Publications Abd Allah, A; Wang, P; Richt, J; Sreevatsan, S. 2012 Y145Stop is sufficient to induce de novo generation of prions. Prion. 6(1):81 8.

Abrahante, J; Johnson, TJ; Hunter, S; and Maheswaran, S; Haugland, M; Bayles, D; and Briggs, R. 2012. Draft genome sequences of two virulent serotypes of avian Pasteurella multocida. Journal of Bacteriology, October.

Andersen, M; Alston, J; Pardey, P. 2012. Capital use intensity and productivity biases. Journal of Productivity Analysis; 37(1):59 71.

Anderson, JA; Wiersma, JJ; Linkert, GL; Kolmer, JA; Jin, Y; Dill Macky, R; Wiersma, JV; Hareland, GA; and Busch, RH. 2012. Registration of Sabin Wheat. J. Plant Registrations 6:174 179.

Anderson, JA; Wiersma, JJ; Linkert, GL; Kolmer, JA; Jin, Y; Dill Macky, R; Wiersma, JV; Hareland, GA; and Busch, RH. 2012. Registration of Tom Wheat. J. Plant Registrations 6:180 185.

Anderson, MZ; Baller, JA; Dulmage, K; Wigen, L; and Berman, J. 2012. The three clades of the telomere associated 1 TLO gene family of Candida albicans have different splicing, localization and expression features. Eukaryotic Cell, 11(10): 1268 1275.

Aoki, T; Ward, TJ; Kistler, HC; and ODonnell, K. 2012. Systematics, phylogeny and trichothecene mycotoxin potential of Fusarium head blight pathogens. Mycotoxins 62: 91 102.

Ashfield, T; Egan, AN; Pfeil, BE; Chen, NWG; Podicheti, R; Ratnaparkhe, MB; Ameline Torregrosa, C; Denny, R; Cannon, S; Doyle, JJ; Geffroy, V; Roe, BA; Saghai Maroof, MA; Young, ND; Innes, RW. 2012. The impact of polyploidy on the evolution of a complex NB LRR resistance gene cluster in soybean. Plant Physiology 159: 344 354.

Asplen, M; Bruns, E; David, A; Denison, RF; Epstein, B; Kaiser, MC; Kaser, JM; Lacroix, L; Mohl, EK; Quiram, G; et al. 2012. Do trade offs have explanatory power for the evolution of organismal interactions? Evolution; 66(5):1297 1307.

Bakker, MG; Bradeen, JM; and Kinkel, LL. 2012. Effects of plant host species and plant community richness on streptomycete community structure. FEMS Microbology Ecology.

Bakker, MG; Tu, ZJ; Bradeen, JM; and Kinkel, LL. 2012. Implications of pyrosequencing error correction for biological data interpretation. PLoS ONE 7(8):e44357.

Bakule, P; Fleming, DG; Sukhorukov, O; Ishida, K; Pratt, F; Momose, T; Torikai, E; Mielke, SL; Garrett, BC; Peterson, KA; et al. 2012. State selected reaction of muonium with vibrationally excited H 2. Journal of Physical Chemistry Letters; 3(19):2755 2760.

Baller, JA; Gao, J; Stamenova, R; Curcio, MJ; Voytas, DF. 2012. A nucleosomal surface defines an integration hotspot for the Saccharomyces cerevisiae Ty1 retrotransposon. Genome Res. 22:704 13.

Bannantine, JP; Wu, CW; Hsu, C; Zhou, S; Schwartz, DC; Bayles, DO; Paustian, ML; Alt, DP; Sreevatsan, S; Kapur, V; Talaat, AM. 2012. Genome sequencing of ovine isolates of Mycobacterium avium subspecies paratuberculosis offers insights into host association. BMC Genomics. 13:89.

Barbieri, M; Marcel, TC; Niks, RE; Francia, E; Pasquariello, M; Mazzamurro, V; Garvin, DF; and Pecchioni, N. 2012. QTLs for resistance to the false brome rust Puccinia brachypodii in the model grass Brachypodium distachyon L. Genome 55:152 163

Barnes, AMT; Ballering, KS; Leibman, RS; Wells, CL; Dunny, GM. 2012. Enterococcus faecalis produces abundant extracellular structures containing DNA in the absence of cell lysis during early biofilm formation. MBio 3(4):e00193 12. Doi:101128/mBio00193 12.

Barney, BM; Mann, RL; Ohlert, JM. 2012. Identification of a Residue Affecting Fatty Alcohol Selectivity in Wax Ester Synthase. Applied and Environmental Microbiology. In Press.

Barney, BM; Wahlen, BD; Garner, E; Wei, J; Seefeldt, LC. 2012. Differences in Substrate Specificities of Five Bacterial Wax Ester Synthases. Applied and Environmental Microbiology. 78, pg. 5734 5745.

Barrero, JM; Jacobsen, JV; Talbot, MJ; White, RG; Swain, SM; Garvin. D.F., and Gubler, F. 2012. Analysis of seed dormancy and light quality effects on germination in Brachypodium distachyon. New Phytologist 193: 376 386.

Bedell VM, Wang Y, Campbell JM, Poshusta TL, Starker CG, Krug Ii RG, Tan W, Penheiter SG, Ma AC, Leung AY, Fahrenkrug SC, Carlson DF, Voytas DF, Clark KJ, Essner JJ, Ekker SC. 2012. In vivo genome editing using a high efficiency TALEN system. Nature.

Berger, G.L., S. Liu, M.D. Hall, W.S. Brooks, S. Chao, G.J. Muehlbauer, B. K. Baik, and C.A. Griffey. 2012. Marker trait associations in Virginia Tech winter barley identified using genome wide mapping. Theor. Appl. Genet. DOI: 10.1007/s00122 012 2011 7.

Bergerson R.J., Collier L.S., Sarver A.L., Been R.A., Lugthart S., Diers M.D., Zuber J., Rappaport A.R., Nixon M.J., Silverstein K.A., Fan D., Lamblin A.F., Wolff L., Kersey J.H., Delwel R., Lowe S.W., OSullivan M.G., Kogan S.C., Adams D.J., Largaespada D.A. 2012. An insertional mutagenesis screen identifies genes that cooperate with Mll AF9 in a murine leukemogenesis model. Blood. 119:4512 4523.

Berman, J and L. Hadany. 2012 Does stress induce (para)sex? Implications for Candida albicans evolution. Trends in Genetics, 28: 1 7.

Berman, J. 2012. Quick Guide: Candida albicans. Current Biology 22(16):R620 22.

Bernales, Varinia S.; Aleksandr V. Marenich; Renato Contreras; Christopher J. Cramer; Donald G. Truhlar. 2012. Quantum mechanical continuum solvation models for ionic liquids. Journal of Physical Chemistry B; 116(30):9122 9129.

Bethke, G., Pecher, P. Eschen Lippold, L. Tsuda, K., Katagiri, F., Glazebrook, J., Scheel, D., and Lee, J. 2012. Activation of the Arabidopsis thaliana mitogen activated protein kinase MPK11 by the flagellin derived elicitor peptide, flg22. Mol. Plant Microbe Interact 25, 471 480.

Biever J., D. Brinkman, and G. Gardner (2012) Is UVR8 the UV B Photoreceptor in Etiolated Arabidopsis Seedlings? Abstract # P11013 (Poster), Plant Biology 2012, Annual Meeting of the American Society of Plant Biologists, Austin, Texas, July 20 24, 2011.

Biliouris, Konstantinos; David Babson; Claudia Schmidt Dannert; Yiannis Kaznessis (Profiled Authors: Yiannis Kaznessis; Claudia Schmidt Dannert; David M Babson). 2012. Stochastic simulations of a synthetic bacteria yeast ecosystem. BMC Systems Biology; ():58 .

Blake V.C., J.G. Kling, P.M. Hayes, J. Jannink, S.R. Jillella, J. Lee, D.E. Matthews, S. Chao, T.J. Close, G.J. Muehlbauer, K.P. Smith, R.P. Wise and J.A. Dickerson. 2012. The Hordeum Toolbox: The Barley Coordinated Agricultural Project Genotype and Phenotype Resource. The Plant Genome 5:81 91

Bolintineanu, Dan S.; Victor Vivcharuk; Yiannis N. Kaznessis (Profiled Author: Yiannis Kaznessis). 2012. Multiscale models of the antimicrobial peptide protegrin 1 on gram negative bacteria membranes. International Journal of Molecular Sciences; 13(9):11000 11011.

Bolon, Y.E., Vance, C.P. 2012. Characterization of the Linkage Group I seed protein QTL in soybean. In: Wilson, R.F., editor. Designing Soybeans for 21st Century Markets. Urbana, Illinois: American Oil Chemists Society. p. 175 195.

Boswell PG, Carr PW, Cohen JD, Hegeman AD. 2012. Easy and accurate calculation of programmed temperature gas chromatographic retention times by back calculation of temperature and hold up time profiles. Journal of Chromatography A 1263:179 188.

Boswell, P. G., Carr, P. W., Cohen, J. D., and Hegeman, A. D. 2012. Easy and Accurate Calculation of Programmed Temperature Gas Chromatographic Retention Times by Back Calculation of Temperature and Hold up Time Profiles, J Chromatogr A, 1263: 179 88.

Botanga, C.J., Bethke, G., Chen, Z., Gallie, D.R., Fiehn, O., and Glazebrook, J. 2012. Metabolite profiling of Arabidopsis inoculated with Alternaria brassicicola reveals that ascorbate reduces disease severity. Molecular Plant Microbe Interactions. In press.

Bowman, AS; Sreevatsan, S; Killian, M; et al. 2012, July. Molecular evidence for interspecies transmission of H3N2pM/H3N2v influenza A viruses at an Ohio agricultural fair. Emerg Microbes Infect 1: e33; doi:10.1038/emi.2012.33

Brutinel, E.D. and J.A. Gralnick. 2012. Preferential utilization of D lactate by Shewanella oneidensis. Appl Environ Microbiol. 78(23):8474 6.

Brutinel, E.D. and J.A. Gralnick. 2012. Shuttling Happens: soluble flavin mediators of extracellular electron transfer in Shewanella. Appl Microbiol Biotechnol. 93(1):41 8.

Brutinel, E.D. and JA. Gralnick. 2012. Anomalies of the anaerobic TCA cycle in Shewanella oneidensis revealed by Tn seq. Mol Microbiol. 86(2):273 83.

Burrack, L.S. and Berman, J. 2012. Neocentromeres and epigenetically inherited features of centromeres. Chromosome Res. DOI 10.1007/s10577 012 9296 x.

Burrack, L.S. and Berman, J. 2012. Flexibility of centromere and kinetochore structures. Trends in Genetics. 28:204 212.

Byappanahalli, M.N., T. Yan, M. Hamilton, S. Ishii, R. S. Fujioka, R. L. Whitman, and M. J. Sadowsky. 2012. The population structure of Escherichia coli isolated from subtropical and temperate soils. Sci. Tot. Environ. 417 418:273 279.

Byung Gee Kim, Sailesh Malla, Mattheos Koffas, Romas Kazlauskas. 2012. Production of 7 O methyl aromadendrin, a medicinally valuable flavonoid, in Escherichia coli. Appl. Environ. Microbiol. 78, 684 694. doi:10.1128/AEM.06274 11

Carlson DF, Tan W, Lillico SG, Stverakova D, Proudfoot C, Christian M, Voytas DF, Long CR, Whitelaw CB, Fahrenkrug SC. 2012. Efficient TALEN mediated gene knockout in livestock. Proc Natl Acad Sci U S A.;109(43):17382 7.

Carrie A. Eberle; Benjamin M. Clasen; Neil O. Anderson; Alan G. Smith. 2012. A novel pollen tube growth assay utilizing a transmitting tract ablated Nicotiana tabacum style. Sexual Plant Reproduction. 25(1):27 37.

Caserta, E., Haemig, H.A.H. Manias, D.A., Tomsic, J., Grundy, F.J., Henkin, T.M. and Dunny, G.M. 2012. In vivo and in vitro analyses of regulation of the pheromone responsive prgQ promoter by the PrgX pheromone receptor protein. J. Bacteriol. 194(13): 3386. Doi: 10.1128/JB.00364 12.

Castell Miller, C. V., and Samac, D. A. 2012. Population genetic structure, gene flow and recombination of Cochliobolus miyabeanus on cultivated wildrice (Zizania palustris). Plant Pathology Doi: 10.1111/j.1365 3059.2011.02581.x

Castro Melchor, M., Le, H., and Hu, W S. 2012. Time series microarray data analysis. Adv. Biochem. Eng. Biotechnol., 127, 27 70. (DOI:10.1007/10_2011_116)

Cavanagh C, Chao S, Wang S, Huang BE, Stephen S et al. 2012. Genome wide comparative diversity uncovers multiple targets of selection for improvement in a worldwide sample of hexaploid wheat landrace and cultivars. In Review.

Chander Y, Jindal N, Sreevatsan S, Stallknecht DE, Goyal SM. 2012 Sep 8. Molecular and phylogenetic analysis of matrix gene of avian influenza viruses isolated from wild birds and live bird markets in the USA. Influenza Other Respi Viruses. doi: 10.1111/irv.12003. [Epub ahead of print] PubMed PMID: 22958470.

Chandola, Varun; Arindam Banerjee; Vipin Kumar. 2012. Anomaly detection for discrete sequences: A survey. IEEE Transactions on Knowledge and Data Engineering; 24(5):823 839.

Chen, C., Xiao, Y., Li, X., and Ni, M. 2012. Light regulated stomatal aperture in Arabidopsis. Molecular Plant 5(3): 566 572.

Choudhary, Swati; Maureen B. Quin; Mark A. Sanders; Ethan T. Johnson; Claudia Schmidt Dannert. 2012. Engineered protein nano compartments for targeted enzyme localization. PLoS ONE; 7(3):.

Christian ML, Demorest ZL, Starker CG, Osborn MJ, Nyquist MD, Zhang Y, Carlson DF, Bradley P, Bogdanove AJ, Voytas DF. 2012. Targeting G with TAL Effectors: A Comparison of Activities of TALENs Constructed with NN and NK Repeat Variable Di Residues.PLoS One. 7(9):e45383.

Coursolle, D. and J.A. Gralnick. 2012. Reconstruction of extracellular respiratory pathways for iron(III) reduction in Shewanella oneidensis strain MR 1. Front Microbiol. 3:56.

Cui, Y., Lee, M.Y., Huo, N., Bragg, J., Yan, L., Yuan, C., Li, C., Holditch, S.J., Xie, J., Luo, M., Li, D., Yu, J., Martin, J., Schackwitz, W., Gu, Y.Q., Vogel, J.P., Jackson, A.O., Liu, Z., and Garvin, D.F. 2012. Fine mapping of the Bsr1 barley stripe mosaic virus resistance gene in the model grass Brachypodium distachyon. PLoS ONE 7:e38333.

Curtin SJ, Kantar MB, Yoon HW, Whaley AM, Schlueter JA, Stupar RM. 2012. Co expression of soybean Dicer like genes in response to stress and development. Funct Integr Genomics, In press.

Curtin SJ, Voytas DF, Stupar RM. 2012. Genome Engineering of Crops with Designer Nucleases. Plant Genome 5: 42 50.

Dahlem TJ, Hoshijima K, Jurynec MJ, Gunther D, Starker CG, Locke AS, Weis AM, Voytas DF, Grunwald DJ. 2012. Simple methods for generating and detecting locus specific mutations induced with TALENs in the zebrafish genome. PLoS Genet. 8(8):e1002861.

Da Hye Jung, Kwon Young Choi, Eunok Jung, Wonji Choi, Hyungdon Yun, Romas J. Kazlauskas, Byung Gee Kim. 2012. Bioconversion of p coumaric acid to p hydroxystyrene using phenolic acid decarboxylase from B. amyloliquefaciens in biphasic reaction system. Appl. Environ. Microbiol. 2012, 00, 000 0000; doi: 10.1007/s00253 012 4358 8.

Dal Bosco C, Dovzhenko A, Liu X, Worner N, Rensch T, Eismann M, Eimer S, Hegermann J, Paponov IA, Ruperti B, Heberle Bors E, Touraev A, Cohen JD, Palme K. 2012. The endoplasmic reticulum localized PIN8 is a pollen specific auxin carrier involved in intracellular auxin homeostasis. Plant Journal 71:860 870.

Daniel R. Bond; Sarah M. Strycharz Glaven; Leonard M. Tender; Cesar I. Torres (Profiled Author: Daniel R Bond). 2012. On electron transport through geobacter biofilms ChemSusChem;5(6):1099 1105.

Danzeisen, J.L., Kim, H.B., Isaacson, R.E., Tu, Z.J., and Johnson, T.J. 2011. Modulations of the chicken cecal microbiome and metagenome in response to anticoccidial and growth promoter treatment. PLoS ONE 6:e27949.

Danzeisen, J.L., Wannemuehler, W., Nolan, L.K., and Johnson, T.J. 2012, Sept. Comparison of multilocus sequence analysis and virulence genotyping of Escherichia coli from live birds, retail poultry meat, and human extraintestinal infection. Accepted for publication in Avian Diseases, in press.

Davidson MB, Katou Y, Keszthelyi A, Sing TL, Xia T, Ou J, Vaisica JA, Thevakumaran N, Marjavaara L, Myers CL, Chabes A, Shirahige K, Brown GW. 2012. Endogenous DNA replication stress results in expansion of dNTP pools and a mutator phenotype. EMBO J. 2012 Jan 10;31(4):895 907.

DeLu (Tyler) Yin, Romas J. Kazlauskas. 2012. Revised molecular basis of the promiscuous carboxylic acid perhydrolase activity in serine hydrolases Chem. Eur. J. 2012, 18, 8130 9; doi:10.1002/chem.201200052

DeLu (Tyler) Yin, Vince Purpero, Ryota Fujii, Qing Jing, Romas J. Kazlauskas. 2012. New structural motif in serine hydrolases for carboxylic acid perhydrolase Chem. Eur J. In press.

Dodge, A.G., L.P. Wackett, and M.J. Sadowsky. 2012. Melamine metabolism by Rhodococcus sp. Mel. Appl. Environ. Microbiol. 78:1397 1403.

Dodge, A.G., Wackett, L.P., and M. J. Sadowsky. 2012. Plasmid localization and organization of melamine degradation genes in Rhodococcus sp. strain Mel. Appl Environ Microbiol. 78:1397 403.

Donahue M, Godden SM, Bey R, Wells S, Oakes JM, Sreevatsan S, Stabel J, Fetrow J. 2012 May. Heat treatment of colostrum on commercial dairy farms decreases colostrum microbial counts while maintaining colostrum immunoglobulin G concentrations. J Dairy Sci. 95(5):2697 702. PubMed PMID: 22541498.

Doyle EL, Booher NJ, Standage DS, Voytas DF, Brendel VP, Vandyk JK, Bogdanove AJ. 2012. TAL Effector Nucleotide Targeter (TALE NT) 2.0: tools for TAL effector design and target prediction. Nucleic Acids Res. 40:W117 22.

E. W. Krumholz, H. Yang, P. Weisenhorn, C. S. Henry, I. G. L. Libourel. 2012. Genome wide metabolic network reconstruction of the picoalga Ostreococcus. J. Exp. Bot. 63, 2353.

Eichten SR, Vaughn MW, Hermanson PJ, Springer NM. 2012. Variation in DNA methylation patterns is more common among maize inbreds than among tissues. The Plant Genome doi: 10.3835/plantgenome2012.06.0009

Ellis LBM, Wackett LP. 2012. Use of the University of Minnesota Biocatalysis/ Biodegradation Database for Study of Microbial Degradation. Microbial Informatics and Experiment, 2: 1

Emily Bruns; Martin Carson; Georgiana May (Profiled Author: Georgiana May). 2012. Pathogen and host genotype differently affectpathogen fitness through their effects on differentlife history stages. BMC Evolutionary Biology; ():135 .

Eom JS, Choi SB, Ward JM, Jeon JS. 2012. The mechanism of phloem loading in rice (Oryza sativa). Mol Cells 33: 431 438

Epstein, Brendan; Antoine Branca; Joann Mudge; Arvind K. Bharti; Roman Briskine; Andrew D. Farmer; Masayuki Sugawara; Nevin D. Young; Michael J. Sadowsky; Peter Tiffin. 2012. Population Genomics of the Facultatively Mutualistic Bacteria Sinorhizobium meliloti and S. medicae. PLoS Genetics; 8(8):.

Esther E. McGinnis; Mary H. Meyer; Alan G. Smith. 2012. Analysis of U.S. genetically engineered crop regulation and litigation. Crop Science. 52(3):991 1002.

Faghmous, James H.; Yashu Chamber; Shyam Boriah; Stefan Liess; Vipin Kumar; Frode Vikebo; Michel Dos Sontos Mesquita. 2012. A novel and scalable spatio temporal technique for ocean eddy monitoring. Proceedings of the National Conference on Artificial Intelligence; 1():281 287.

Fang Z, Gonzales AM, Durbin ML, Meyer KKT, Miller BH, Volz KM, Clegg MT, Morrell PL. 2012. Tracing the geographic origin of weedy Ipomoea purpurea (common morning glory) in the Southeastern United States. (In Review)

Fang Z, Eule Nashoba A, Powers C, Kono TY, Morrell PL, Smith KP. 2012. Comparative analysis identifies the contributions of exotic donors to disease resistance in a barley experimental population. (In Review)

Fang Z, Pyhajarvi T, Weber AL, Dawe RK, Glaubitz JC, Sanchez Gonzalez JD, Ross Ibarra C, Doebley J, Morrell PL, Ross Ibarra J. 2012. Megabase scale inversion polymorphism in the wild ancestor of maize. Genetics 191: 883 894.

Fang, Gang; Gaurav Pandey; Wen Wang; Manish Gupta; Michael Steinbach; Vipin Kumar. 2012. Mining low support discriminative patterns from dense and high dimensional data. IEEE Transactions on Knowledge and Data Engineering; 24(2):279 294.

Fang, Gang; Majda Haznadar; Wen Wang; Haoyu Yu; Michael Steinbach; Timothy R. Church; William S. Oetting; Brian van Ness; Vipin Kumar. 2012. High order SNP combinations associated with complex diseases: Efficient discovery, statistical power and functional interactions. PLoS ONE; 7(4):.

Fengli Fu; Daniel F. Voytas. 2012. Zinc Finger Database (ZiFDB) v2.0: a comprehensive database of C2H2 zinc fingers and engineered zinc finger arrays. Nucleic Acids Research; doi: 10.1093/nar/gks1167

Ferreira, J., Park, Y., Hu, W S., Ko, C.C. 2012. Multipotent progenitor cell aggregates for expansion, osteogenic differentiation and in vivo tracing with AAV vector serotype 6. Gene Therapy, (In press. 2012). doi: 10.1038/gt.2012.16.

Fink, R.C., E. P. Black, Z. Hou, M. Sugawara, M. J. Sadowsky, and F. Diez Gonzalez. 2012. Transcriptional Responses of Escherichia coli K 12 and O157:H7 Associated with Lettuce Leaves. Appl. Environ. Microbiol. 78:1752 64.

Fisk, S., A. Cuesta Marcos, L. Cistue, J. Russell, K.P Smith, P. Baenziger, Z. Bedo, A. Corey, T. Filichkin, I. Karsai, R. Waugh, P. Hayes. 2012. FR H3: A New QTL to Assist in the Development of Fall Sown Barley with Superior Low Temperature Tolerance. Theor. Appl. Genet. DOI 10.1007/s00122 012 1982 8.

Flynn, C.M., K.A. Hunt, J.A. Gralnick and F. Srienc. 2012. Construction and elementary model analysis of a metabolic model for Shewanella oneidensis MR 1. Biosystems. 107(2):120 8.

Frank, K.L., Barnes, A.M.T., Grindle, S.M., Manias, D.A., Schlievert, P.M., and Dunny, G.M. 2012. Use of Recombinase Based In Vivo Expression Technology To Characterize Enterococcus faecalis Gene Expression during Infection Identifies In Vivo Expressed Antisense RNAs and Implicates the Protease Eep in Pathogenesis. Infect. Immun. 80(2):539. DOI: 10.1128/IAI.05964 11.

Frey, P. A. and Hegeman A. D. 2012. Chemical and Stereochemical Actins of UDP galactose 4 Epimerase, Acc. Chem. Res., in press.

George, SJ, Barney, BM, Mitra, D, Igarashi, RY, Guo, Y, Dean, DR, Cramer, SP, Seefeldt, LC. 2012. EXAFS and NRVS Reveal a Conformational Distortion of the FeMo cofactor in the MoFe Nitrogenase Propargyl Alcohol Complex. Journal of Inorganic Biochemistry. 112, pages 85 92.

Gerami Nejad, Forche, A., McClellan, M., and Berman, J. 2012. Analysis of protein function in clinical Candida albicans isolates. Yeast. 29(8):303 309. PMID: 22777821; NIHMSID#390377.

Giuseppe, A., Sanseverino, W., Rombauts, S., Van der Peer, Y., Bradeen, J., Carputo, D., Frusciante, L., and Ercolano, M.R. 2012. Overview of tomato candidate pathogen recognition genes reveals important Solanum R loci dynamics. New Phytologist.

Gnanandarajah, J.S., Johnson, T.J., Kim, H.B., Abrahante, J.E., Lulich, J.P., and Murtaugh, M.P. 2012. Comparative fecal microbiota of dogs with and without calcium oxalate stones.

Goblirsch, B.R., J.A. Frias, L.P. Wackett, and C.M. Wilmot. 2012. Crystal structures of Xanthomonas campestris OleA reveal features that promote head to head condensation of two long chain fatty acids. Biochemistry 51: 4138 4146.

Gonzales AM, Fang Z, Durbin ML, Meyer KKT, Clegg MT, Morrell PL. 2012. Nucleotide sequence diversity of floral pigment genes in Mexican populations of Ipomoea purpurea (morning glory) accord with a neutral model of evolution. J of Heredity doi:10.1093/jhered/ess059

Gora PJ, Reinders, A, Ward JM. 2012. A novel fluorescent assay for sucrose transporters. Plant Methods 8: 13

Grayson T. Wawrzyn; Maureen B. Quin; Swati Choudhary; Fernando Lopez Gallego; Claudia Schmidt Dannert. 2012. Draft genome of omphalotus olearius provides a predictive framework for sesquiterpenoid natural product biosynthesis in basidiomycota. Chemistry and Biology; 19(6):772 783.

Habibollah, G., C.W. Hiebert, T. Zegeye, S. Liu, M. Dilawari, T. Tsilo, J.A. Anderson, M.N. Rouse, Y. Jin, and T. Fetch. 2012. Inheritance of resistance to Ug99 stem rust in wheat cultivar Norin 40 and genetic mapping of Sr42. Theor. Appl. Genet. 125:817 824.

Hamilton, M.J., A. R. Weingarden, M. J. Sadowsky, and A. Khoruts. 2012. Standardized Frozen Preparation for Transplantation of Fecal Microbiota for Recurrent Clostridium difficile Infection. Am. J. Gastroenterol. doi: 10.1038/ajg.2011.482. PMID: 22290405

Han, Jaebeom; Donald G. Truhlar; Jiali Gao. 2012. Optimization of the explicit polarization (X Pol) potential using a hybrid density functional. Theoretical Chemistry Accounts;131(3):1 15.

Hansen, Travis; Miki Hondzo; Mara T. Mashek; Douglas G. Mashek; Paul A. Lefebvre. 2012. Algal swimming velocities signal fatty acid accumulation. Biotechnology and Bioengineering.

Haran KP, Godden S, Boxrud D, Jawahir S, Bender JB, Sreevatsan S. 2012 Mar. Prevalence and Characterization of Staphylococcus aureus, including Methicillin Resistant Staphylococcus aureus from Bulk Tank Milk from Minnesota Dairy Farms. J Clin Microbiol. 50(3):688 95. Epub 2011 Dec 14. PubMed PMID: 22170937; PubMed Central PMCID: PMC3295154.

Hu, W S. 2012. Cell Culture Bioprocess Engineering. Ebook ( http://www.cellprocessbook.com/ ) and printed book (Amazon).

Hu, W S., Zeng, A P. 2012. Genomics and Systems Biology of Mammalian Cell Culture. Adv. Biochem. Eng. Biotechnol. Vol. 127. Springer pub.

Huang, Y., B. Millet, K. Beaubien, S. Dahl, B. Steffenson, K. Smith, G. Muehlbauer. 2012. Haplotype diversity and population structure in cultivated and wild barley evaluated for Fusarium head blight responses. Theor. Appl. Genet. DOI 10.1007/s00122 012 2006 4.

Hufford MB, Xu X, van Heerwaarden J, Pyhajarvi T, Chia J M, Cartwright RA, Elshire RJ, Glaubitz JC, Guill KE, Kaeppler SM, Lai J, Morrell PL, Shannon LM, Song C, Springer NM, Swanson Wagner RA, Tiffin P, Wang J, Zhang G, Doebley J, McMullen MD, Ware D, Buckler ES, Yang S, Ross Ibarra J. 2012. Comparative population genomics of maize domestication and improvement. Nature Genetics 44(7):808 811.

Hufford, Matthew B.; Xun Xu; Joost Van Heerwaarden; Tanja Pyhajarvi; Jer Ming Chia; Reed A. Cartwright; Robert J. Elshire; Jeffrey C. Glaubitz; Kate E. Guill; Shawn M. Kaeppler; et al. 2012. Comparative population genomics of maize domestication and improvement. Nature Genetics; 44(7):808 811.

Igarashi, D., Tsuda, K., and Katagiri, F. 2012. The Peptide Growth Factor, Phytosulfokine, Attenuates Pattern Triggered Immunity. Plant J. 71, 194 204.

Jacquemin, Denis; Yan Zhao; Rosendo Valero; Carlo Adamo; Ilaria Ciofini; Donald G. Truhlar. 2012. Verdict: Time dependent density functional theory not guilty of large errors for cyanines. Journal of Chemical Theory and Computation;8(4):1255 1259.

Jareonmit, P., M. Mehta, M. J. Sadowsky, and K. Sajjaphan. 2012. Phylogenetic and phenotypic analyses of arsenic reducing bacteria isolated from an old tin mine area in Thailand. World Journal of Microbiology and Biotechnology. doi:10.1007/s11274 012 1034 1

Ji Young Ryu, Jiyoung Seo, Joong Hoon Ahn, Michael J. Sadowsky, and Hor Gil Hur. 2012. Transcriptional Control of Isoeugenol Monooxygenase of Pseudomonas nitroreducens Jin1 in E. coli. Biosci. Biotechnol. Biochemi. 76:1891 1896.

Johnson, T.J. and Lang, K. 2012. IncA/C plasmids: an emerging threat to human and animal health? Mobile Genetic Elements 2:55 58.

Johnson, T.J., Bielek, E.M., Fortini, D., Hansen, L.H., Hasman, H., Debroy, C., Nolan, L.K., and Carattoli, A. 2012. Expansion of the IncX plasmid family for improved identification and typing of novel plasmids in drug resistant Enterobacteriaceae. Plasmid 68:43 50.

Johnson, T.J., Wannemuehler, Y.W., Kariyawasam, S., Johnson, J.R., Logue, C.M., and Nolan, L.K. 2012. Prevalence of avian pathogenic Escherichia coli strain APEC O1 genomic islands and assessment of its zoonotic potential. Journal of Bacteriology 194:2846 2853.

Jonkers, W., Dong, Y., Broz, K., and Kistler, H.C. 2012. The Wor1 like protein Fgp1 regulates pathogenicity, toxin synthesis and reproduction in the phytopathogenic fungus Fusarium graminearum. PLoS Pathogens 8(5): e1002724.

Jonkers, W., Rodriguez Estrada, A.E., Lee, K., Breakspear, A., May, G. and Kistler, H.C. 2012. Metabolome and transcriptome of the interaction between Ustilago maydis and Fusarium verticillioides in vitro. Applied and Environmental Microbiology 78: 3656 3667.

Jordan, N.R., L. Aldrich Wolfe, S.C. Huerd, D.L. Larson, and G. Muehlbauer. 2012. Soil occupancy effects of invasive and native grassland plant species on composition and diversity of mycorrhizal associations. Invasive Plant Science and Management (In press)

Joshi D, Harris NB, Waters R, Thacker T, Mathema B, Krieswirth B, Sreevatsan S. 2012 Sep 19. Single nucleotide polymorphisms in Mycobacterium bovis genome resolve phylogenetic relationships. J Clin Microbiol. [Epub ahead of print] PubMed PMID: 22993186.

Jung, H. J. G., Samac, D. A., and Sarath, G. 2012. Modifying crops to increase cell wall digestibility. Plant Sci. 185 186:65 77.

Justen VL, Fritz VA, Cohen JD. 2012. Seasonal variation in glucosinolate accumulation in turnips grown under photoselective nettings. Hort Environ Biotechnol 53:108 115.

Kamber, T., T. Lansdell, C. A. Ishimaru, V. O. Stockwell, T. H. M. Smits, and B. Duffy. 2012. Characterization of the antibacterial peptide herbicolin I biosynthetic operon in Pantoea vagans biocontrol strain C9 1 and incidence in Pantoea species. Appl. Environ. Microbiol. (in press)

Kane, A.L., D.R. Bond and J.A. Gralnick. 2012. Electrochemical analysis of Shewanella oneidensis engineered to bind gold electrodes. ACS Synth Biol. DOI: 10.1021/sb300042w

Kantar M, Betts K, Hulke BS, Stupar RM, Wyse D. 2012. Breaking Tuber Dormancy in Helianthus tuberosus L. and Interspecific Hybrids of Helianthus annuus L. x Helianthus tuberosus. Hort Sci 47:1342 1346.

Katagiri, F. 2012. Toward Predictive Biology in Plant Immunity. Induction of Resistance in Plants by Pathogens, Eds. Rodrigues, F. et al. (Universidade Federal de Vicosa, MG, Brazil), pp. 239 256. ISBN 978 85 8179 025 0.

Kauffman, C. and George Karypis. 2012. Computational Tools for Protein DNA Interactions. WIREs Data Mining and Knowledge Discovery, 2: 14 28.

Kauffman, C. Karypis, G. 2012. Coarse and Fine grained Models for Proteins: Evaluation by Decoy Discrimination. Proteins (in press).

Kawale, Jaya; Snigdhansu Chatterjee; Dominick Ormsby; Karsten Steinhaeuser; Stefan Liess; Vipin Kumar. 2012. Testing the significance of spatio temporal teleconnection patterns. Proceedings of the ACM SIGKDD International Conference on Knowledge Discovery and Data Mining; ():642 650.

Kim HB, Borewicz K, White BA, Singer RS, Sreevatsan S, Tu ZJ, Isaacson RE. 2012 Sep 6. Microbial shifts in the swine distal gut in response to the treatment with antimicrobial growth promoter, tylosin. Proc Natl Acad Sci U S A. 2012 Sep 18;109(38):15485 90. Epub PubMed PMID: 22955886; PubMed Central PMCID: PMC3458334.

Kim Y.C., Jahren N., Stone M.D., Udeshi N.D., Markowski T.W., Witthuhn B.A., Shabanowitz J., Hunt D.F. and Neil E. Olszewski N.E. 2012. Identification and Origin of N linked β D N acetylglucosamine Monosaccharide Modifications on Arabidopsis thaliana Proteins. Plant Physiol. doi: http:/ / dx. doi. org/ 10. 1104/ pp. 112. 208900

Koch E, Costanzo M, Bellay J, Deshpande R, Chatfield Reed K, Chua G, DUrso G, Andrews B, Boone C, Myers CL. 2012. Conserved rules govern genetic interaction degree across species. Genome Biology.

Konstantinos Biliouris; David Babson; Claudia Schmidt Dannert; Yiannis Kaznessis. 2012. Stochastic simulations of a synthetic bacteria yeast ecosystem. BMC Systems Biology; ():58 .

Kurbanov, Elbek K.; Hannah R. Leverentz; Donald G. Truhlar; Elizabeth A. Amin. 2012. Electrostatically embedded many body expansion for neutral and charged metalloenzyme model systems. Journal of Chemical Theory and Computation; 8(1):1 5.

Kwon young Choi, Eun Ok Jung, Da Hye Jung, Bishnu Pandey, Hyungdon Yun, Hyung yun Park, Byung gee Kim, Romas J. Kazlauskas. 2012. Cloning, expression and characterization of CYP102D1, a self sufficient P450 monooxygenases from Streptomyces avermitilis. FEBS J. 2012, 279, 1650 1662; doi: 10.1111/j.1742 4658.2011.08462.x.

Kynast, R.G., D.W. Davis, R.L. Phillips, and H.W. Rines. 2012. Gamete formation via meiotic nuclear restitution generates fertile amphiploid F1 (oat x maize) plants. Sexual Plant Reproduction 25:111 122.

L. Jean Patterson; Seraphin Kuate; Mara Daltabuit Test; Qingsheng Li; Peng Xiao; Katherine McKinnon; Janet DiPasquale; Anthony Cristillo; David Venzon; Ashley Haase; et al. 2012. Replicating adenovirus simian immunodeficiency virus (SIV) vectors efficiently prime siv specific systemic and mucosal immune responses by targeting myeloid dendritic cells and persisting in rectal macrophages, regardless of immunization route. Clinical and Vaccine Immunology; 19(5):629 637.

Lamont EA, Bannantine JP, Armien A, Sanjiv Kumar DA, Sreevatsan S. 2012. Mycobacterium avium subspecies paratuberculosis produces spores. PLoS One. 7(1):e30648. Epub 2012 Jan 24. PubMed PMID: 22292005; PubMed Central PMCID: PMC3265505.

Lamont EA, Davis WC, Eckstein T, Sreevatsan S. 2012. Mycobacterium avium subsp. paratuberculosis Induces Phagosome Acidification at the Epithelium to Promote Calcium Dependent IL 1β Production and Macrophage Recruitment. Infection and Immunity 80 (9) 3225 3235.

Lang, K.L., Danzeisen, J.L., Xu, W., and Johnson, T.J. 2012. Transcriptome mapping of pAR060302, a blaCMY 2 positive, IncA/C broad host range plasmid. Applied and Environmental Microbiology 78:3379 3386.

Le, H. Kabbur, S. Pollastrini, L. Sun, Z. Mills, K. Johnson, K. Karypis, G. and Hu, W. S. 2012. Multivariate Analysis of Cell Culture Bioprocess Data Lactate Consumption as Process Indicator. Journal of Biotechnology, Vol. 162, pp. 210 223, 2012.

Lebarbenchon C, Sreevatsan S, Lefevre T, Yang M, Ramakrishnan MA, Brown JD, Stallknecht DE. 2012 Aug 1. Reassortant influenza A viruses in wild duck populations: effects on viral shedding and persistence in water. Proc Biol Sci. 2012 Oct 7;279(1744):3967 75. Epub. PubMed PMID: 22859590; PubMed Central PMCID: PMC3427581.

Leverentz, Hannah R.; Katie A. Maerzke; Samuel J. Keasler; J. Ilja Siepmann; Donald G. Truhlar. 2012. Electrostatically embedded many body method for dipole moments, partial atomic charges, and charge transfer. Physical Chemistry Chemical Physics; 14(21):7669 7678.

Levsen, Nicholas D.; Peter Tiffin; Matthew S. Olson. 2012. Pleistocene speciation in the genus populus (salicaceae). Systematic Biology; 61(3):401 412.

Lewis IA, Shortreed MR, Hegeman AD, Markley JD. 2012. Novel NMR and MS Approaches to Metabolomics. The Handbook of Metabolomics, Methods in Pharmacology and Toxicology, Teresa Whei Mei Fan et al. Eds., Springer Science & Business Media, New York, vol. 17, 199 230, DOI 10.1007/978 1 61779 618 0_7.

Li CY, Leopold AL, Sander GW, Shanks JV, Zhao L, Gibson SI. 2012. The ORCA2 Transcription Factor Plays a Key Role in Regulation of the Terpenoid Indole Alkaloid Pathway. Submitted.

Li, L., K. Petsch, R. Shimizu, S. Liu, W.W. Xu, K. Ying, J. Yu, M.J. Scanlon, P.S. Schnable, M.C.P. Timmermans, N.M. Springer, and G.J. Muehlbauer. Mendelian and non Mendelian regulation of gene expression in the maize shoot apex. PLoS Genetics (In press).

Li, X., C. Zhu, C T. Yeh, W. Wu, F. Tian, G. Bai, E.S. Buckler, G.J. Muehlbauer, M.C.P. Timmermans, M.J. Scanlon, P.S. Schnable and J. Yu. 2012. Genic and non genic contributions to quantitative trait variation in maize as detected via GWAS. Genome Research (In press).

Li, X; Daniel J. OSullivan (Profiled Author: Daniel J OSullivan). 2012. Contribution of the Actinobacteria to the growing diversity of lantibiotics. Biotechnology Letters; ():1 13.

Liu S, Ying K, Yeh C T, Yang J, Swanson Wagner RA, Wu W, Richmond T, Gerhardt DJ, Albert TJ, Lai J, Springer NM, Nettleton D, Jeddeloh JA, Schnable PS. 2012. De Novo CNV are frequently generated via segregation of non allelic homologs. The Plant Journal 72:390 399.

Liu X, Gardner G, Cohen JD. 2012. Evaluation of the transport of indole 3 butyric acid in Arabidopsis thaliana hypocotyls by stable isotope labeling and gas chromatography mass spectrometry. Plant Physiology 158:1988 2000.

Liu X, Hegeman AD, Gardner G, and Cohen, JD. 2012. Protocol: High throughput and quantitative assays of auxin and auxin precursors from minute tissue samples, Plant Methods, 8(1): 31.

Liu, N., Y. Xu, S. Hossain, N. Huang, D. Coursolle, J.A. Gralnick and E.M. Boon. 2012. Nitric oxide regulation of cyclic di GMP synthesis and hydrolysis in Shewanella woodyi. Biochemistry. 51(10):2087 99.

Liu, X., A. D. Hegeman, G. Gardner, and J. D. Cohen. 2012. Protocol: High throughput and quantitative assays of auxin and auxin precursors from minute tissue samples. Plant Methods. 8: 31.

Liu, X., J. Wu, G. Clark, S. Lundy, M. Lim, D. Arnold, J. Chan, W. Tang, G. K. Muday, G. Gardner, and S. J. Roux. October 15, 2012. Role for apyrases in polar auxin transport in Arabidopsis, Plant Physiol. pp.112.202887.

Liu, X., L. Barkawi, G. Gardner, and J. D. Cohen. 2012. Transport of Indole 3 Butyric Acid and Indole 3 Acetic Acid in Arabidopsis Hypocotyls Using Stable Isotope Labeling, Plant Physiol. 158: 1988 2000.

Liu, Ying; Daniel R. Bond, 2012. Long distance electron transfer by G. sulfurreducens biofilms results in accumulation of reduced c type cytochromes. ChemSusChem;5(6):1047 1053.

Logue, C.M., Doetkott, C., Mangiamele, P., Wannemuehler, Y.M., Johnson, T.J., Tivendale, K.A., Li, G., Sherwood, J., and Nolan, L.K. 2012. Genotypic and phenotypic traits that distinguish neonatal meningitis Escherichia coli from fecal E. coli isolates of healthy human hosts.

Lorenz, A., Smith, K.P., and Jannink, J.L. 2012. Potential and optimization of genomic selection for Fusarium head blight resistance in six row barley. Crop Sci. 52:1609 1621.

Lukoyanov, D, Yang, Z Y, Barney, BM, Dean, DR, Seefeldt, LC, Hoffman, BM. 2012. Unification of Reaction Pathway and Kinetic Scheme for N2 reduction Catalyzed by Nitrogenase. Proceedings of the National Academy of Sciences. 109, pages 5583 5587.

Lynne, A.M., Kariyawasam, S., Wannemeuhler, Y.M., Johnson, T.J., Johnson, S.J., Sinha, A.S., Lynne, D.K., Moon H.W., Jordan D.M., Logue, C.M., Foley, S.L., and Nolan, L.K. 2012. Recombinant Iss as a potential vaccine for avian colibacillosis. Avian Diseases 56:192 199.

Makarevitch I, Thompson A, Muehlbauer GJ, Springer NM. 2012. Maize Zmbrd1 gene encodes a brassinosteroid C 6 Oxidase. PLoS One 7(1):e30798.

Marenich, Aleksandr V.; Steven V. Jerome; Christopher J. Cramer; Donald G. Truhlar. 2012. Charge model 5: An extension of hirshfeld population analysis for the accurate description of molecular interactions in gaseous and condensed phases. Journal of Chemical Theory and Computation; 8(2):527 541.

Marenich, Aleksandr V.; Wendu Ding; Christopher J. Cramer; Donald G. Truhlar. 2012. Resolution of a challenge for solvation modeling: Calculation of dicarboxylic acid dissociation constants using mixed discrete continuum solvation models. Journal of Physical Chemistry Letters; 3(11):1437 1442.

Matthew A. Andersen; Julian M. Alston; Philip G. Pardey. 2012. Erratum: Capital services in U.S. Agriculture: Concepts, comparisons, and the treatment of interest rates: An error and a correction. American Journal of Agricultural Economics; 94(5):1247 1248.

McHale LK, Haun WJ, Xu WW, Bhaskar PB, Anderson JE, Hyten DL, Gerhardt DJ, Jeddeloh JA, Stupar RM. 2012. Structural variants in the soybean genome localize to clusters of biotic stress response genes. Plant Physiol 159: 1295 1308.

Menke, J., Dong, Y., and Kistler, H.C. 2012. Fusarium graminearum Tri12p influences virulence to wheat and trichothecene accumulation. Molecular Plant Microbe Interactions 25:1408 1418.

Menzel WI, Chen W P, Hegeman AD, and Cohen JD. 2012. Qualitative and Quantitative Screening of Amino Acids in Plant Tissues. High Throughput Phenotyping in Plants: Methods and Protocols, Normanly J. Ed. Methods in Molecular Biology, vol. 918, 165 178.

Mielke, Steven L.; Donald G. Truhlar. 2012. Accelerating the convergence and reducing the variance of path integral calculations of quantum mechanical free energies by using local reference Potentials. Journal of Chemical Theory and Computation; 8(5):1589 1596.

Ming Zeng; Ashley T. Haase; Timothy W. Schacker (Profiled Authors: Ashley T Haase; Timothy W Schacker). 2012. Lymphoid tissue structure and HIV 1 infection: Life or death for T cells. Trends in Immunology; 33(6):306 314.

Ming Zeng; Mirko Paiardini; Jessica C. Engram; Greg J. Beilman; Jeffrey G. Chipman; Timothy W. Schacker; Guido Silvestri; Ashley T. Haase. 2012. Critical role of CD4 T cells in maintaining lymphoid tissue structure for immune cell homeostasis and reconstitution. Blood; 120(9):1856 4867.

Ming Zeng; Peter J. Southern; Cavan S. Reilly; Greg J. Beilman; Jeffrey G. Chipman; Timothy W. Schacker; Ashley T. Haase. 2012. Lymphoid tissue damage in HIV 1 infection depletes naive T cells and limits T cell reconstitution after antiretroviral therapy. PLoS Pathogens; 8(1):.

Mitri C, Vernick KD. 2012. Anopheles gambiae pathogen susceptibility: the intersection of genetics, immunity and ecology. Curr Opin Microbiol.

Moeller, D.A., M.A. Geber, V.M. Eckhart, & P. Tiffin. 2012. Reduced pollinator service and elevated pollen limitation at the geographic range limit of an annual plant. Ecology 93:1036 1048.

Moeller, David A.; Monica A. Geber; Vincent M. Eckhart; Peter Tiffin. 2012. Reduced pollinator service and elevated pollen limitation at the geographic range limit of an annual plant. Ecology; 93(5):1036 1048.

Molla B, Byrne M, Abley M, Mathews J, Jackson CR, Fedorka Cray P, Sreevatsan S, Wang P, Gebreyes WA. 2012. Epidemiology and Genotypic Characteristics of Methicillin Resistant Staphylococcus aureus Strains of Porcine Origin. J Clin Microbiol. 50(11):3687 93. doi: 10.1128/JCM.01971 12.

Mollov, D. Lockhart, B., Zlesak, D.C., Olszewski, N. 2012. Complete nucleotide sequence of rose yellow vein virus, a member of the family Caulimoviridae having a novel genome organization. Arch Virol DOI 10.1007/s00705 012 1547 9

Morrell PL, Buckler ES, Ross Ibarra J. 2012. Crop genomics: advances and applications. Nat Rev Genet 13: 85 96.

Mossey, P. and Das, A. 2012. Expression of Agrobacterium tumefaciens octopine Ti plasmid virB8 gene is regulated by translational coupling. Plasmid (in press).

Mulukutla, B., Crammer, M. and Hu, W. S. 2012. On metabolic shift to lactate consumption in fed batch culture of mammalian cells. Metabol. Eng. 14, 138 49. (PMID:22244936)

Nachimuthu, Santhanamoorthi; Jiali Gao; Donald G. Truhlar. 2012. A benchmark test suite for proton transfer energies and its use to test electronic structure model chemistries. Chemical Physics; 400():8 12.

Ning, X, Michael Walters, and George Karypis. 2012. Improved Machine Learning Models for Predicting Selective Compounds. Journal of Chemical Information and Modeling, 52 (1), pp. 38 50.

Okagaki, R., S. Cho, W.M. Kruger, W.W. Xu, S. Heinen and G.J. Muehlbauer. 2012. The barley UNICULM2 gene resides in a centromeric region and may be associated with signaling and stress responses. Functional & Integrative Genomics DOI 10.1007/s10142 012 0299 7.

ORourke J A, Yang S W, Miller S S et al. 2012. An RNA seq atlas of Pi deficient white lupin: a guide to phosphorus acclimation in plants. Plant Physiol. 160: in press

OSullivan, D. 2012. Developing antimicrobial dairy ingredients. Food Technology; 66(6):44 50.

Paape T, Zhou P, Branca A, Briskine R, Young ND, Tiffin P. 2012. Fine scale population recombination rates, hotspots and correlates of recombination in the Medicago truncatula genome. Genome Biology and Evolution 4: 726 737.

Paape, Timothy; Peng Zhou; Antoine Branca; Roman Briskine; Nevin Young; Peter Tiffin. 2012. Fine scale population recombination rates, hotspots, and correlates of recombination in the Medicago truncatula genome. Genome Biology and Evolution; 4(5):726 737.

Palaria, A; Ivy Johnson Kanda; Daniel J. OSullivan (Profiled Author: Daniel J OSullivan). 2012. Effect of a synbiotic yogurt on levels of fecal bifidobacteria, clostridia, and enterobacteria. Applied and Environmental Microbiology; 78(4):933 940.

Papajak, Ewa; Donald G. Truhlar. 2012. What are the most efficient basis set strategies for correlated wave function calculations of reaction energies and barrier heights. Journal of Chemical Physics; 137(6):.

Papajak, Ewa; Prasenjit Seal; Xuefei Xu; Donald G. Truhlar. 2012. Thermochemistry of radicals formed by hydrogen abstraction from 1 butanol, 2 methyl 1 propanol, and butanal. Journal of Chemical Physics; 137(10):.

Patterson, S.K., Borewicz, K., Johnson, T.J., Xu, W., and Isaacson, R.E. 2012. Characterization and differential gene expression between two phenotypic phase variants in Salmonella enterica serovar Typhimurium.

Pettengill, J.B., & D.A. Moeller. 2012. Phylogeography of speciation: allopatric divergence and secondary contact between outcrossing and selfing Clarkia. Molecular Ecology 21:4578 4592.

Pettengill, J.B., & D.A. Moeller. 2012. Tempo and mode of mating system evolution between incipient Clarkia species. Evolution 66:1210 1225.

Peverati, Roberto; Donald G. Truhlar. 2012. An improved and broadly accurate local approximation to the exchange correlation density functional: The MN12 L functional for electronic structure calculations in chemistry and physics. Physical Chemistry Chemical Physics; 14(38):13171 13174.

Peverati, Roberto; Donald G. Truhlar. 2012. Exchange correlation functional with good accuracy for both structural and energetic properties while depending only on the density and its gradient. Journal of Chemical Theory and Computation; 8(7):2310 2319.

Peverati, Roberto; Donald G. Truhlar. 2012. M11 L: A local density functional that provides improved accuracy for electronic structure calculations in chemistry and physics. Journal of Physical Chemistry Letters; 3(1):117 124.

Peverati, Roberto; Donald G. Truhlar. 2012. Performance of the M11 and M11 L density functionals for calculations of electronic excitation energies by adiabatic time dependent density functional theory. Physical Chemistry Chemical Physics; 14(32):11363 11370.

Peverati, Roberto; Donald G. Truhlar. 2012. Performance of the M11 L density functional for bandgaps and lattice constants of unary and binary semiconductors. Journal of Chemical Physics; 136(13):.

Philip A. Mudd; Mauricio A. Martins; Adam J. Ericsen; Damien C. Tully; Karen A. Power; Alex T. Bean; Shari M. Piaskowski; Lijie Duan; Aaron Seese; Adrianne D. Gladden; et al. 2012. Vaccine induced CD8 + T cells control AIDS virus replication. Nature.

Pileggi, M., S.A. Pileggi, L.R. Olchanheski, P. A. da Silva, A. M. Munoz Gonzalez, W. C. Koskinen, B. Barber, and M. J. Sadowsky. 2012. Isolation of mesotrione degrading bacteria from aquatic environments in Brazil. Chemosphere. 86:1127 1132.

Qi, Y. and Katagiri, F. 2012. Membrane microdomain may be a platform for immune signaling. Plant Signal Behavior 7, 454 456.

Quirin, E.A., Mann, H., Meyer, R.S., Traini, A., Chiusano, M.L., Litt, A., and Bradeen, J.M. 2012. Evolutionary meta analysis of Solanaceous resistance gene and Solanum resistance gene analog sequences and a practical framework for cross species comparisons. Molecular Plant Microbe Interactions 25:603 612.

R. Bender, P. Klinkenberg, Z. Jiang, B. Bauer, G. Karypis, N. Nguyen, M. Perera, B. Nikolau, and C. Carter. 2012. Function Genomics of Nectar Production in Brassicaceae. Flora, 2007(7), pp. 491 496.

Radmer, L., Tesfaye, M., Somers, D. A., Temple, S. J., Vance, C. P. and Samac, D. A. 2012. Aluminum resistance mechanisms in oat (Avena sativa L.). Plant Soil 351:121 134.

Reategui, E., E. Reynolds, L. Kasinkas, A. Aggarwal, M. J. Sadowsky, A. Aksan A, and L. P. Wackett. 2012 Silica gel encapsulated AtzA biocatalyst for atrazine biodegradation. Appl. Microbiol. Biotechnol. PMID: 22228259.

Reinders A, Sun Y, Karvonen KL, Ward JM. 2012. Identification of amino acids important for substrate specificity in sucrose transporters using gene shuffling. J Biol Chem 287 30296 30304

Reinders, A, Sivitz, AB, Ward JM. 2012. Evolution of plant sucrose uptake transporters (SUTs). Front. Plant Sci. 3: 00022

Rezwan, Ahmed, and George Karypis. 2012. Algorithms for Mining the Evolution of Conserved Relational States in Dynamic Networks. Knowledge and Information Systems (in press).

Rodriguez Estrada, A.E., Jonkers, W., Kistler, H.C. and May, G. 2012. Interactions between Fusarium verticillioides, Ustilago maydis, and Zea mays: an endophyte, a pathogen, and their shared plant host. Fungal Genetics and Biology 49: 578 587.

Romas J. Kazlauskas, Uwe T. Bornscheuer. 2012. Enzyme catalytic promiscuity: expanding the catalytic action of enzymes to new reactions. Comprehensive Chirality, H. Yamamoto, E. Carreira, vol. 7, 465 480; doi: 10.1016/B978 0 08 095167 6.00729 1

Romas J. Kazlauskas. 2012. Biology evolves to fight chemistry. Chem. Biol. 2012, 19, 435 437; doi: 10.1016/j.chembiol.2012.04.004.

Rouse, M.N., I.C. Nava, S. Chao, J.A. Anderson, and Y. Jin. 2012. Identification of markers linked to the race Ug99 effective stem rust resistance gene Sr28 in wheat (Triticum aestivum L.). Theor. Appl. Genet. 125: 877 885.

Samac, D. A., and Foster Hartnett, D. 2012. Effect of glyphosate application on foliar diseases in glyphosate tolerant alfalfa. Plant Dis. 96:1104 1110.

Sandford, E.E., Orr, M., Li, X., Zhou, H., Johnson, T.J., Kariyawasam, S., Liu, P., Nolan, L.K., and Lamont, S. 2012. Strong Concordance Between Transcriptomic Patterns of Spleen and Peripheral Blood Leukocytes in Response to Avian Pathogenic Escherichia coli.

Sandford, E.E., Orr, M., Shelby, M., Li, X., Zhou, H., Johnson, T.J., Kariyawasam, S., Liu, P., Nolan, L.K., and Lamont, S.J. 2012. Leukocyte Transcriptome from Chickens Infected with Avian Pathogenic Escherichia coli Identifies Pathways Associated with Resistance. Results In Immunology 2:44 53.

Seal, Prasenjit; Ewa Papajak; Donald G. Truhlar. 2012. Kinetics of the hydrogen abstraction from carbon 3 of 1 butanol by hydroperoxyl radical: Multi structural variational transition state calculations of a reaction with 262 conformations of the transition state. Journal of Physical Chemistry Letters; 3(2):264 271.

Seal, Prasenjit; Ewa Papajak; Tao Yu; Donald G. Truhlar. 2012. Statistical thermodynamics of 1 butanol, 2 methyl 1 propanol, and butanal. Journal of Chemical Physics;136(3):.

Seffernick, J.L., J.S. Erickson, S.M. Cameron, S. Cho, A.G. Dodge, J. Richman, M.J. Sadowsky, and L.P. Wackett. 2012. Defining the cyanuric acid hydrolase (AtzD)/barbiturase protein family. J. Bacteriol. 194:4579 4588.

Seo. ,J, J.Y. Ryu, J. Han, J. H. Ahn, M. J. Sadowsky, H.G. Hur HG, and Y. Chong. 2012. Amino acid substitutions in naphthalene dioxygenase from Pseudomonas sp. strain NCIB 9816 4 result in regio and stereo specific hydroxylation of flavanone and isoflavanone. Appl Microbiol Biotechnol. PMID: 22391970

Sharifpoor S, van Dyk D, Costanzo M, Baryshnikova A, Friesen H, Douglas AC, Youn JY, Vandersluis B, Myers CL, Papp B, Boone C, Andrews BJ. 2012. Functional wiring of the yeast kinome revealed by global analysis of genetic network motifs. Genome Res.

Shepard, S.M., Danzeisen, J.L., Isaacson, R.E., Seemann, T., Achtman, M., and Johnson, T.J. 2012. Genome sequences and phylogenetic analysis of K88 and F18 positive porcine enterotoxigenic Escherichia coli. Journal of Bacteriology 194:395 405.

Shin, S., J.A. Torres Acosta, S.J. Heinen, S. McCormick, M. Lemmens, P.M.K. Paris, F. Berthiller, G. Adam and G.J. Muehlbauer. 2012. Transgenic Arabidopsis thaliana expressing a barley UDP glucosyltransferase exhibit resistance to the mycotoxin deoxynivalenol. J. Exp. Bot. 63:4731 4740.

Shivaraju, M., Unruh, J., Slaughter, B.D., Mattingly, M., Berman, J. and Gerton J.L. 2012. Cell cycle coupled structural oscillation of centromeric nucleosomes in yeast. Cell. 150(2): 304 316.

Shu, C. C., Chatterjee, A., Hu, W. S., Ramkrishna, D. 2012. Modeling of Gene Regulatory Processes by Population Mediated Signaling. New Applications of Population Balances. Chem. Eng. Sci., 70, 188 199.

Simons, K., J.A. Anderson, M. Mergoum, J.D. Faris, D.L. Klindworth, S.S. Xu, C. Sneller, J. B. Ohm, G.A. Hareland, M.C. Edwards, and S. Chao. 2012. Genetic mapping analysis of bread making quality traits in spring wheat. Crop Sci. 52:2182 2197.

Smadbeck, P.; Y.N. Kaznessis. 2012. Efficient moment matrix generation for arbitrary chemical networks. Chemical Engineering Science; 84():612 618.

Song, Z,, Vail. A., Sadowsky, M.J., Schilling, J.S. 2012. Competition between two wood degrading fungi with distinct influences on residues. FEMS Microbiol Ecol. 79:109 17.

Spartz, A.K., S.H. Lee, J.P. Wenger, N. Gonzalez, H. Itoh, D. Inze, W.A. Peer, A.S. Murphy, P. Overvoorde, and W.M. Gray. 2012. The SAUR19 subfamily of SMALL AUXIN UP RNA genes promote cell expansion. Plant J. 70:978 90.

Springer NM. Epigenetics and crop improvement. 2012. Trends in Genetics doi:pii: S0168 9525(12)00168 0.

Stanton Geddes, John; Peter Tiffin; Ruth G. Shaw. 2012. Role of climate and competitors in limiting fitness across range edges of an annual plant. Ecology; 93(7):1604 1613.

Stanton Geddes, John; Ruth G. Shaw; Peter Tiffin. 2012. Interactions between soil habitat and geographic range location affect plant fitness. PLoS ONE; 7(5):.

Steiner E., Efroni I., Gopalraj M., Saathoff K., Tseng, T S*, Kieffer M., Eshed Y., Olszewski N.E., Weiss D. 2012. The Arabidopsis O GlcNAc transferase SPINDLY interacts with class I TCPs to facilitate cytokinin responses in leaves and flowers. The Plant Cell 24: 96 108.; doi:10.1105/tpc.111.093518

Stephen R. Keller; Nicholas Levsen; Matthew S. Olson; Peter Tiffin. 2012. Local adaptation in the flowering time gene network of balsam poplar, populus balsamifera L. Molecular Biology and Evolution; 29(10):3143 3152.

Sun Y, Lin Z, Reinders A, Ward JM. 2012. Functionally important amino acids in rice sucrose transporter OsSUT1 Biochemistry 51: 3284 3291

Sun Y, Ward JM. 2012. Arg188 in rice sucrose transporter OsSUT1 is crucial for substrate transport. BMC Biochemistry (in press)

Sun, X., Kang, X., and Ni, M. 2012. Hypersensitive to Red and Blue 1 and its modification by Protein Phosphatase 7 are implicated in the control of Arabidopsis stomatal aperture. PLoS Genetics 8(5): e1002674.

Sun, Xiaoqing. 2012. Dissecting the mechanism for regulation of hydrogenase gene expression in the green alga Chlamydomonas reinhardtii using the RSP3 reporter. Ph.D. Thesis, University of Minnesota.

Susana Goncalves; Stephen P. Miller; Maria A. Carrondo; Anthony M. Dean; Pedro M. Matias (Profiled Authors: Antony M Dean; Stephen P Miller). 2012. Induced fit and the catalytic mechanism of isocitrate dehydrogenase. Biochemistry; 51(36):7098 7115.

Swanson Wagner RA, Briskine R, Schaefer R, Hufford MB, Ross Ibarra J, Myers CL, Tiffin P, Springer NM. 2012. Reshaping of the maize transcriptome by domestication. Proc Natl Acad Sci USA, 109(29):11878 11883.

Tagarelli, A. and George Karypis. 2012. A Segment based Approach to Clustering Multi Topic Documents. Knowledge and Information Systems (in press).

Takacs, E.M., J. Li, L. Ponnala, D. Janick Buckner, J. Yu, G.J. Muehlbauer, M.C.P. Timmermans, P.S. Schnable, Q. Sun, D. Nettleton and M.J. Scanlon. 2012. Ontogeny of the maize shoot apical meristem. The Plant Cell 24:3219 3234.

Tegeder M, Ward JM. 2012. Molecular evolution of AAP and LHT amino acid transporters in the plant kingdom. Front. Plant Sci. 3: 00021

The International Barley Genome Consortium. 2012. A physical, genetical and functional sequence assembly of the barley genome. Nature doi:10.1038/nature11543.

Tiburcio M, Niang M, Deplaine G, Perrot S, Bischoff E, Ndour PA, Silvestrini F, Khattab A, Milon G, David PH, Hardeman M, Vernick KD, Sauerwein RW, Preiser PR, Mercereau Puijalon O, Buffet P, Alano P, Lavazec C. 2012. A switch in infected erythrocyte deformability at the maturation and blood circulation of Plasmodium falciparum transmission stages. Blood. 119(24):e172 80. PMCID: 3382942.

Tishchenko, Oksana; Donald G. Truhlar. 2012. Benchmark Ab initio calculations of the barrier height and transition state geometry for hydrogen abstraction from a phenolic antioxidant by a peroxy radical and its use to assess the performance of density functionals. Journal of Physical Chemistry Letters; 3(19):2834 2839.

Truhlar, Donald G. 2012. Are molecular orbitals delocalized? Journal of Chemical Education; 89(5):573 574.

Truman, W.M.D. and Glazebrook, J. 2012. Co expression analysis identifies putative targets for CBP60g and SARD1 regulation. BMC Plant Biology, in press.

Tsuda, K., Qi, Y., Nguyen, L.V., Bethke, G., Tsuda, Y., Glazebrook, J., and Katagiri, F. 2012. An efficient Agrobacterium mediated transient transformation of Arabidopsis. Plant J. 69:713 719. DOI: 10.1111/j.1365 313X.2011.04819.x.

Unno, Tatsuya & Di, Doris Y W & Jeonghwan, Jang & Suh, Yaeseul & Sadowsky, Michael J & Hur, Hor Gil. 2012. Integrated Online System for a Pyrosequencing Based Microbial Source Tracking Method that Targets Bacteroidetes 16S rDNA. Environ. Sci. Technol. 46:93 987.

Unrean, Pornkamol; Friedrich Srienc. 2012. Predicting the adaptive evolution of Thermoanaerobacterium saccharolyticum. Journal of Biotechnology; 158(4):259 266.

Uwe T. Bornscheuer, Gjalt Huisman, Romas J. Kazlauskas, Stefan Lutz, Jeffrey Moore, Karen Robins. 2012. Engineering the third wave of biocatalysis. Nature. 485, 185 194; doi: 10.1038/nature11117.

Uwe T. Bornscheuer, Romas J. Kazlauskas. 2012, May. Enzymatic catalytic promiscuity and the design of new enzyme catalyzed reactions. Enzyme Catalysis in Organic Synthesis, 3rd edition. K. Drauz, H. Groger, O. pp1695 1733; doi: 10.1002/9783527639861.ch41

Valberg S, Sponseller B, Hegeman AD, Earing J, Bender J, Martinson K, Patterson S, and Sweetman L. 2012. Seasonal pasture myopathy/atypical myopathy in North America associated with ingestion of hypoglycin A within seeds of the box elder tree, Equine Vet J, accepted. DOI: 10.1111/j.2042 3306.2012.00684.x

Wackett, L.P. and L.B.M. Ellis. 2012. MiniReview: Microbial transformation of organic compounds. Micro. Inf. Exp. 2:1 doi:10.1186/2042 5783 2 1

Wang, Bo; Donald G. Truhlar. 2012. Partial atomic charges and screened charge models of the electrostatic potential. Journal of Chemical Theory and Computation; 8(6):1989 1998.

Wang, Yingjie; Carlos P. Sosa; Alessandro Cembran; Donald G. Truhlar; Jiali Gao. 2012. Multilevel X Pol: A fragment based method with mixed quantum mechanical representations of different fragments. Journal of Physical Chemistry B; 116(23):6781 6788.

Wawrzyn, Grayson T.; Sarah E. Bloch; Claudia Schmidt Dannert. 2012. Discovery and characterization of terpenoid biosynthetic pathways of fungi. Methods in Enzymology; 515():83 105.

Waybrant B, Pearce TR, Wang P, Sreevatsan S, Kokkoli E. 2012 Sep 12. Development and characterization of an aptamer binding ligand of fractalkine using domain targeted SELEX. Chem Commun (Camb). 48(80):10043 5. PubMed PMID: 22936337.

Wolf, V.C., A. Gassmann, B.M. Clasen, A.G. Smith, C. Muller. 2012. Genetic and chemical variation of Tanacetum vulgare in plants of native and invasive origin. Biological Control. 61:240 245.

Wonphatcharachai M, Wang P, Enomoto S, Webby R, Gramer M, Amonsin A, Sreevatsan S. 2012. Neutralizing DNA aptamers against Influenza A H3N2 viruses. J. Clin. Microbiol.

Xing Liu; Lana Barkawi; Gary Gardner; Jerry D. Cohen. 2012. Transport of indole 3 butyric acid and indole 3 acetic acid in Arabidopsis hypocotyls using stable isotope labeling. Plant Physiology; 158(4):1988 2000.

Xu, Xuefei; Donald G. Truhlar. 2012. Performance of effective core potentials for density functional calculations on 3d transition metals. Journal of Chemical Theory and Computation; 8(1):80 90.

Xu, Xuefei; Ewa Papajak; Jingjing Zheng; Donald G. Truhlar. 2012. Multi structural variational transition state theory: Kinetics of the 1,5 hydrogen shift isomerization of the 1 butoxyl radical including all structures and torsional anharmonicity. Physical Chemistry Chemical Physics;14(12):4204 4216.

Xu, Xuefei; Tao Yu; Ewa Papajak; Donald G. Truhlar. 2012. Multistructural variational transition state theory: Kinetics of the hydrogen abstraction from carbon 2 of 2 methyl 1 propanol by hydroperoxyl radical including all structures and torsional anharmonicity. Journal of Physical Chemistry A; 116(43):10480 10487.

Yi, T and Morrell, PL. 2012. (in press). Introduction of major exotic economic plants. In: Hong, D and Blackmore, S (eds.). Plants of China.

Young ND, Bharti AK. 2012. Genome enabled insights into legume biology. Annual Review of Plant Biology 12: 193 201.

Yu, Tao; Jingjing Zheng; Donald G. Truhlar. 2012. Multipath variational transition state theory: Rate constant of the 1,4 hydrogen shift isomerization of the 2 cyclohexylethyl radical. Journal of Physical Chemistry A 2012;116(1):297 308.

Yu, Tao; Jingjing Zheng; Donald G. Truhlar. 2012. Statistical thermodynamics of the isomerization reaction between n heptane and isoheptane. Physical Chemistry Chemical Physics 2012;14(2):482 494.

Zhang Y, Zhang F, Li X, Baller JA, Qi Y, Starker CG, Bogdanove AJ, Voytas DF. 2012, Nov 2. TALENs enable efficient plant genome engineering. Plant Physiol.

Zhang, Peng; Donald G. Truhlar; Jiali Gao. 2012. Fragment based quantum mechanical methods for periodic systems with Ewald summation and mean image charge convention for long range electrostatic interactions. Physical Chemistry Chemical Physics; 14(21):7821 7829.

Zhang, Peng; Luke Fiedler; Hannah R. Leverentz; Donald G. Truhlar; Jiali Gao. 2012. Erratum: Polarized molecular orbital chemistry. 2. The PMO method (Journal of Chemical Theory and Computation.7 (857 867) DOI:10.1021/ct100638g)) Journal of Chemical Theory and Computation; 8(8):2983 . 09.

Zhao, Yan; Hou T. Ng; Roberto Peverati; Donald G. Truhlar. 2012. Benchmark database for ylidic bond dissociation energies and its use for assessments of electronic structure methods. Journal of Chemical Theory and Computation; 8(8):2824 2834.

Zheng, Jingjing; Donald G. Truhlar. 2012. Multi path variational transition state theory for chemical reaction rates of complex polyatomic species: Ethanol + OH reactions. Faraday Discussions; 157():59 88.

Zheng, Jingjing; Roberta J. Rocha; Marina Pelegrini; Luiz F. A. Ferrao; Edson F. V. Carvalho; Orlando Roberto Neto; Francisco B. C. MacHado; Donald G. Truhlar. 2012.A product branching ratio controlled by vibrational adiabaticity and variational effects: Kinetics of the H + trans N 2H 2 reactions. Journal of Chemical Physics; 136(18):.

Zheng, Jingjing; Steven L. Mielke; Kenneth L. Clarkson; Donald G. Truhlar. 2012. MSTor: A program for calculating partition functions, free energies, enthalpies, entropies, and heat capacities of complex molecules including torsional anharmonicity. Computer Physics Communications; 183(8):1803 1812.

Zhou, H., G. Muehlbauer and B.J. Steffenson. 2012. Population structure and linkage disequilibrium in elite barley breeding germplasm from the United States. J. Zhejiang Univ. 13:438 451.

Zhuang, F. George Karypis, Xia Ning, Qing He, and Zhongzhi Shi. 2012. Milti view Learning via Probabilistic Latent Semantic Analysis. Information Sciences, 199, 20 30.