions on ComputationalBiology and Bioinformatics,14(4):844–855, July 2017.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Xu:2012:AI

[XTL12a] Yun Xu, Da Teng, and Yim-ing Lei. 2011 annual in-dex. IEEE/ACM Trans-actions on ComputationalBiology and Bioinformat-ics, 9(1):??, January 2012.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Xu:2012:RL

[XTL12b] Yun Xu, Da Teng, and Yim-ing Lei. 2011 reviewerslist. IEEE/ACM Transac-tions on Computational Bi-ology and Bioinformatics, 9(1):316–318, January 2012.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Xu:2012:MLM

[XTL12c] Yun Xu, Da Teng, andYiming Lei. MinePhos:

a literature mining sys-tem for protein phoshphory-lation information extrac-tion. IEEE/ACM Transac-tions on Computational Bi-ology and Bioinformatics, 9(1):311–315, January 2012.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Xu:2005:FRP

[Xu05] Jinbo Xu. Fold recognitionby predicted alignment ac-curacy. IEEE/ACM Trans-actions on ComputationalBiology and Bioinformatics,2(2):157–165, April 2005.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Xu:2013:ENE

[Xu13] Ying Xu. Editorial fromthe new Editor-in–Chief.IEEE/ACM Transactionson Computational Biologyand Bioinformatics, 10(1):1, January 2013. CODENITCBCY. ISSN 1545-5963(print), 1557-9964 (elec-tronic).

Xu:2014:EEC

[Xu14a] Ying Xu. Editorial from theEditor-in-Chief. IEEE/ACMTransactions on Computa-tional Biology and Bioin-formatics, 11(1):1, January2014. CODEN ITCBCY.ISSN 1545-5963 (print),1557-9964 (electronic).

REFERENCES 355

Xu:2014:RAE

[Xu14b] Ying Xu. Reviewer appreci-ation editorial. IEEE/ACMTransactions on Computa-tional Biology and Bioinfor-matics, 11(4):613, July 2014.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Xu:2015:EEC

[Xu15] Ying Xu. Editorial from theEditor-in-Chief. IEEE/ACMTransactions on Computa-tional Biology and Bioin-formatics, 12(1):1, January2015. CODEN ITCBCY.ISSN 1545-5963 (print),1557-9964 (electronic).

Xu:2016:IDA

[XW16] Xiaoyi Xu and MinghuiWang. Inferring disease asso-ciated phosphorylation sitesvia random walk on multi-layer heterogeneous network.IEEE/ACM Transactionson Computational Biologyand Bioinformatics, 13(5):836–844, September 2016.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Xie:2015:LFA

[XWC15] Minzhu Xie, Jianxin Wang,and Xin Chen. LGH: afast and accurate algorithmfor single individual haplo-typing based on a two-locuslinkage graph. IEEE/ACMTransactions on Computa-


Xu:2007:IGR

[XWF07] Rui Xu, Donald Wunsch II,and Ronald Frank. In-ference of genetic regula-tory networks with recurrentneural network models us-ing particle swarm optimiza-tion. IEEE/ACM Transac-tions on Computational Bi-ology and Bioinformatics, 4(4):681–692, October 2007.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Xie:2016:AHA

[XXM+16] Jiang Xie, Chaojuan Xi-ang, Jin Ma, Jun Tan,Tieqiao Wen, Jinzhi Lei,and Qing Nie. An adap-tive hybrid algorithm forglobal network alignment.IEEE/ACM Transactions onComputational Biology andBioinformatics, 13(3):483–493, May 2016. CODENITCBCY. ISSN 1545-5963(print), 1557-9964 (elec-tronic).

Xiao:2020:CDW

[XYYZ20] Ming Xiao, Xiangyu Yang,Jun Yu, and Le Zhang.CGIDLA: Developing theWeb server for CpG Is-land related density and

REFERENCES 356

LAUPs (lineage-associatedunderrepresented permuta-tions) study. IEEE/ACMTransactions on Computa-tional Biology and Bioin-formatics, 17(6):2148–2154,November 2020. CODENITCBCY. ISSN 1545-5963(print), 1557-9964 (elec-tronic). URL https://dl.acm.org/doi/10.1109/TCBB.2019.2935971.

Xie:2019:EEM

[XYZ19] Wen-Bin Xie, Hong Yan, andXing-Ming Zhao. EmDL:Extracting miRNA–drug in-teractions from literature.IEEE/ACM Transactionson Computational Biologyand Bioinformatics, 16(5):1722–1728, September 2019.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Xiong:2007:DDK

[XZC07] Huilin Xiong, Ya Zhang,and Xue-Wen Chen. Data-dependent kernel machinesfor microarray data classifi-cation. IEEE/ACM Trans-actions on ComputationalBiology and Bioinformatics,4(4):583–595, October 2007.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Xie:2015:CTC

[XZG15] Xiaojing Xie, ShuigengZhou, and Jihong Guan.CoGI: Towards compress-ing genomes as an image.


Xu:2018:ESB

[XZG+18] Biao Xu, Yong Zhang, Dun-wei Gong, Yinan Guo, andMiao Rong. Environmentsensitivity-based cooperativeco-evolutionary algorithmsfor dynamic multi-objectiveoptimization. IEEE/ACMTransactions on Computa-tional Biology and Bioin-formatics, 15(6):1877–1890,November 2018. CODENITCBCY. ISSN 1545-5963(print), 1557-9964 (elec-tronic).

Xu:2014:BSB

[XZY+14] Yanxun Xu, Xiaofeng Zheng,Yuan Yuan, Marcos R. Es-tecio, Jean-Pierre Issa, PengQiu, Yuan Ji, and ShoudanLiang. BM-SNP: a Bayesianmodel for SNP calling us-ing high throughput se-quencing data. IEEE/ACMTransactions on Computa-tional Biology and Bioin-formatics, 11(6):1038–1044,November 2014. CODENITCBCY. ISSN 1545-5963(print), 1557-9964 (elec-tronic).

Yang:2013:PEL

[YAB13] Ye Yang, Farnoosh A.

REFERENCES 357

Aghababazadeh, and David R.Bickel. Parametric esti-mation of the local falsediscovery rate for identi-fying genetic associations.IEEE/ACM Transactions onComputational Biology andBioinformatics, 10(1):98–108, January 2013. CODENITCBCY. ISSN 1545-5963(print), 1557-9964 (elec-tronic).

Yu:2008:CAA

[YB08] Zeyun Yu and Chandra-jit Bajaj. Computa-tional approaches for au-tomatic structural analysisof large biomolecular com-plexes. IEEE/ACM Transac-tions on Computational Bi-ology and Bioinformatics, 5(4):568–582, October 2008.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

You:2010:UGP

[YBGB10] Liwen You, Vladimir Bru-sic, Marcus Gallagher, andMikael Boden. Using Gaus-sian process with test re-jection to detect T-cell epi-topes in pathogen genomes.IEEE/ACM Transactions onComputational Biology andBioinformatics, 7(4):741–751, October 2010. CODENITCBCY. ISSN 1545-5963(print), 1557-9964 (elec-tronic).

Yin:2008:NAC

[YC08] Zong-Xian Yin and Jung-Hsien Chiang. Novelalgorithm for coexpres-sion detection in time-varying microarray datasets. IEEE/ACM Transac-tions on Computational Bi-ology and Bioinformatics, 5(1):120–135, January 2008.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Yuan:2012:SRN

[YCCM12] Yinyin Yuan, Christina Cur-tis, Carlos Caldas, and Flo-rian Markowetz. A sparseregulatory network of copy-number driven gene ex-pression reveals putativebreast cancer oncogenes.IEEE/ACM Transactions onComputational Biology andBioinformatics, 9(4):947–954, July 2012. CODENITCBCY. ISSN 1545-5963(print), 1557-9964 (elec-tronic).

Yazdani:2020:BFP

[YCCY20] Hossein Yazdani, Leo L.Cheng, David C. Chris-tiani, and Azam Yazdani.Bounded fuzzy possibilisticmethod reveals informationabout lung cancer throughanalysis of metabolomics.IEEE/ACM Transactions onComputational Biology andBioinformatics, 17(2):526–535, March 2020. CODENITCBCY. ISSN 1545-5963

REFERENCES 358

(print), 1557-9964 (elec-tronic). URL https://dl.acm.org/doi/abs/10.1109/TCBB.2018.2869757.

Yu:2013:HFC

[YCY+13] Zhiwen Yu, Hantao Chen,Jane You, Guoqiang Han,and Le Li. Hybrid fuzzycluster ensemble frame-work for tumor cluster-ing from biomolecular data.IEEE/ACM Transactions onComputational Biology andBioinformatics, 10(3):657–670, May 2013. CODENITCBCY. ISSN 1545-5963(print), 1557-9964 (elec-tronic).

Yu:2014:DSB

[YCY+14] Zhiwen Yu, HongshengChen, Jane You, Hau-SanWong, Jiming Liu, Le Li,and Guoqiang Han. Dou-ble selection based semi-supervised clustering ensem-ble for tumor clusteringfrom gene expression pro-files. IEEE/ACM Trans-actions on ComputationalBiology and Bioinformatics,11(4):727–740, July 2014.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Yu:2015:AFC

[YCY+15] Zhiwen Yu, Hantao Chen,Jane You, Jiming Liu, Hau-San Wong, Guoqiang Han,and Le Li. Adaptive fuzzyconsensus clustering frame-

work for clustering analysisof cancer data. IEEE/ACMTransactions on Computa-tional Biology and Bioinfor-matics, 12(4):887–901, July2015. CODEN ITCBCY.ISSN 1545-5963 (print),1557-9964 (electronic).

Yang:2012:MPD

[YCYC12] Cheng-Hong Yang, Yu-HueiCheng, Cheng-Huei Yang,and Li-Yeh Chuang. Mu-tagenic primer design formismatch PCR-RFLP SNPgenotyping using a geneticalgorithm. IEEE/ACMTransactions on Computa-tional Biology and Bioinfor-matics, 9(3):837–845, May2012. CODEN ITCBCY.ISSN 1545-5963 (print),1557-9964 (electronic).

Yuan:2018:GIH

[YCZ+18] Lin Yuan, Fanglin Chen,Ling-Li Zeng, Lubin Wang,and Dewen Hu. Gender iden-tification of human brain im-age with a novel 3D descrip-tor. IEEE/ACM Transac-tions on Computational Bi-ology and Bioinformatics,15(2):551–561, March 2018.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Yao:2008:EAE

[YDM+08] Peggy Yao, Ankur Dhanik,Nathan Marz, Ryan Prop-per, Charles Kou, GuanfengLiu, Henry van den Bedem,

REFERENCES 359

Jean-Claude Latombe, In-bal Halperin-Landsberg, andRuss B. Altman. Efficientalgorithms to explore con-formation spaces of flexibleprotein loops. IEEE/ACMTransactions on Computa-tional Biology and Bioinfor-matics, 5(4):534–545, Octo-ber 2008. CODEN ITCBCY.ISSN 1545-5963 (print),1557-9964 (electronic).

Yan:2020:BPM

[YDW+20] Cheng Yan, Guihua Duan,Fang-Xiang Wu, Yi Pan,and Jianxin Wang. BR-WMDA:Predicting microbe-disease associations based onsimilarities and bi-randomwalk on disease and mi-crobe networks. IEEE/ACMTransactions on Computa-tional Biology and Bioin-formatics, 17(5):1595–1604,September 2020. CODENITCBCY. ISSN 1545-5963(print), 1557-9964 (elec-tronic). URL https://dl.acm.org/doi/10.1109/TCBB.2019.2907626.

Yoo:2017:IIK

[YFCM17] Boyoung Yoo, Fazle ElahiFaisal, Huili Chen, and Ti-jana Milenkovic. Improv-ing identification of key play-ers in aging via network de-noising and core inference.IEEE/ACM Transactionson Computational Biologyand Bioinformatics, 14(5):1056–1069, September 2017.CODEN ITCBCY. ISSN


Yu:2016:PPF

[YFWZ16] Guoxian Yu, GuangyuanFu, Jun Wang, and Hai-long Zhu. Predicting pro-tein function via semanticintegration of multiple net-works. IEEE/ACM Trans-actions on ComputationalBiology and Bioinformatics,13(2):220–232, March 2016.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Yu:2018:NPN

[YFWZ18] Guoxian Yu, GuangyuanFu, Jun Wang, and Ying-wen Zhao. NewGOA: Pre-dicting new GO annota-tions of proteins by bi-random walks on a hybridgraph. IEEE/ACM Trans-actions on ComputationalBiology and Bioinformatics,15(4):1390–1402, July 2018.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Yu:2019:HPB

[YG19] Liang Yu and Lin Gao. Hu-man pathway-based diseasenetwork. IEEE/ACM Trans-actions on ComputationalBiology and Bioinformatics,16(4):1240–1249, July 2019.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

REFERENCES 360

Yan:2020:GES

[YGFC20] Da Yan, Xin Gao, Samah J.Fodeh, and Jake Y. Chen.Guest editorial for se-lected papers from BIOKDD2018 and DMBIH 2018.IEEE/ACM Transactionson Computational Biologyand Bioinformatics, 17(6):1832–1834, November 2020.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic). URL https://dl.acm.org/doi/10.1109/TCBB.2020.3020443.

Yuan:2019:IMO

[YGY+19] Lin Yuan, Le-Hang Guo,Chang-An Yuan, YouhuaZhang, Kyungsook Han,Asoke K. Nandi, BarryHonig, and De-Shuang Huang.Integration of multi-omicsdata for gene regulatorynetwork inference and ap-plication to breast cancer.IEEE/ACM Transactions onComputational Biology andBioinformatics, 16(3):782–791, May 2019. CODENITCBCY. ISSN 1545-5963(print), 1557-9964 (elec-tronic).

Yu:2013:NFV

[YH13] Hong-Jie Yu and De-ShuangHuang. Normalized featurevectors: a novel alignment-free sequence comparisonmethod based on the num-bers of adjacent amino acids.IEEE/ACM Transactions onComputational Biology and

Bioinformatics, 10(2):457–467, March 2013. CODENITCBCY. ISSN 1545-5963(print), 1557-9964 (elec-tronic).

Yu:2012:SGS

[YHB12] Lei Yu, Yue Han, andMichael E. Berens. Stablegene selection from microar-ray data via sample weight-ing. IEEE/ACM Transac-tions on Computational Bi-ology and Bioinformatics, 9(1):262–272, January 2012.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Yang:2019:RHD

[YHCS19] Xi Yang, Guoqiang Han,Hongmin Cai, and YanSong. Recovering hidden di-agonal structures via non-negative matrix factorizationwith multiple constraints.IEEE/ACM Transactionson Computational Biologyand Bioinformatics, 16(5):1760–1772, September 2019.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Yu:2015:EEA

[YHV+15] Qiang Yu, Hongwei Huo,Jeffrey Scott Vitter, JunHuan, and Yakov Nekrich.An efficient exact algorithmfor the motif stem searchproblem over large alpha-bets. IEEE/ACM Trans-actions on Computational

REFERENCES 361


Yang:2013:CPP

[YHY13] Chao Yang, Zengyou He, andWeichuan Yu. A combi-natorial perspective of theprotein inference problem.IEEE/ACM Transactionson Computational Biologyand Bioinformatics, 10(6):1542–1547, November 2013.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Yang:2012:PRP

[YHYY12] Chao Yang, Zengyou He,Can Yang, and WeichuanYu. Peptide rerankingwith protein-peptide cor-respondence and precur-sor peak intensity informa-tion. IEEE/ACM Transac-tions on Computational Bi-ology and Bioinformatics, 9(4):1212–1219, July 2012.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

You:2019:EEL

[YHZ+19] Zhu-Hong You, Wen-ZhunHuang, Shanwen Zhang,Yu-An Huang, Chang-QingYu, and Li-Ping Li. Anefficient ensemble learn-ing approach for predict-ing protein-protein interac-tions by integrating pro-

tein primary sequence andevolutionary information.IEEE/ACM Transactions onComputational Biology andBioinformatics, 16(3):809–817, May 2019. CODENITCBCY. ISSN 1545-5963(print), 1557-9964 (elec-tronic).

Yan:2017:NNP

[YKW17] Yan, Anthony J. Kusa-lik, and Fang-Xiang Wu.NovoExD: De novo peptidesequencing for ETD/ECDspectra. IEEE/ACM Trans-actions on ComputationalBiology and Bioinformatics,14(2):337–344, March 2017.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Yerneni:2018:IIS

[YKWK18] Satwica Yerneni, Ishita K.Khan, Qing Wei, andDaisuke Kihara. IAS: In-teraction specific GO termassociations for predict-ing protein-protein interac-tion networks. IEEE/ACMTransactions on Computa-tional Biology and Bioin-formatics, 15(4):1247–1258,July 2018. CODEN ITCBCY.ISSN 1545-5963 (print),1557-9964 (electronic).

Yoon:2012:SLP

[YL12] Yongwook Yoon and Gary Ge-unbae Lee. Subcellular lo-calization prediction throughboosting association rules.

REFERENCES 362

IEEE/ACM Transactions onComputational Biology andBioinformatics, 9(2):609–618, March 2012. CODENITCBCY. ISSN 1545-5963(print), 1557-9964 (elec-tronic).

Yang:2020:CBM

[YLC20] Cheng-Hong Yang, Yu-DaLin, and Li-Yeh Chuang.Class balanced multifactordimensionality reduction todetect gene–gene interac-tions. IEEE/ACM Trans-actions on ComputationalBiology and Bioinformatics,17(1):71–81, January 2020.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic). URL https://dl.acm.org/doi/abs/10.1109/TCBB.2018.2858776.

Yang:2013:EBC

[YLCC13] Cheng-Hong Yang, Yu-DaLin, Li-Yeh Chaung, andHsueh-Wei Chang. Evalu-ation of breast cancer sus-ceptibility using improvedgenetic algorithms to gen-erate genotype SNP bar-codes. IEEE/ACM Trans-actions on ComputationalBiology and Bioinformatics,10(2):361–371, March 2013.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Ye:2015:GAM

[YlCW+15] Yongtao Ye, David Wai lokCheung, Yadong Wang, Siu-

Ming Yiu, Qing Zhang, Tak-Wah Lam, and Hing-FungTing. GLProbs: align-ing multiple sequences adap-tively. IEEE/ACM Trans-actions on ComputationalBiology and Bioinformatics,12(1):67–78, January 2015.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Yu:2015:DCP

[YLH+15] Dong-Jun Yu, Yang Li, JunHu, Xibei Yang, Jing-YuYang, and Hong-Bin Shen.Disulfide connectivity pre-diction based on modelledprotein 3D structural infor-mation and random forest re-gression. IEEE/ACM Trans-actions on ComputationalBiology and Bioinformatics,12(3):611–621, May 2015.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Yu:2006:MPA

[YLL+06] Weichuan Yu, Xiaoye Li,Junfeng Liu, Baolin Wu,Kenneth R. Williams, andHongyu Zhao. Multiplepeak alignment in sequentialdata analysis: a scale-space-based approach. IEEE/ACMTransactions on Computa-tional Biology and Bioinfor-matics, 3(3):208–219, July2006. CODEN ITCBCY.ISSN 1545-5963 (print),1557-9964 (electronic).

REFERENCES 363

Ye:2004:UUD

[YLXJ04] Jieping Ye, Tao Li, TaoXiong, and Ravi Janardan.Using uncorrelated discrimi-nant analysis for tissue clas-sification with gene expres-sion data. IEEE/ACMTransactions on Computa-tional Biology and Bioinfor-matics, 1(4):181–190, Octo-ber 2004. CODEN ITCBCY.ISSN 1545-5963 (print),1557-9964 (electronic).

Yan:2017:TNW

[YLXS17] Zhangming Yan, Ke Liu,Shunian Xiang, and ZhirongSun. txCoords: a novelWeb application for tran-scriptomic peak re-mapping.IEEE/ACM Transactions onComputational Biology andBioinformatics, 14(3):746–748, May 2017. CODENITCBCY. ISSN 1545-5963(print), 1557-9964 (elec-tronic).

Yu:2012:STS

[YLY+12] Zhiwen Yu, Le Li, Jane You,Hau-San Wong, and Guo-qiang Han. SC3: Triple spec-tral clustering-based consen-sus Clustering framework forclass discovery from can-cer gene expression profiles.IEEE/ACM Transactionson Computational Biologyand Bioinformatics, 9(6):1751–1765, November 2012.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Yang:2011:RFS

[YM11] Feng Yang and K. Z.Mao. Robust feature se-lection for microarray databased on multicriterion fu-sion. IEEE/ACM Transac-tions on Computational Bi-ology and Bioinformatics, 8(4):1080–1092, July 2011.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Yeganeh:2020:CDA

[YM20] Pourya Naderi Yeganeh andM. Taghi Mostafavi. Causaldisturbance analysis: anovel graph centrality basedmethod for pathway enrich-ment analysis. IEEE/ACMTransactions on Computa-tional Biology and Bioin-formatics, 17(5):1613–1624,September 2020. CODENITCBCY. ISSN 1545-5963(print), 1557-9964 (elec-tronic). URL https://dl.acm.org/doi/10.1109/TCBB.2019.2907246.

Yoo:2014:ICM

[YMT+14] Paul D. Yoo, Sami Muhai-dat, Kamal Taha, JamalBentahar, and AbdallahShami. Intelligent consen-sus modeling for proline cis-trans isomerization predic-tion. IEEE/ACM Trans-actions on ComputationalBiology and Bioinformatics,11(1):26–32, January 2014.CODEN ITCBCY. ISSN

REFERENCES 364


Yang:2012:IXT

[YMW+12] Pengyi Yang, Jie Ma, Peng-hao Wang, Yunping Zhu,Bing B. Zhou, and Yee HwaYang. Improving X!Tandemon peptide identificationfrom mass spectrometryby self-boosted percolator.IEEE/ACM Transactionson Computational Biologyand Bioinformatics, 9(5):1273–1280, September 2012.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Yu:2014:IEL

[YN14] Hualong Yu and Jun Ni.An improved ensemble learn-ing method for classifyinghigh-dimensional and im-balanced biomedicine data.IEEE/ACM Transactions onComputational Biology andBioinformatics, 11(4):657–666, July 2014. CODENITCBCY. ISSN 1545-5963(print), 1557-9964 (elec-tronic).

Yoon:2005:DCB

[YNBM05] Sungroh Yoon, ChristineNardini, Luca Benini, andGiovanni De Micheli. Dis-covering coherent biclus-ters from gene expressiondata using zero-suppressedbinary decision diagrams.IEEE/ACM Transactions onComputational Biology and

Bioinformatics, 2(4):339–354, October 2005. CODENITCBCY. ISSN 1545-5963(print), 1557-9964 (elec-tronic).

Yue:2018:SGS

[YNN+18] Zongliang Yue, Michael T.Neylon, Thanh Nguyen,Timothy Ratliff, and Jake Y.Chen. “Super Gene Set”causal relationship discov-ery from functional genomicsdata. IEEE/ACM Trans-actions on ComputationalBiology and Bioinformatics,15(6):1991–1998, November2018. CODEN ITCBCY.ISSN 1545-5963 (print),1557-9964 (electronic).

Yip:2007:SIS

[YNWC07] Andy M. Yip, Michael K.Ng, Edmond H. Wu, andTony F. Chan. Strate-gies for identifying statis-tically significant dense re-gions in microarray data.IEEE/ACM Transactions onComputational Biology andBioinformatics, 4(3):415–429, July 2007. CODENITCBCY. ISSN 1545-5963(print), 1557-9964 (elec-tronic).

Yoruk:2011:CSM

[YOGY11] Erdem Yoruk, Michael F.Ochs, Donald Geman, andLaurent Younes. A compre-hensive statistical model forcell signaling. IEEE/ACMTransactions on Computa-

REFERENCES 365

tional Biology and Bioinfor-matics, 8(3):592–606, May/June 2011. CODENITCBCY. ISSN 1545-5963(print), 1557-9964 (elec-tronic).

Yukinawa:2009:OAB

[YOKI09] Naoto Yukinawa, ShigeyukiOba, Kikuya Kato, and ShinIshii. Optimal aggrega-tion of binary classifiers formulticlass cancer diagnosisusing gene expression pro-files. IEEE/ACM Trans-actions on ComputationalBiology and Bioinformatics,6(2):333–343, April 2009.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Yu:2013:HCH

[YP13] Tianwei Yu and Hesen Peng.Hierarchical clustering ofhigh-throughput expressiondata based on general depen-dences. IEEE/ACM Trans-actions on ComputationalBiology and Bioinformatics,10(4):1080–1085, July 2013.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Yu:2011:INR

[YPS11] Tianwei Yu, Hesen Peng, andWei Sun. Incorporating non-linear relationships in mi-croarray missing value impu-tation. IEEE/ACM Trans-actions on ComputationalBiology and Bioinformat-

ics, 8(3):723–731, May/June2011. CODEN ITCBCY.ISSN 1545-5963 (print),1557-9964 (electronic).

Yu:2013:PFP

[YRD+13] Guoxian Yu, Huzefa Rang-wala, Carlotta Domeniconi,Guoji Zhang, and Zhi-wen Yu. Protein func-tion prediction using multi-label ensemble classifica-tion. IEEE/ACM Transac-tions on Computational Bi-ology and Bioinformatics, 10(4):1, July 2013. CODENITCBCY. ISSN 1545-5963(print), 1557-9964 (elec-tronic).

Yu:2014:EPF

[YRD+14a] Guoxian Yu, Huzefa Rang-wala, Carlotta Domeniconi,Guoji Zhang, and ZhiwenYu. Erratum to “Proteinfunction prediction usingmultilabel ensemble classifi-cation”. IEEE/ACM Trans-actions on ComputationalBiology and Bioinformat-ics, 11(1):265, January 2014.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Yu:2014:PFP

[YRD+14b] Guoxian Yu, Huzefa Rang-wala, Carlotta Domeniconi,Guoji Zhang, and ZhiwenYu. Protein function predic-tion with incomplete anno-tations. IEEE/ACM Trans-actions on Computational

REFERENCES 366


Yu:2015:PPF

[YRD+15] Guoxian Yu, Huzefa Rang-wala, Carlotta Domeni-coni, Guoji Zhang, and ZiliZhang. Predicting proteinfunction using multiple ker-nels. IEEE/ACM Transac-tions on Computational Bi-ology and Bioinformatics, 12(1):219–233, January 2015.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Yu:2020:LBE

[YRL+20] Xinyi Yu, Wenge Rong, Jing-shuang Liu, Deyu Zhou,Yuanxin Ouyang, and ZhangXiong. LSTM-based end-to-end framework for biomedi-cal event extraction. IEEE/ACM Transactions on Com-putational Biology and Bioin-formatics, 17(6):2029–2039,November 2020. CODENITCBCY. ISSN 1545-5963(print), 1557-9964 (elec-tronic). URL https://dl.acm.org/doi/10.1109/TCBB.2019.2916346.

Yoo:2017:GES

[YS17] Illhoi Yoo and AmardaShehu. Guest editorial forspecial section on BIBM2014. IEEE/ACM Trans-actions on Computational


Yan:2013:CNE

[YSC13] Su Yan, W. Scott Spangler,and Ying Chen. Chemicalname extraction based onautomatic training data gen-eration and rich feature set.IEEE/ACM Transactionson Computational Biologyand Bioinformatics, 10(5):1218–1233, September 2013.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Yamanishi:2019:GEA

[YSC19] Yoshihiro Yamanishi, Ya-subumi Sakakibara, and Yi-Ping Phoebe Chen. Guesteditorial for the 16th AsiaPacific Bioinformatics Con-ference. IEEE/ACM Trans-actions on ComputationalBiology and Bioinformat-ics, 16(1):1–2, January 2019.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Yao:2020:ADP

[YSGZ20] Heng Yao, Yunjia Shi, Ji-hong Guan, and ShuigengZhou. Accurately detect-ing protein complexes bygraph embedding and com-bining functions with inter-actions. IEEE/ACM Trans-actions on Computational

REFERENCES 367

Biology and Bioinformatics,17(3):777–787, May 2020.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic). URL https://dl.acm.org/doi/10.1109/TCBB.2019.2897769.

Yu:2017:PND

[YSW+17] Liang Yu, Ruidan Su,Bingbo Wang, Long Zhang,Yapeng Zou, Jing Zhang,and Lin Gao. Predictionof novel drugs for hepato-cellular carcinoma based onmulti-source random walk.IEEE/ACM Transactions onComputational Biology andBioinformatics, 14(4):966–977, July 2017. CODENITCBCY. ISSN 1545-5963(print), 1557-9964 (elec-tronic).

Yang:2015:FDW

[YTLL15] Lina Yang, Yuan YanTang, Yang Lu, and HuiwuLuo. A fractal dimen-sion and wavelet transformbased method for proteinsequence similarity analy-sis. IEEE/ACM Transac-tions on Computational Bi-ology and Bioinformatics,12(2):348–369, March 2015.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Yu:2020:NGF

[YWF+20] Guoxian Yu, Keyao Wang,Guangyuan Fu, Maozu Guo,and Jun Wang. NMFGO:

Gene function predictionvia nonnegative matrix fac-torization with gene ontol-ogy. IEEE/ACM Transac-tions on Computational Bi-ology and Bioinformatics, 17(1):238–249, January 2020.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic). URL https://dl.acm.org/doi/abs/10.1109/TCBB.2018.2861379.

Yang:2007:MFE

[YWK+07] Jing Yang, Sarawan Wongsa,Visakan Kadirkamanathan,Stephen A. Billings, andPhillip C. Wright. Metabolicflux estimation — a self-adaptive evolutionary algo-rithm with singular value de-composition. IEEE/ACMTransactions on Computa-tional Biology and Bioinfor-matics, 4(1):126–138, Jan-uary 2007. CODEN ITCBCY.ISSN 1545-5963 (print),1557-9964 (electronic).

Yan:2019:DMP

[YWN+19] Cheng Yan, Jianxin Wang,Peng Ni, Wei Lan, Fang-Xiang Wu, and Yi Pan.DNRLMF–MDA: Predict-ing microRNA-Disease asso-ciations based on similari-ties of microRNAs and dis-eases. IEEE/ACM Transac-tions on Computational Bi-ology and Bioinformatics, 16(1):233–243, January 2019.CODEN ITCBCY. ISSN

REFERENCES 368


Yu:2018:NFN

[YWW+18] Chunjiang Yu, Wentao Wu,Jing Wang, Yuxin Lin, Yang,Jiajia Chen, Fei Zhu, andBairong Shen. NGS-FC:a next-generation sequenc-ing data format converter.IEEE/ACM Transactionson Computational Biologyand Bioinformatics, 15(5):1683–1691, September 2018.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Yang:2020:DDF

[YWW20] Shengping Yang, Mitchell S.Wachtel, and JiangrongWu. DFseq: Distribution-free method to detect dif-ferential gene expressionfor RNA-sequencing data.IEEE/ACM Transactions onComputational Biology andBioinformatics, 17(2):558–565, March 2020. CODENITCBCY. ISSN 1545-5963(print), 1557-9964 (elec-tronic). URL https://dl.acm.org/doi/abs/10.1109/TCBB.2018.2866994.

Yin:2016:EPT

[YXS16] Xi Yin, Ying-Ying Xu, andHong-Bin Shen. Enhanc-ing the prediction of trans-membrane β-barrel segmentswith chain learning and fea-ture sparse representation.IEEE/ACM Transactions


Yang:2013:FNF

[YXYC13] Jiaoyun Yang, Yun Xu,Xiaohui Yao, and Guo-liang Chen. FNphasing:a novel fast heuristic algo-rithm for haplotype phas-ing based on flow networkmodel. IEEE/ACM Trans-actions on ComputationalBiology and Bioinformatics,10(2):372–382, March 2013.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Yuan:2017:NPB

[YZG+17] Lin Yuan, Lin Zhu, Wei-LiGuo, Xiaobo Zhou, YouhuaZhang, Zhenhua Huang, andDe-Shuang Huang. Noncon-vex penalty based low-rankrepresentation and sparse re-gression for eQTL mapping.IEEE/ACM Transactionson Computational Biologyand Bioinformatics, 14(5):1154–1164, September 2017.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Yang:2019:PFI

[YZG+19] Runtao Yang, ChengjinZhang, Rui Gao, Lina Zhang,and Qing Song. Predict-ing FAD interacting residues

REFERENCES 369

with feature selection andcomprehensive sequence de-scriptors. IEEE/ACMTransactions on Computa-tional Biology and Bioin-formatics, 16(6):2046–2056,November 2019. CODENITCBCY. ISSN 1545-5963(print), 1557-9964 (elec-tronic). URL https://dl.acm.org/doi/abs/10.1109/TCBB.2018.2824332.

Zhu:2009:GGA

[ZACS09] Qian Zhu, Zaky Adam,Vicky Choi, and DavidSankoff. Generalized geneadjacencies, graph band-width, and clusters in yeastevolution. IEEE/ACMTransactions on Computa-tional Biology and Bioinfor-matics, 6(2):213–220, April2009. CODEN ITCBCY.ISSN 1545-5963 (print),1557-9964 (electronic).

Zare:2020:PSC

[ZANN20] Fatima Zare, Sardar Ansari,Kayvan Najarian, and SheidaNabavi. Preprocessing se-quence coverage data formore precise detection ofcopy number variations.IEEE/ACM Transactions onComputational Biology andBioinformatics, 17(3):868–876, May 2020. CODENITCBCY. ISSN 1545-5963(print), 1557-9964 (elec-tronic). URL https://dl.acm.org/doi/10.1109/TCBB.2018.2869738.

Zhu:2011:GMA

[ZAZ11] Dongxiao Zhu, Lipi Acharya,and Hui Zhang. A gener-alized multivariate approachto pattern discovery fromreplicated and incompletegenome-wide measurements.IEEE/ACM Transactionson Computational Biologyand Bioinformatics, 8(5):1153–1169, September 2011.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Zimek:2010:SHF

[ZBFK10] Arthur Zimek, Fabian Buch-wald, Eibe Frank, and Ste-fan Kramer. A study of hi-erarchical and flat classifica-tion of proteins. IEEE/ACMTransactions on Computa-tional Biology and Bioinfor-matics, 7(3):563–571, July2010. CODEN ITCBCY.ISSN 1545-5963 (print),1557-9964 (electronic).

Zhao:2011:MKI

[ZC11] Xin Zhao and Leo Wang-Kit Cheung. Multiclasskernel-imbedded Gaussianprocesses for microarray dataanalysis. IEEE/ACM Trans-actions on ComputationalBiology and Bioinformatics,8(4):1041–1053, July 2011.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

REFERENCES 370

Zhou:2014:GEA

[ZC14] Shuigeng Zhou and Yi-Ping Phoebe Chen. Guesteditorial for the 12th AsiaPacific Bioinformatics Con-ference. IEEE/ACM Trans-actions on ComputationalBiology and Bioinformatics,11(4):614–615, July 2014.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Zhang:2015:GES

[ZC15] Shihua Zhang and Luo-nan Chen. Guest edito-rial for special section onISB/TBC 2014. IEEE/ACMTransactions on Computa-tional Biology and Bioin-formatics, 12(5):1074–1075,September 2015. CODENITCBCY. ISSN 1545-5963(print), 1557-9964 (elec-tronic).

Zhang:2018:HSB

[ZCG+18] Jian Zhang, Haiting Chai,Bo Gao, Guifu Yang, andZhiqiang Ma. HEME-sPred: Structure-basedligand-specific heme bindingresidues prediction by usingfast-adaptive ensemble learn-ing scheme. IEEE/ACMTransactions on Computa-tional Biology and Bioin-formatics, 15(1):147–156,January 2018. CODENITCBCY. ISSN 1545-5963(print), 1557-9964 (elec-tronic).

Zhou:2019:E

[ZCM19] Shuigeng Zhou, Yi-Ping PhoebeChen, and Hiroshi Mamit-suka. Editorial. IEEE/ACMTransactions on Computa-tional Biology and Bioin-formatics, 16(2):350–351,March 2019. CODENITCBCY. ISSN 1545-5963(print), 1557-9964 (elec-tronic). URL https://dl.acm.org/doi/abs/10.1109/TCBB.2018.2827138.

Zhang:2017:TPI

[ZCR+17] Fa Zhang, Yu Chen, FeiRen, Xuan Wang, ZhiyongLiu, and Xiaohua Wan. Atwo-phase improved correla-tion method for automaticparticle selection in Cryo-EM. IEEE/ACM Transac-tions on Computational Bi-ology and Bioinformatics,14(2):316–325, March 2017.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Zhu:2019:ARC

[ZCWW19] Wenliang Zhu, Xiaohe Chen,Yan Wang, and LirongWang. Arrhythmia recog-nition and classification us-ing ECG morphology andsegment feature analysis.IEEE/ACM Transactions onComputational Biology andBioinformatics, 16(1):131–138, January 2019. CODENITCBCY. ISSN 1545-5963(print), 1557-9964 (elec-tronic).

REFERENCES 371

Zhang:2012:FIF

[ZD12] Xiao-Fei Zhang and Dao-Qing Dai. A frameworkfor incorporating functionalinterrelationships into pro-tein function prediction algo-rithms. IEEE/ACM Trans-actions on ComputationalBiology and Bioinformat-ics, 9(3):740–753, May 2012.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Zhang:2017:TDP

[ZD17] Bo Zhang and HaibinDuan. Three-dimensionalpath planning for unin-habited combat aerial ve-hicle based on predator-prey pigeon-inspired opti-mization in dynamic environ-ment. IEEE/ACM Transac-tions on Computational Bi-ology and Bioinformatics, 14(1):97–107, January 2017.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Zhang:2012:PCD

[ZDL12] Xiao-Fei Zhang, Dao-QingDai, and Xiao-Xin Li. Pro-tein complexes discoverybased on protein-protein in-teraction data via a regular-ized sparse generative net-work model. IEEE/ACMTransactions on Computa-tional Biology and Bioinfor-matics, 9(3):857–870, May2012. CODEN ITCBCY.


Zeng:2019:NLP

[ZDL+19] Zexian Zeng, Yu Deng, Xi-aoyu Li, Tristan Naumann,and Yuan Luo. Natural lan-guage processing for EHR-based computational pheno-typing. IEEE/ACM Trans-actions on ComputationalBiology and Bioinformat-ics, 16(1):139–153, January2019. CODEN ITCBCY.ISSN 1545-5963 (print),1557-9964 (electronic).

Zhu:2017:ISI

[ZDYH17] Lin Zhu, Su-Ping Deng,Zhu-Hong You, and De-Shuang Huang. Identify-ing spurious interactions inthe protein-protein interac-tion networks using localsimilarity preserving embed-ding. IEEE/ACM Trans-actions on ComputationalBiology and Bioinformatics,14(2):345–352, March 2017.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Zhao:2020:INF

[ZFZ+20] Jin Zhao, Haodi Feng,Daming Zhu, Chi Zhang,and Ying Xu. IsoTree:a new framework for denovo transcriptome assem-bly from RNA-seq reads.IEEE/ACM Transactions onComputational Biology andBioinformatics, 17(3):938–

REFERENCES 372

948, May 2020. CODENITCBCY. ISSN 1545-5963(print), 1557-9964 (elec-tronic). URL https://dl.acm.org/doi/10.1109/TCBB.2018.2808350.

Zhao:2019:PPI

[ZG19] Zhenni Zhao and XinqiGong. Protein–protein in-teraction interface residuepair prediction based ondeep learning architecture.IEEE/ACM Transactionson Computational Biologyand Bioinformatics, 16(5):1753–1759, September 2019.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Zoppis:2012:MIO

[ZGB+12] Italo Zoppis, Erica Gianazza,Massimiliano Borsani, CliziaChinello, Veronica Mainini,Carmen Galbusera, CarloFerrarese, Gloria Galim-berti, Sandro Sorbi, Bar-bara Borroni, Fulvio Magni,Marco Antoniotti, and Gi-ancarlo Mauri. Mutual in-formation optimization formass spectra data align-ment. IEEE/ACM Trans-actions on ComputationalBiology and Bioinformat-ics, 9(3):934–939, May 2012.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Zhang:2005:PMF

[ZGC+05] Jingfen Zhang, Wen Gao,

Jinjin Cai, Simin He, RongZeng, and Runsheng Chen.Predicting molecular formu-las of fragment ions withisotope patterns in tandemmass spectra. IEEE/ACMTransactions on Computa-tional Biology and Bioinfor-matics, 2(3):217–230, July2005. CODEN ITCBCY.ISSN 1545-5963 (print),1557-9964 (electronic).

Zhu:2016:CPE

[ZGDH16] Lin Zhu, Wei-Li Guo, Su-Ping Deng, and De-ShuangHuang. ChIP–PIT: Enhanc-ing the analysis of ChIP-Seqdata using convex-relaxedpair-wise interaction tensordecomposition. IEEE/ACMTransactions on Computa-tional Biology and Bioinfor-matics, 13(1):55–63, January2016. CODEN ITCBCY.ISSN 1545-5963 (print),1557-9964 (electronic).

Zhang:2020:EMM

[ZGZ+20] Jingsong Zhang, JianmeiGuo, Ming Zhang, XiangtianYu, Xiaoqing Yu, WeifengGuo, Tao Zeng, and Luo-nan Chen. Efficient min-ing multi-mers in a vari-ety of biological sequences.IEEE/ACM Transactions onComputational Biology andBioinformatics, 17(3):949–958, May 2020. CODENITCBCY. ISSN 1545-5963(print), 1557-9964 (elec-tronic). URL https://

REFERENCES 373


Zhang:2007:SSS

[Zha07] Louxin Zhang. Superiorityof spaced seeds for homologysearch. IEEE/ACM Trans-actions on ComputationalBiology and Bioinformat-ics, 4(3):496–505, July 2007.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Zhang:2011:GTS

[Zha11] Louxin Zhang. From genetrees to species trees II:Species tree inference byminimizing deep coalescenceevents. IEEE/ACM Trans-actions on ComputationalBiology and Bioinformatics,8(6):1685–1691, November2011. CODEN ITCBCY.ISSN 1545-5963 (print),1557-9964 (electronic).

Zhao:2016:DMS

[Zha16] Xing-Ming Zhao. Datamining in systems biology.IEEE/ACM Transactions onComputational Biology andBioinformatics, 13(6):1003,November 2016. CODENITCBCY. ISSN 1545-5963(print), 1557-9964 (elec-tronic).

Zhang:2017:ENE

[Zha17] Aidong Zhang. Editorialfrom the new Editor-in-Chief. IEEE/ACM Trans-actions on Computational

Biology and Bioinformat-ics, 14(2):251, March 2017.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Zhang:2018:AIP

[Zha18] Xizhe Zhang. Altering in-dispensable proteins in con-trolling directed human pro-tein interaction network.IEEE/ACM Transactionson Computational Biologyand Bioinformatics, 15(6):2074–2078, November 2018.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Zhu:2019:TSS

[ZHE19] Lu Zhu, Ralf Hofestadt,and Martin Ester. Tissue-specific subcellular localiza-tion prediction using multi-label Markov random fields.IEEE/ACM Transactionson Computational Biologyand Bioinformatics, 16(5):1471–1482, September 2019.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Zhang:2005:SGN

[ZHEB05] Shaojie Zhang, Brian Haas,Eleazar Eskin, and VineetBafna. Searching genomesfor noncoding RNA usingFastR. IEEE/ACM Transac-tions on Computational Bi-ology and Bioinformatics, 2(4):366–379, October 2005.CODEN ITCBCY. ISSN

REFERENCES 374


Zheng:2020:DDA

[ZHG20] Jingyi Zheng, Fushing Hsieh,and Linqiang Ge. A data-driven approach to pre-dict and classify epilepticseizures from brain-wide cal-cium imaging video data.IEEE/ACM Transactionson Computational Biologyand Bioinformatics, 17(6):1858–1870, November 2020.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic). URL https://dl.acm.org/doi/10.1109/TCBB.2019.2895077.

Zhang:2017:MVC

[ZHJ17] Yong Zhang, Xiaohua Hu,and Xingpeng Jiang. Multi-view clustering of mi-crobiome samples by ro-bust similarity network fu-sion and spectral cluster-ing. IEEE/ACM Transac-tions on Computational Bi-ology and Bioinformatics,14(2):264–271, March 2017.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Zhao:2014:CGE

[ZHL+14] Liang Zhao, Steven C. H.Hoi, Zhenhua Li, Lim-soon Wong, Hung Nguyen,and Jinyan Li. Couplinggraphs, efficient algorithmsand B-cell epitope predic-tion. IEEE/ACM Trans-actions on Computational


Zhang:2007:MCU

[ZHSS07] Runxuan Zhang, Guang-BinHuang, N. Sundararajan,and P. Saratchandran. Mul-ticategory classification us-ing an extreme learning ma-chine for microarray geneexpression cancer diagno-sis. IEEE/ACM Trans-actions on ComputationalBiology and Bioinformat-ics, 4(3):485–495, July 2007.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Zhang:2020:ISO

[ZHZ+20] Rongrong Zhang, Ming Hu,Yu Zhu, Zhaohui Qin,Ke Deng, and Jun S. Liu.Inferring spatial organiza-tion of individual topolog-ically associated domainsvia piecewise helical model.IEEE/ACM Transactions onComputational Biology andBioinformatics, 17(2):647–656, March 2020. CODENITCBCY. ISSN 1545-5963(print), 1557-9964 (elec-tronic). URL https://dl.acm.org/doi/abs/10.1109/TCBB.2018.2865349.

Zhao:2016:PBN

[ZK16] Yun-Bo Zhao and J. Krish-nan. Probabilistic Boolean

REFERENCES 375

network modelling and anal-ysis framework for mRNAtranslation. IEEE/ACMTransactions on Computa-tional Biology and Bioinfor-matics, 13(4):754–766, 2016.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Zhao:2018:BMV

[ZKL18] Yize Zhao, Jian Kang, andQi Long. Bayesian mul-tiresolution variable selec-tion for ultra-high dimen-sional neuroimaging data.IEEE/ACM Transactions onComputational Biology andBioinformatics, 15(2):537–550, March 2018. CODENITCBCY. ISSN 1545-5963(print), 1557-9964 (elec-tronic).

Zhi:2007:CBA

[ZKP+07] Degui Zhi, Uri Keich, PavelPevzner, Steffen Heber, andHaixu Tang. Correctingbase-assignment errors in re-peat regions of shotgun as-sembly. IEEE/ACM Trans-actions on ComputationalBiology and Bioinformatics,4(1):54–64, January 2007.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Zhang:2019:TGP

[ZKW19] Jiao Zhang, Sam Kwong,and Ka-Chun Wong. To-Bio: Global pathway simi-larity search based on topo-

logical and biological fea-tures. IEEE/ACM Transac-tions on Computational Bi-ology and Bioinformatics, 16(1):336–349, January 2019.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Zrimec:2015:FPD

[ZL15] Jan Zrimec and Ales La-panje. Fast prediction ofDNA melting bubbles usingDNA thermodynamic sta-bility. IEEE/ACM Trans-actions on ComputationalBiology and Bioinformatics,12(5):1137–1145, September2015. CODEN ITCBCY.ISSN 1545-5963 (print),1557-9964 (electronic).

Zou:2019:AML

[ZL19] Quan Zou and Qi Liu.Advanced machine learningtechniques for bioinformat-ics. IEEE/ACM Transac-tions on Computational Bi-ology and Bioinformatics, 16(4):1182–1183, July 2019.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Zhang:2012:QDS

[ZLH12] Yong Zhang, Peng Li, andGarng Huang. Quanti-fying dynamic stability ofgenetic memory circuits.IEEE/ACM Transactions onComputational Biology andBioinformatics, 9(3):871–884, May 2012. CODEN

REFERENCES 376


Zhang:2017:CPP

[ZLH+17] Lin Zhang, Hui Liu, YufeiHuang, Xuesong Wang, Yi-dong Chen, and Jia Meng.Cancer progression predic-tion using gene interac-tion regularized elastic net.IEEE/ACM Transactions onComputational Biology andBioinformatics, 14(1):145–154, January 2017. CODENITCBCY. ISSN 1545-5963(print), 1557-9964 (elec-tronic).

Zeng:2020:DCF

[ZLH+20] Xiangxiang Zeng, YinglaiLin, Yuying He, Linyuan Lu,Xiaoping Min, and AlfonsoRodrıguez-Paton. Deep col-laborative filtering for pre-diction of disease genes.IEEE/ACM Transactionson Computational Biologyand Bioinformatics, 17(5):1639–1647, September 2020.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic). URL https://dl.acm.org/doi/10.1109/TCBB.2019.2907536.

Zheng:2017:CFF

[ZLJT17] Shaoqiu Zheng, Junzhi Li,Andreas Janecek, and YingTan. A cooperative frame-work for fireworks algo-rithm. IEEE/ACM Trans-actions on Computational


Zhang:2020:ODP

[ZLL+20] Yuan Zhang, Haihong Liu,Zhouhong Li, ZhonghuaMiao, and Jin Zhou. Os-cillatory dynamics of p53-Mdm2 circuit in response toDNA damage caused by ion-izing radiation. IEEE/ACMTransactions on Computa-tional Biology and Bioin-formatics, 17(5):1703–1713,September 2020. CODENITCBCY. ISSN 1545-5963(print), 1557-9964 (elec-tronic). URL https://dl.acm.org/doi/10.1109/TCBB.2019.2899574.

Zheng:2017:MMA

[ZLLS17] Weihua Zheng, Kenli Li,Keqin Li, and Hing Che-ung So. A modified multi-ple alignment Fast FourierTransform with higher effi-ciency. IEEE/ACM Trans-actions on ComputationalBiology and Bioinformatics,14(3):634–645, May 2017.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Zeng:2017:PVD

[ZLLZ17] Xiangxiang Zeng, YuanluLiao, Yuansheng Liu, andQuan Zou. Predictionand validation of disease

REFERENCES 377

genes using HeteSim scores.IEEE/ACM Transactions onComputational Biology andBioinformatics, 14(3):687–695, May 2017. CODENITCBCY. ISSN 1545-5963(print), 1557-9964 (elec-tronic).

Zhang:2016:IGM

[ZLPW16] Ya Zhang, Ao Li, ChenPeng, and Minghui Wang.Improve glioblastoma mul-tiforme prognosis predictionby using feature selectionand multiple kernel learning.IEEE/ACM Transactionson Computational Biologyand Bioinformatics, 13(5):825–835, September 2016.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Zhu:2015:PIM

[ZLS+15] Xiangyuan Zhu, Kenli Li,Ahmad Salah, Lin Shi, andKeqin Li. Parallel implemen-tation of MAFFT on CUDA-enabled graphics hardware.IEEE/ACM Transactions onComputational Biology andBioinformatics, 12(1):205–218, January 2015. CODENITCBCY. ISSN 1545-5963(print), 1557-9964 (elec-tronic).

Zhang:2019:CMV

[ZLS+19] Jun-Ping Zhang, Yi Liu, WeiSun, Xiao-Yang Zhao, La Ta,and Wei-Sheng Guo. Charac-teristics of myosin V proces-

sivity. IEEE/ACM Transac-tions on Computational Bi-ology and Bioinformatics, 16(4):1302–1308, July 2019.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Zhang:2011:PTN

[ZLW+11] Peng Zhang, HouqiangLi, Honghui Wang, WongStephen, and Xiaobo Zhou.Peak tree: a new tool formultiscale hierarchical rep-resentation and peak detec-tion of mass spectrometrydata. IEEE/ACM Transac-tions on Computational Bi-ology and Bioinformatics, 8(4):1054–1066, July 2011.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Zhou:2020:EPD

[ZLX+20] Jiyun Zhou, Qin Lu, RuifengXu, Lin Gui, and HongpengWang. EL LSTM: Predic-tion of DNA-binding residuefrom protein sequence bycombining long short-termmemory and ensemble learn-ing. IEEE/ACM Transac-tions on Computational Bi-ology and Bioinformatics, 17(1):124–135, January 2020.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic). URL https://dl.acm.org/doi/abs/10.1109/TCBB.2018.2858806.

REFERENCES 378

Zhang:2019:DPC

[ZLXL19] Yi-Yan Zhang, Qin Li,Yi Xin, and Wei-Qi Lv. Dif-ferentiating prostate cancerfrom benign prostatic hy-perplasia using PSAD basedon machine learning: Single-center retrospective study inChina. IEEE/ACM Trans-actions on ComputationalBiology and Bioinformatics,16(3):936–941, May 2019.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Zhang:2012:HSP

[ZLY+12] Yijia Zhang, Hongfei Lin,Zhihao Yang, Jian Wang,and Yanpeng Li. Hashsubgraph pairwise kernelfor protein-protein interac-tion extraction. IEEE/ACMTransactions on Computa-tional Biology and Bioinfor-matics, 9(4):1190–1202, July2012. CODEN ITCBCY.ISSN 1545-5963 (print),1557-9964 (electronic).

Zhang:2013:PCP

[ZLY+13] Yijia Zhang, Hongfei Lin,Zhihao Yang, Jian Wang,Yanpeng Li, and Bo Xu.Protein complex predictionin large ontology attributedprotein-protein interactionnetworks. IEEE/ACMTransactions on Computa-tional Biology and Bioinfor-matics, 10(3):729–741, May2013. CODEN ITCBCY.


Zhang:2006:SGR

[ZLZ06] Chaolin Zhang, Xuesong Lu,and Xuegong Zhang. Sig-nificance of gene ranking forclassification of microarraysamples. IEEE/ACM Trans-actions on ComputationalBiology and Bioinformat-ics, 3(3):312–320, July 2006.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Zhang:2019:EPH

[ZLZ+19] Xiaolong Zhang, Xiaoli Lin,Jiafu Zhao, Qianqian Huang,and Xin Xu. Efficiently pre-dicting hot spots in PPIsby combining random for-est and synthetic minor-ity over-sampling technique.IEEE/ACM Transactions onComputational Biology andBioinformatics, 16(3):774–781, May 2019. CODENITCBCY. ISSN 1545-5963(print), 1557-9964 (elec-tronic).

Zheng:2020:GEI

[ZLZ20] Jie Zheng, Jinyan Li, andYun Zheng. Guest ed-itorial for the 29th In-ternational Conference onGenome Informatics (GIW2018). IEEE/ACM Trans-actions on ComputationalBiology and Bioinformatics,17(3):726–727, May 2020.CODEN ITCBCY. ISSN

REFERENCES 379

1545-5963 (print), 1557-9964(electronic). URL https://dl.acm.org/doi/10.1109/TCBB.2020.2978606.

Zhang:2012:RRN

[ZM12] Xiuwei Zhang and BernardM. E. Moret. Refining regu-latory networks through phy-logenetic transfer of informa-tion. IEEE/ACM Transac-tions on Computational Bi-ology and Bioinformatics, 9(4):1032–1045, July 2012.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Zhou:2014:DSC

[ZMC+14] Cheng Zhou, Pieter Meysman,Boris Cule, Kris Laukens,and Bart Goethals. Dis-covery of spatially cohe-sive itemsets in three-dimensional protein struc-tures. IEEE/ACM Trans-actions on ComputationalBiology and Bioinformat-ics, 11(5):814–825, Septem-ber 2014. CODEN ITCBCY.ISSN 1545-5963 (print),1557-9964 (electronic).

Zhang:2017:DCN

[ZmCXS17] Yue Zhang, Yiu ming Che-ung, Bo Xu, and WeifengSu. Detection copy num-ber variants from NGS withsparse and smooth con-straints. IEEE/ACM Trans-actions on ComputationalBiology and Bioinformatics,14(4):856–867, July 2017.


Zeller:2014:GAP

[ZMP+14] Michael Zeller, Christophe N.Magnan, Vishal R. Patel,Paul Rigor, Leonard Sender,and Pierre Baldi. A ge-nomic analysis pipeline andits application to pediatriccancers. IEEE/ACM Trans-actions on ComputationalBiology and Bioinformat-ics, 11(5):826–839, Septem-ber 2014. CODEN ITCBCY.ISSN 1545-5963 (print),1557-9964 (electronic).

Zarai:2018:CAC

[ZMST18] Yoram Zarai, Michael Mar-galiot, Eduardo D. Sontag,and Tamir Tuller. Control-lability analysis and controlsynthesis for the ribosomeflow model. IEEE/ACMTransactions on Computa-tional Biology and Bioin-formatics, 15(4):1351–1364,July 2018. CODEN ITCBCY.ISSN 1545-5963 (print),1557-9964 (electronic).

Zarai:2013:EES

[ZMT13] Yoram Zarai, Michael Mar-galiot, and Tamir Tuller.Explicit expression for thesteady-state translation ratein the infinite-dimensionalhomogeneous ribosome flowmodel. IEEE/ACM Trans-actions on ComputationalBiology and Bioinformatics,

REFERENCES 380


Zarai:2014:MPT

[ZMT14] Yoram Zarai, Michael Mar-galiot, and Tamir Tuller.Maximizing protein transla-tion rate in the ribosomeflow model: the homoge-neous case. IEEE/ACMTransactions on Computa-tional Biology and Bioin-formatics, 11(6):1184–1195,November 2014. CODENITCBCY. ISSN 1545-5963(print), 1557-9964 (elec-tronic).

Zou:2013:BNM

[Zou13] Yi Ming Zou. Boolean net-works with multiexpressionsand parameters. IEEE/ACMTransactions on Computa-tional Biology and Bioinfor-matics, 10(3):584–592, May2013. CODEN ITCBCY.ISSN 1545-5963 (print),1557-9964 (electronic).

Zhu:2010:IFP

[ZOZ10] Zexuan Zhu, Yew-Soon Ong,and Jacek M. Zurada. Iden-tification of full and par-tial class relevant genes.IEEE/ACM Transactions onComputational Biology andBioinformatics, 7(2):263–277, April 2010. CODENITCBCY. ISSN 1545-5963(print), 1557-9964 (elec-tronic).

Zhang:2019:BNC

[ZPW+19] Lu Zhang, Qiuping Pan,Yue Wang, Xintao Wu, andXinghua Shi. Bayesiannetwork construction andgenotype-phenotype infer-ence using GWAS statis-tics. IEEE/ACM Transac-tions on Computational Bi-ology and Bioinformatics,16(2):475–489, March 2019.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic). URL https://dl.acm.org/doi/abs/10.1109/TCBB.2017.2779498.

Zhang:2019:DPD

[ZRK19] Huanan Zhang, David Roe,and Rui Kuang. Detectingpopulation-differentiation copynumber variants in humanpopulation tree by sparsegroup selection. IEEE/ACMTransactions on Computa-tional Biology and Bioin-formatics, 16(2):538–549,March 2019. CODENITCBCY. ISSN 1545-5963(print), 1557-9964 (elec-tronic). URL https://dl.acm.org/doi/abs/10.1109/TCBB.2017.2779481.

Zhou:2018:BNR

[ZS18] Jie Zhou and Yuan-YuanShi. A bipartite networkand resource transfer-basedapproach to infer lncRNA-environmental factor associ-ations. IEEE/ACM Trans-actions on ComputationalBiology and Bioinformatics,

REFERENCES 381

15(3):753–759, May 2018.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Zhong:2019:FEF

[ZS19] Hua Zhong and MingzhouSong. A fast exact func-tional test for directional as-sociation and cancer biologyapplications. IEEE/ACMTransactions on Computa-tional Biology and Bioinfor-matics, 16(3):818–826, May2019. CODEN ITCBCY.ISSN 1545-5963 (print),1557-9964 (electronic).

Zhou:2010:FNN

[ZSC+10] Jianjun Zhou, Jorg Sander,Zhipeng Cai, Lusheng Wang,and Guohui Lin. Find-ing the nearest neighborsin biological databases us-ing less distance computa-tions. IEEE/ACM Transac-tions on Computational Bi-ology and Bioinformatics, 7(4):669–680, October 2010.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Zhao:2008:ICG

[ZSD08] Wentao Zhao, Erchin Ser-pedin, and Edward R.Dougherty. Inferring connec-tivity of genetic regulatorynetworks using information-theoretic criteria. IEEE/ACM Transactions on Com-putational Biology and Bioin-formatics, 5(2):262–274, April


Zhan:2014:PEM

[ZSY+14] Choujun Zhan, Wuchao Situ,Lam Fat Yeung, Peter Wai-Ming Tsang, and GenkeYang. A parameter estima-tion method for biologicalsystems modelled by ODE/DDE models using splineapproximation and differ-ential evolution algorithm.IEEE/ACM Transactionson Computational Biologyand Bioinformatics, 11(6):1066–1076, November 2014.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Zhu:2013:EAZ

[ZW13] Daming Zhu and LushengWang. An exact algo-rithm for the zero exemplarbreakpoint distance prob-lem. IEEE/ACM Transac-tions on Computational Bi-ology and Bioinformatics,10(6):1469–1477, November2013. CODEN ITCBCY.ISSN 1545-5963 (print),1557-9964 (electronic).

Zhang:2019:IFI

[ZW19] Wei Zhang and Shu-LinWang. An integrated frame-work for identifying mutateddriver pathway and cancerprogression. IEEE/ACMTransactions on Computa-tional Biology and Bioin-

REFERENCES 382

formatics, 16(2):455–464,March 2019. CODENITCBCY. ISSN 1545-5963(print), 1557-9964 (elec-tronic). URL https://dl.acm.org/doi/abs/10.1109/TCBB.2017.2788016.

Zhang:2015:III

[ZWC15] Xian Zhang, Ligang Wu,and Shaochun Cui. Animproved integral inequal-ity to stability analysis ofgenetic regulatory networkswith interval time-varyingdelays. IEEE/ACM Trans-actions on ComputationalBiology and Bioinformatics,12(2):398–409, March 2015.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Zhang:2017:CFG

[ZWcF17] Jing Zhang, Hao Wang, andWu chun Feng. cuBLASTP:Fine-grained parallelizationof protein sequence search onCPU + GPU. IEEE/ACMTransactions on Computa-tional Biology and Bioinfor-matics, 14(4):830–843, July2017. CODEN ITCBCY.ISSN 1545-5963 (print),1557-9964 (electronic).

Zhong:2017:PII

[ZWD+17] Jiancheng Zhong, JianxingWang, Xiaojun Ding, ZhenZhang, Min Li, Fang-XiangWu, and Yi Pan. Proteininference from the integra-tion of tandem MS data

and interactome networks.IEEE/ACM Transactionson Computational Biologyand Bioinformatics, 14(6):1399–1409, November 2017.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Zheng:2020:IIC

[ZWDR20] Huiru Zheng, Haiying Wang,Richard J. Dewhurst, andRainer Roehe. Improv-ing the inference of co-occurrence networks in thebovine rumen microbiome.IEEE/ACM Transactions onComputational Biology andBioinformatics, 17(3):858–867, May 2020. CODENITCBCY. ISSN 1545-5963(print), 1557-9964 (elec-tronic). URL https://dl.acm.org/doi/10.1109/TCBB.2018.2879342.

Zhang:2017:MOP

[ZwGC17] Yong Zhang, Dun wei Gong,and Jian Cheng. Multi-objective particle swarm op-timization approach for cost-based feature selection inclassification. IEEE/ACMTransactions on Computa-tional Biology and Bioinfor-matics, 14(1):64–75, January2017. CODEN ITCBCY.ISSN 1545-5963 (print),1557-9964 (electronic).

Zhang:2019:MLP

[ZWHC19] Li Zhang, Ho-Chun Wu,Cheuk-Hei Ho, and Shing-

REFERENCES 383

Chow Chan. A multi-Laplacian prior and aug-mented Lagrangian approachto the exploratory anal-ysis of time-varying geneand transcriptional regula-tory networks for gene mi-croarray data. IEEE/ACMTransactions on Computa-tional Biology and Bioin-formatics, 16(6):1816–1829,November 2019. CODENITCBCY. ISSN 1545-5963(print), 1557-9964 (elec-tronic). URL https://dl.acm.org/doi/abs/10.1109/TCBB.2018.2828810.

Zhao:2011:ASB

[ZWL11] Liang Zhao, Limsoon Wong,and Jinyan Li. Antibody-specified B-cell epitope pre-diction in line with the prin-ciple of context-awareness.IEEE/ACM Transactionson Computational Biologyand Bioinformatics, 8(6):1483–1494, November 2011.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Zeng:2012:HES

[ZWL+12] Nianyin Zeng, Zidong Wang,Yurong Li, Min Du, and Xi-aohui Liu. A hybrid EKFand switching PSO algo-rithm for joint state and pa-rameter estimation of lat-eral flow immunoassay mod-els. IEEE/ACM Transac-tions on Computational Bi-ology and Bioinformatics, 9


Zhang:2014:SBN

[ZWL14a] Hao Zhang, Xingyuan Wang,and Xiaohui Lin. Syn-chronization of Boolean net-works with different updateschemes. IEEE/ACM Trans-actions on ComputationalBiology and Bioinformat-ics, 11(5):965–972, Septem-ber 2014. CODEN ITCBCY.ISSN 1545-5963 (print),1557-9964 (electronic).

Zhao:2014:DPC

[ZWL+14b] Bihai Zhao, Jianxin Wang,Min Li, Fang-Xiang Wu,and Yi Pan. Detectingprotein complexes basedon uncertain graph model.IEEE/ACM Transactions onComputational Biology andBioinformatics, 11(3):486–497, May 2014. CODENITCBCY. ISSN 1545-5963(print), 1557-9964 (elec-tronic).

Zhang:2015:SAS

[ZWL15] Hao Zhang, Xingyuan Wang,and Xiaohui Lin. Syn-chronization of asynchronousswitched Boolean network.IEEE/ACM Transactionson Computational Biologyand Bioinformatics, 12(6):1449–1456, November 2015.CODEN ITCBCY. ISSN

REFERENCES 384


Zhang:2020:TSD

[ZWM+20] Gui-Jun Zhang, Xiao-QiWang, Lai-Fa Ma, Liu-Jing Wang, Jun Hu, andXiao-Gen Zhou. Two-stage distance feature-basedoptimization algorithm forDe novo protein structureprediction. IEEE/ACMTransactions on Computa-tional Biology and Bioin-formatics, 17(6):2119–2130,November 2020. CODENITCBCY. ISSN 1545-5963(print), 1557-9964 (elec-tronic). URL https://dl.acm.org/doi/10.1109/TCBB.2019.2917452.

Zhang:2018:CTC

[ZWS+18] Lijun Zhang, Ming Wang,Nicholas W. Sterling, Eun-Young Lee, Paul J. Eslinger,Daymond Wagner, Guang-wei Du, Mechelle M. Lewis,Young Truong, F. DuBoisBowman, and Xuemei Huang.Cortical thinning and cogni-tive impairment in Parkin-son’s disease without demen-tia. IEEE/ACM Transac-tions on Computational Bi-ology and Bioinformatics,15(2):570–580, March 2018.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Zhang:2012:NUF

[ZWSX12] Shaohong Zhang, Hau-San

Wong, Ying Shen, andDongqing Xie. A new un-supervised feature rankingmethod for gene expressiondata based on consensusaffinity. IEEE/ACM Trans-actions on ComputationalBiology and Bioinformatics,9(4):1257–1263, July 2012.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Zheng:2017:AOI

[ZWW17] Huiru Zheng, ChaoyangWang, and Haiying Wang.Analysis of organization ofthe interactome using dom-inating sets: a case studyon cell cycle interaction net-works. IEEE/ACM Trans-actions on ComputationalBiology and Bioinformatics,14(2):282–289, March 2017.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Zhang:2020:LPL

[ZWXL20] Tianyi Zhang, MinghuiWang, Jianing Xi, andAo Li. LPGNMF: Predict-ing long non-coding RNAand protein interaction us-ing graph regularized non-negative matrix factoriza-tion. IEEE/ACM Transac-tions on Computational Bi-ology and Bioinformatics, 17(1):189–197, January 2020.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic). URL https:/

REFERENCES 385


Zhu:2010:FSG

[ZWY+10] Shenghuo Zhu, DingdingWang, Kai Yu, Tao Li,and Yihong Gong. Featureselection for gene expres-sion using model-based en-tropy. IEEE/ACM Trans-actions on ComputationalBiology and Bioinformatics,7(1):25–36, January 2010.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Zhang:2016:GAS

[ZWZ16] Xian Zhang, Ligang Wu,and Jiahua Zou. Globallyasymptotic stability analy-sis for genetic regulatory net-works with mixed delays: anM -matrix-based approach.IEEE/ACM Transactions onComputational Biology andBioinformatics, 13(1):135–147, January 2016. CODENITCBCY. ISSN 1545-5963(print), 1557-9964 (elec-tronic).

Zhang:2016:MCS

[ZWZS16] Jingsong Zhang, YinglinWang, Chao Zhang, andYongyong Shi. Mining con-tiguous sequential genera-tors in biological sequences.IEEE/ACM Transactionson Computational Biologyand Bioinformatics, 13(5):855–867, September 2016.CODEN ITCBCY. ISSN


Zhao:2011:ASM

[ZXB11] Wenqi Zhao, Guoliang Xu,and Chandrajit L. Ba-jaj. An algebraic splinemodel of molecular surfacesfor energetic computations.IEEE/ACM Transactionson Computational Biologyand Bioinformatics, 8(6):1458–1467, November 2011.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Zhang:2018:CDE

[ZXLZ18a] Wei Zhang, Jia Xu, YuanyuanLi, and Xiufen Zou. Correc-tion to “Detecting EssentialProteins Based on NetworkTopology, Gene ExpressionData, and Gene OntologyInformation”. IEEE/ACMTransactions on Computa-tional Biology and Bioin-formatics, 15(3):1035, May2018. CODEN ITCBCY.ISSN 1545-5963 (print),1557-9964 (electronic). See[ZXLZ18b].

Zhang:2018:DEP

[ZXLZ18b] Wei Zhang, Jia Xu, YuanyuanLi, and Xiufen Zou. De-tecting essential proteinsbased on network topol-ogy, gene expression data,and gene ontology informa-tion. IEEE/ACM Transac-tions on Computational Bi-ology and Bioinformatics, 15

REFERENCES 386

(1):109–116, January 2018.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic). See correction[ZXLZ18a].

Zhang:2020:PEP

[ZXZ20] Wei Zhang, Jia Xu, and Xi-ufen Zou. Predicting es-sential proteins by integrat-ing network topology, sub-cellular localization informa-tion, gene expression pro-file and GO annotation data.IEEE/ACM Transactionson Computational Biologyand Bioinformatics, 17(6):2053–2061, November 2020.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic). URL https://dl.acm.org/doi/10.1109/TCBB.2019.2916038.

Zhao:2020:MNM

[ZY20] Lan Zhao and Hong Yan.MCNF: a novel methodfor cancer subtyping by in-tegrating multi-omics andclinical data. IEEE/ACMTransactions on Computa-tional Biology and Bioin-formatics, 17(5):1682–1690,September 2020. CODENITCBCY. ISSN 1545-5963(print), 1557-9964 (elec-tronic). URL https://dl.acm.org/doi/10.1109/TCBB.2019.2910515.

Zhou:2018:STM

[ZYF+18] Xichuan Zhou, Fan Yang,Yujie Feng, Qin Li, FangTang, Shengdong Hu, Zhi

Lin, and Lei Zhang. Aspatial-temporal method todetect global influenza epi-demics using heterogeneousdata collected from the In-ternet. IEEE/ACM Trans-actions on ComputationalBiology and Bioinformatics,15(3):802–812, May 2018.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Zhou:2019:CCK

[ZYN+19] Huiwei Zhou, Yunlong Yang,Shixian Ning, Zhuang Liu,Chengkun Lang, Yingyu Lin,and Degen Huang. Combin-ing context and knowledgerepresentations for chemical-disease relation extraction.IEEE/ACM Transactionson Computational Biologyand Bioinformatics, 16(6):1879–1889, November 2019.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic). URL https://dl.acm.org/doi/abs/10.1109/TCBB.2018.2838661.

Zhou:2013:MAD

[ZYW+13] Xiaowei Zhou, Can Yang, Xi-ang Wan, Hongyu Zhao, andWeichuan Yu. Multisam-ple aCGH data analysis viatotal variation and spectralregularization. IEEE/ACMTransactions on Computa-tional Biology and Bioin-formatics, 10(1):230–235,January 2013. CODENITCBCY. ISSN 1545-5963

REFERENCES 387


Zhang:2017:PCI

[ZYW17] Jianhua Zhang, Zhong Yin,and Rubin Wang. Pat-tern classification of instan-taneous cognitive task-loadthrough GMM clustering,Laplacian eigenmap, and en-semble SVMs. IEEE/ACMTransactions on Computa-tional Biology and Bioinfor-matics, 14(4):947–965, July2017. CODEN ITCBCY.ISSN 1545-5963 (print),1557-9964 (electronic).

Zhang:2013:SAM

[ZZ13] Wei Zhang and XiufenZou. Systematic anal-ysis of the mechanismsof virus-triggered Type IIFN signaling pathwaysthrough mathematical mod-eling. IEEE/ACM Trans-actions on ComputationalBiology and Bioinformatics,10(3):771–779, May 2013.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Zheng:2014:EIL

[ZZ14] Yu Zheng and LouxinZhang. Effect of incom-plete lineage sorting on tree-reconciliation-based infer-ence of gene duplication.IEEE/ACM Transactions onComputational Biology andBioinformatics, 11(3):477–485, May 2014. CODEN


Zhang:2015:NMD

[ZZ15] Wei Zhang and Xiufen Zou.A new method for detect-ing protein complexes basedon the three node cliques.IEEE/ACM Transactions onComputational Biology andBioinformatics, 12(4):879–886, July 2015. CODENITCBCY. ISSN 1545-5963(print), 1557-9964 (elec-tronic).

Zhang:2018:DMD

[ZZ18] Junhua Zhang and ShihuaZhang. The discovery ofmutated driver pathways incancer: Models and algo-rithms. IEEE/ACM Trans-actions on ComputationalBiology and Bioinformatics,15(3):988–998, May 2018.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Zhang:2020:CCM

[ZZ20] Lihua Zhang and Shi-hua Zhang. Compari-son of computational meth-ods for imputing single-cell RNA-sequencing data.IEEE/ACM Transactions onComputational Biology andBioinformatics, 17(2):376–389, March 2020. CODENITCBCY. ISSN 1545-5963(print), 1557-9964 (elec-tronic). URL https:/

REFERENCES 388


Zhang:2020:WSC

[ZZBH20] Qinhu Zhang, Lin Zhu, Wen-zheng Bao, and De-ShuangHuang. Weakly-supervisedconvolutional neural net-work architecture for pre-dicting protein–DNA bind-ing. IEEE/ACM Transac-tions on Computational Bi-ology and Bioinformatics,17(2):679–689, March 2020.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic). URL https://dl.acm.org/doi/abs/10.1109/TCBB.2018.2864203.

Zhang:2019:IMH

[ZZCD19] Jingpu Zhang, Zuping Zhang,Zhigang Chen, and LeiDeng. Integrating mul-tiple heterogeneous net-works for novel LncRNA-disease association infer-ence. IEEE/ACM Trans-actions on ComputationalBiology and Bioinformatics,16(2):396–406, March 2019.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic). URL https://dl.acm.org/doi/abs/10.1109/TCBB.2017.2701379.

Zeng:2010:SSC

[ZZCY10] Jia Zeng, Xiao-Yu Zhao,Xiao-Qin Cao, and HongYan. SCS: Signal, con-text, and structure fea-tures for genome-wide hu-man promoter recognition.


Zhu:2013:ISI

[ZZDW13] Yuan Zhu, Xiao-Fei Zhang,Dao-Qing Dai, and Meng-Yun Wu. Identifying spu-rious interactions and pre-dicting missing interactionsin the protein-protein in-teraction networks via agenerative network model.IEEE/ACM Transactions onComputational Biology andBioinformatics, 10(1):219–225, January 2013. CODENITCBCY. ISSN 1545-5963(print), 1557-9964 (elec-tronic).

Zhu:2013:IDB

[ZZDY13] Yuan Zhu, Weiqiang Zhou,Dao-Qing Dai, and HongYan. Identification ofDNA-binding and protein-binding proteins using en-hanced graph wavelet fea-tures. IEEE/ACM Trans-actions on ComputationalBiology and Bioinformatics,10(4):1017–1031, July 2013.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Zhang:2019:KLS

[ZZF+19] Zuping Zhang, Jingpu Zhang,Chao Fan, Yongjun Tang,

REFERENCES 389

and Lei Deng. KAT-ZLGO: Large-scale predic-tion of LncRNA functionsby using the KATZ mea-sure based on multiple net-works. IEEE/ACM Trans-actions on ComputationalBiology and Bioinformatics,16(2):407–416, March 2019.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic). URL https://dl.acm.org/doi/abs/10.1109/TCBB.2017.2704587.

Zhang:2018:DED

[ZZH18a] Hongbo Zhang, Lin Zhu,and De-Shuang Huang. Dis-cMLA: an efficient discrim-inative Motif learning algo-rithm over high-throughputdatasets. IEEE/ACM Trans-actions on ComputationalBiology and Bioinformatics,15(6):1810–1820, November2018. CODEN ITCBCY.ISSN 1545-5963 (print),1557-9964 (electronic).

Zhu:2018:LLM

[ZZH18b] Lin Zhu, Hong-Bo Zhang,and De-Shuang Huang.LMMO: a large margin ap-proach for refining regula-tory motifs. IEEE/ACMTransactions on Computa-tional Biology and Bioinfor-matics, 15(3):913–925, May2018. CODEN ITCBCY.ISSN 1545-5963 (print),1557-9964 (electronic).

Zhang:2019:HOC

[ZZH19] Qinhu Zhang, Lin Zhu, andDe-Shuang Huang. High-order convolutional neuralnetwork architecture for pre-dicting DNA-protein bindingsites. IEEE/ACM Transac-tions on Computational Bi-ology and Bioinformatics, 16(4):1184–1192, July 2019.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Zamanighomi:2018:GRN

[ZZKW18] Mahdi Zamanighomi, MostafaZamanian, Michael Kim-ber, and Zhengdao Wang.Gene regulatory network in-ference from perturbed time-series expression data viaordered dynamical expan-sion of non-steady state ac-tors. IEEE/ACM Transac-tions on Computational Bi-ology and Bioinformatics, 15(4):1093–1106, July 2018.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Zhang:2017:AIB

[ZZM17] Kuize Zhang, Lijun Zhang,and Shaoshuai Mou. Anapplication of invertibilityof Boolean control net-works to the control ofthe mammalian cell cy-cle. IEEE/ACM Transac-tions on Computational Bi-ology and Bioinformatics, 14(1):225–229, January 2017.CODEN ITCBCY. ISSN

REFERENCES 390


Zheng:2011:MBS

[ZZN+11a] Chun-Hou Zheng, Lei Zhang,To-Yee Ng, Chi KeungShiu, and De-Shuang Huang.Metasample-based sparserepresentation for tumorclassification. IEEE/ACMTransactions on Computa-tional Biology and Bioin-formatics, 8(5):1273–1282,September 2011. CODENITCBCY. ISSN 1545-5963(print), 1557-9964 (elec-tronic).

Zheng:2011:MPD

[ZZN+11b] Chun-Hou Zheng, Lei Zhang,Vincent To-Yee Ng, Chi Ke-ung Shiu, and D.-S. Huang.Molecular pattern discoverybased on penalized matrixdecomposition. IEEE/ACMTransactions on Computa-tional Biology and Bioin-formatics, 8(6):1592–1603,November 2011. CODENITCBCY. ISSN 1545-5963(print), 1557-9964 (elec-tronic).

Zhang:2015:FMA

[ZZN15] Shuqin Zhang, Hongyu Zhao,and Michael K. Ng. Func-tional module analysis forgene coexpression networkswith network integration.IEEE/ACM Transactionson Computational Biologyand Bioinformatics, 12(5):1146–1160, September 2015.


Zhang:2019:MPM

[ZZRPZ19] Xuan Zhang, Quan Zou, Al-fonso Rodriguez-Paton, andXiangxiang Zeng. Meta-path methods for prioritiz-ing candidate disease miR-NAs. IEEE/ACM Transac-tions on Computational Bi-ology and Bioinformatics, 16(1):283–291, January 2019.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Zheng:2007:RNA

[ZZS07] Chunfang Zheng, Qian Zhu,and David Sankoff. Re-moving noise and ambi-guities from comparativemaps in rearrangement anal-ysis. IEEE/ACM Transac-tions on Computational Bi-ology and Bioinformatics, 4(4):515–522, October 2007.CODEN ITCBCY. ISSN1545-5963 (print), 1557-9964(electronic).

Zhang:2018:EMS

[ZZS18] Yue Zhang, Chunfang Zheng,and David Sankoff. Evolu-tionary model for the sta-tistical divergence of paral-ogous and orthologous genepairs generated by wholegenome duplication and spe-ciation. IEEE/ACM Trans-actions on ComputationalBiology and Bioinformatics,

REFERENCES 391


Zhang:2017:EPC

[ZZY+17] Gui-Jun Zhang, Xiao-GenZhou, Xu-Feng Yu, Xiao-HuHao, and Li Yu. Enhanc-ing protein conformationalspace sampling using dis-tance profile-guided differen-tial evolution. IEEE/ACMTransactions on Computa-tional Biology and Bioin-formatics, 14(6):1288–1301,November 2017. CODENITCBCY. ISSN 1545-5963(print), 1557-9964 (elec-tronic).

Zhang:2017:FAE

[ZZZC17] Bei Zhang, Yu-Jun Zheng,Min-Xia Zhang, and Sheng-Yong Chen. Fireworks al-gorithm with enhanced fire-works interaction. IEEE/ACM Transactions on Com-putational Biology and Bioin-formatics, 14(1):42–55, Jan-uary 2017. CODEN ITCBCY.ISSN 1545-5963 (print),1557-9964 (electronic).

Zhang:2019:FSS

[ZZZW19] Jie Zhang, Zhigen Zhao,Kai Zhang, and Zhi Wei.A feature sampling strat-egy for analysis of highdimensional genomic data.IEEE/ACM Transactions onComputational Biology andBioinformatics, 16(2):434–

441, March 2019. CODENITCBCY. ISSN 1545-5963(print), 1557-9964 (elec-tronic). URL https://dl.acm.org/doi/abs/10.1109/TCBB.2017.2779492.