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Bülent Arman Aksoy

e-mail: arman@aksoy.org

web-site: http://arman.aksoy.org mobile: +1-607-793-6850

address: 342 E110th St Apt 2E New York, NY, 10029

Experience

2015 – … Post-doctoral fellow at Icahn School of Medicine, Mount Sinai Hospital

Hammer Lab, Genetics & Genomics Department (info) Advisor: Jeff Hammerbacher

Education

2010 – 2015 Ph.D. in Computational Biology and Medicine Tri-Institutional Training Program in Computational Biology and Medicine at Memorial Sloan-Kettering Cancer Center (info) Advisor: Chris Sander

2004 – 2010 B.Sc. in Molecular Biology & Genetics B.Sc. in Mathematics (double-major)

Bogazici University, Istanbul, Turkey (info) Advisor: A. Nazli Basak

Talks and Workshops

2014/10 Center for Cancer Systems Biology 4th Annual Symposium 15-minute talk on “Prediction of Individualized Therapeutic Vulnerabilities from Cancer Profiles” (info) (CCSB Young Scientist Award)

2014/05 The Cancer Genome Atlas 3rd Annual Scientific Symposium 15-minute talk on “Prediction of Individualized Therapeutic Vulnerabilities from Cancer Profiles” (info / video)

2013/09 National Cancer Center of Korea Led a two-day workshop on cBioPortal for cancer researchers (info)

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Research Interests

Computational Biology Genomics Cancer Biology Systems Biology Pathway Informatics Bioinformatics

Peer Reviews

Bioinformatics BMC Cancer PLOS ONE F1000 Research

Publications

24 publications (3 first author | 9 consortium papers | 2 available as a preprint) Google Scholar Profile: http://bit.ly/arman_gscholar | Impact Story Profile: http://bit.ly/arman_impact

Aksoy BA, Demir E, Babur O, Wang W, Jing X, Schultz N, Sander C. Prediction of individualized therapeutic vulnerabilities in cancer from genomic profiles. Bioinformatics. 30(14):2051-2059, 2014 (full text) [OA] (role: lead)

Aksoy BA, Jacobsen A, Fieldhouse RJ, Lee W, Demir E, Ciriello G, Schultz N, Marks DS, Sander C. Cancer-associated recurrent mutations in RNase III domains of DICER1. bioRxiv preprint. DOI: 10.1101/005686 (full text) [OA] (role: lead)

Aksoy BA, Gao J, Dresdner G, Wang W, Root A, Jing X, Cerami E, Sander C. PiHelper: an open source framework for drug-target and antibody-target data. Bioinformatics Application Note. 29(16):2071-2072, 2013 (full text) [OA] (role: lead)

Gao J, Aksoy BA, Dogrusoz U, Dresdner G, Gross B, Sumer SO, Sun Y, Jacobsen A, Sinha R, Larsson E, Cerami E, Sander C, Schultz N. Integrative Analysis of Complex Cancer Genomics Profiles using the cBioPortal. Science Signaling. 6(269), 2013. (full text) [OA]

Cerami E, Gao J, Dogrusoz U, Gross B, Sumer SO, Aksoy BA, Jacobsen A, …, Sander C, Schultz N. The cBio Cancer Genomics Portal: An Open Platform for Exploring Multidimensional Cancer Genomics Data. Cancer Discovery. 2(5): 401–404,.2012 (full text) [OA] (role: software development)

Ciriello G, Miller ML, Aksoy BA, Senbabaoglu Y, Schultz N, Sander C. Emerging landscape of oncogenic signatures across human cancers. Nature Genetics. 45(10):1127-1133, 2013 (full text) [OA] (role: data collection)

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Arbiza L, Gronau I, Aksoy BA, Hubisz MJ, Gulko B, Keinan A, Siepel A. Genome-wide inference of natural selection on human transcription factor binding sites. Nature Genetics. 45:723-729, 2013. (abstract) (role: data collection, analysis)

The Cancer Genome Atlas Network (… Aksoy BA …) (TCGA Papers) •   Comprehensive molecular portraits of human breast tumours. Nature.

490(7418):61-70, 2012 •   Comprehensive genomic characterization of squamous cell lung cancers.

Nature. 489(7417):519-525, 2012 •   Comprehensive genomic characterization human colon and rectal cancer.

Nature. 487(7407):330-337, 2012 •   Integrated genomic characterization of endometrial carcinoma. Nature.

497(7447):67-73, 2013 •   Genomic and Epigenomic Landscapes of Adult De Novo Acute Myeloid

Leukemia. NEJM. 368:2059-2074, 2013 •   …

(role: member as a cBioPortal developer)

Demir E, Babur O, Rodchenkov I, Aksoy BA, Fukuda K, Gross B, Sumer OS, Bader G, Sander C. Paxtools: A library for accessing, analyzing and creating biological pathway data. PLOS Computational Biology. Vol 9. E1003194, 2013. (full text) [OA] (role: software development)

Babur O, Aksoy BA, Rodchenkov I, Sumer SO, Sander C, Demir E. Pattern seach in BioPAX models. Bioinformatics Application Note. 30(1):139-140, 2014. (full text) [OA] (role: software development)

Babur O, Dogrusoz U, Cakir M, Aksoy BA, Schultz N, Sander C, Demir E. Integrating biological pathways and genomic profiles with ChiBE 2. BMC Genomics. 15:642. 2014. (full text) [OA] (role: software development) Luna A, Babur O, Aksoy BA, Demir E, Sander C. PaxtoolsR: Pathway Analysis in R Using Pathway Commons. bioRxiv preprint (full text) [OA] (role: software development)

Ciriello G, Cerami E, Aksoy BA, Sander C, Schultz C. Using MEMo to Discover Mutual Exclusivity Modules in Cancer. Current Protocols in Bionformatics. 8.17.1-8.17.12. 2013. (abstract) (role: software development)

Babur O, Gonen M, Aksoy BA, Schultz N, Ciriello G, Sander C, Demir E. Systematic identification of cancer driving signaling pathways based on mutual exclusivity of genomic alterations. Genome Biology. 2015. 16:45 (full text) [OA] (role: software development)

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Korkut A, Wang W, Demir E, Aksoy BA, Jing X, Molinelli E, Babur O, Bemis D, Solit DB, Pratilas C, Sander C. Perturbation biology nominates upstream–downstream drug combinations in RAF inhibitor resistant melanoma cells. eLife. 2015. (full text) [OA] (role: software development, analysis)

Miller ML, Reznik E, Gauthier NP, Aksoy BA, Korkut A, Gao J, Ciriello G, Schultz N, Sander C. Pan-cancer analysis of mutation hotspots in protein domains. Cell Systems. 2015. 1(3), 197-209. (full text) [OA] (role: analysis)

   

References

Jeff Hammerbacher MSSM   info (at) hammerlab.org

Chris Sander MSKCC sander (at) cbio.mskcc.org

Gary Bader UofT gary.bader (at) utoronto.ca

Adam Siepel CSHL asiepel (at) cshl.edu

A. Nazli Basak BOUN basak (at) boun.edu.tr