Gerstein, Mark B - Yale University - Biological & Biomedical Sciences

个人简介

After graduating from Harvard summa cum laude with a A.B. in physics in 1989, Prof. Mark Gerstein earned a doctorate in theoretical chemistry and biophysics from Cambridge University in 1993. He did postdoctoral research in bioinformatics at Stanford University from 1993 to 1996. He came to Yale in 1997 as an assistant professor in the Department of Molecular Biophysics and Biochemistry, and since 1999, in the Computer Science Department. He was named an associate professor in 2001, and the following year became co-director of the Yale Computational Biology and Bioinformatics Program. Gerstein has published appreciably in the scientific literature, with >400 publications in total, including a number of them in prominent venues, such as Science, Nature, and Scientific American. His research is focused on bioinformatics, and he is particularly interested in data science & data mining, macromolecular geometry & simulation, and human genome annotation & cancer genomics. PhD Cambridge University (1992) Postdoctoral Fellow Stanford University

研究领域

Biochemistry; Biophysics; DNA; Medical Informatics; Computational Biology; Genomics

近期论文

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The real life of pseudogenes Gerstein, M. and Zheng, D. (2006). The real life of pseudogenes. Sci. Am. 295: 48-55. Integrative annotation of variants from 1092 humans: application to cancer genomics E Khurana, Y Fu, V Colonna, XJ Mu, HM Kang, T Lappalainen, A Sboner, L Lochovsky, J Chen, A Harmanci, J Das, A Abyzov, S Balasubramanian, K Beal, D Chakravarty, D Challis, Y Chen, D Clarke, L Clarke, F Cunningham, US Evani, P Flicek, R Fragoza, E Garrison, R Gibbs, ZH Gumus, J Herrero, N Kitabayashi, Y Kong, K Lage, V Liluashvili, SM Lipkin, DG MacArthur, G Marth, D Muzny, TH Pers, GR Ritchie, JA Rosenfeld, C Sisu, X Wei, M Wilson, Y Xue, F Yu, 1000 Genomes Project Consortium, ET Dermitzakis, H Yu, MA Rubin, C Tyler-Smith, M Gerstein (2013). Science 342: 1235587 Architecture of the human regulatory network derived from ENCODE data. MB Gerstein, A Kundaje, M Hariharan, SG Landt, KK Yan, C Cheng, XJ Mu, E Khurana, J Rozowsky, R Alexander, R Min, P Alves, A Abyzov, N Addleman, N Bhardwaj, AP Boyle, P Cayting, A Charos, DZ Chen, Y Cheng, D Clarke, C Eastman, G Euskirchen, S Frietze, Y Fu, J Gertz, F Grubert, A Harmanci, P Jain, M Kasowski, P Lacroute, J Leng, J Lian, H Monahan, H O'Geen, Z Ouyang, EC Partridge, D Patacsil, F Pauli, D Raha, L Ramirez, TE Reddy, B Reed, M Shi, T Slifer, J Wang, L Wu, X Yang, KY Yip, G Zilberman-Schapira, S Batzoglou, A Sidow, PJ Farnham, RM Myers, SM Weissman, M Snyder (2012). Nature 489:91-100. Relating three-dimensional structures to protein networks provides evolutionary insights. PM Kim, LJ Lu, Y Xia, MB Gerstein (2006). Science 314:1938-41. Despic V, Dejung M, Gu M, Krishnan J, Zhang J, Herzel L, Straube K, Gerstein MB, Butter F, Neugebauer KM: Dynamic RNA-protein interactions underlie the zebrafish maternal-to-zygotic transition. Genome Res. 2017 Apr 5; 2017 Apr 5. PMID: 28381614 Li S, Shuch BM, Gerstein MB: Whole-genome analysis of papillary kidney cancer finds significant noncoding alterations. PLoS Genet. 2017 Mar; 2017 Mar 30. PMID: 28358873 Choo SW, Rayko M, Tan TK, Hari R, Komissarov A, Wee WY, Yurchenko AA, Kliver S, Tamazian G, Antunes A, Wilson RK, Warren WC, Koepfli KP, Minx P, Krasheninnikova K, Kotze A, Dalton DL, Vermaak E, Paterson IC, Dobrynin P, Sitam FT, Rovie-Ryan JJ, Johnson WE, Yusoff AM, Luo SJ, Karuppannan KV, Fang G, Zheng D, Gerstein MB, Lipovich L, O'Brien SJ, Wong GJ: Pangolin genomes and the evolution of mammalian scales and immunity. Genome Res. 2016 Oct; 2016 Aug 10. PMID: 27510566 Cheung KH, Keerthikumar S, Roncaglia P, Subramanian SL, Roth ME, Samuel M, Anand S, Gangoda L, Gould S, Alexander R, Galas D, Gerstein MB, Hill AF, Kitchen RR, Lötvall J, Patel T, Procaccini DC, Quesenberry P, Rozowsky J, Raffai RL, Shypitsyna A, Su AI, Théry C, Vickers K, Wauben MH, Mathivanan S, Milosavljevic A, Laurent LC: Extending gene ontology in the context of extracellular RNA and vesicle communication. J Biomed Semantics. 2016; 2016 Apr 12. PMID: 27076901 Abyzov A, Li S, Gerstein MB: Understanding genome structural variations. Oncotarget. 2016 Feb 16. PMID: 26657727 PsychENCODE Consortium., Akbarian S, Liu C, Knowles JA, Vaccarino FM, Farnham PJ, Crawford GE, Jaffe AE, Pinto D, Dracheva S, Geschwind DH, Mill J, Nairn AC, Abyzov A, Pochareddy S, Prabhakar S, Weissman S, Sullivan PF, State MW, Weng Z, Peters MA, White KP, Gerstein MB, Amiri A, Armoskus C, Ashley-Koch AE, Bae T, Beckel-Mitchener A, Berman BP, Coetzee GA, Coppola G, Francoeur N, Fromer M, Gao R, Grennan K, Herstein J, Kavanagh DH, Ivanov NA, Jiang Y, Kitchen RR, Kozlenkov A, Kundakovic M, Li M, Li Z, Liu S, Mangravite LM, Mattei E, Markenscoff-Papadimitriou E, Navarro FC, North N, Omberg L, Panchision D, Parikshak N, Poschmann J, Price AJ, Purcaro M, Reddy TE, Roussos P, Schreiner S, Scuderi S, Sebra R, Shibata M, Shieh AW, Skarica M, Sun W, Swarup V, Thomas A, Tsuji J, van Bakel H, Wang D, Wang Y, Wang K, Werling DM, Willsey AJ, Witt H, Won H, Wong CC, Wray GA, Wu EY, Xu X, Yao L, Senthil G, Lehner T, Sklar P, Sestan N: The PsychENCODE project. Nat Neurosci. 2015 Dec. PMID: 26605881 Sudmant PH, Rausch T, Gardner EJ, Handsaker RE, Abyzov A, Huddleston J, Zhang Y, Ye K, Jun G, Hsi-Yang Fritz M, Konkel MK, Malhotra A, Stütz AM, Shi X, Paolo Casale F, Chen J, Hormozdiari F, Dayama G, Chen K, Malig M, Chaisson MJ, Walter K, Meiers S, Kashin S, Garrison E, Auton A, Lam HY, Jasmine Mu X, Alkan C, Antaki D, Bae T, Cerveira E, Chines P, Chong Z, Clarke L, Dal E, Ding L, Emery S, Fan X, Gujral M, Kahveci F, Kidd JM, Kong Y, Lameijer EW, McCarthy S, Flicek P, Gibbs RA, Marth G, Mason CE, Menelaou A, Muzny DM, Nelson BJ, Noor A, Parrish NF, Pendleton M, Quitadamo A, Raeder B, Schadt EE, Romanovitch M, Schlattl A, Sebra R, Shabalin AA, Untergasser A, Walker JA, Wang M, Yu F, Zhang C, Zhang J, Zheng-Bradley X, Zhou W, Zichner T, Sebat J, Batzer MA, McCarroll SA, 1000 Genomes Project Consortium., Mills RE, Gerstein MB, Bashir A, Stegle O, Devine SE, Lee C, Eichler EE, Korbel JO: An integrated map of structural variation in 2,504 human genomes. Nature. 2015 Oct 1. PMID: 26432246 Mu JC, Tootoonchi Afshar P, Mohiyuddin M, Chen X, Li J, Bani Asadi N, Gerstein MB, Wong WH, Lam HY: Leveraging long read sequencing from a single individual to provide a comprehensive resource for benchmarking variant calling methods. Sci Rep. 2015 Sep 28; 2015 Sep 28. PMID: 26412485 Fang LT, Afshar PT, Chhibber A, Mohiyuddin M, Fan Y, Mu JC, Gibeling G, Barr S, Asadi NB, Gerstein MB, Koboldt DC, Wang W, Wong WH, Lam HY: An ensemble approach to accurately detect somatic mutations using SomaticSeq. Genome Biol. 2015 Sep 17; 2015 Sep 17. PMID: 26381235 Duffy EE, Rutenberg-Schoenberg M, Stark CD, Kitchen RR, Gerstein MB, Simon MD: Tracking Distinct RNA Populations Using Efficient and Reversible Covalent Chemistry. Mol Cell. 2015 Sep 3. PMID: 26340425 Subramanian SL, Kitchen RR, Alexander R, Carter BS, Cheung KH, Laurent LC, Pico A, Roberts LR, Roth ME, Rozowsky JS, Su AI, Gerstein MB, Milosavljevic A: Integration of extracellular RNA profiling data using metadata, biomedical ontologies and Linked Data technologies. J Extracell Vesicles. 2015; 2015 Aug 28. PMID: 26320941 Mohiyuddin M, Mu JC, Li J, Bani Asadi N, Gerstein MB, Abyzov A, Wong WH, Lam HY: MetaSV: an accurate and integrative structural-variant caller for next generation sequencing. Bioinformatics. 2015 Aug 15; 2015 Apr 10. PMID: 25861968 Abyzov A, Li S, Kim DR, Mohiyuddin M, Stütz AM, Parrish NF, Mu XJ, Clark W, Chen K, Hurles M, Korbel JO, Lam HY, Lee C, Gerstein MB: Analysis of deletion breakpoints from 1,092 humans reveals details of mutation mechanisms. Nat Commun. 2015 Jun 1; 2015 Jun 1. PMID: 26028266 Mu JC, Mohiyuddin M, Li J, Bani Asadi N, Gerstein MB, Abyzov A, Wong WH, Lam HY: VarSim: a high-fidelity simulation and validation framework for high-throughput genome sequencing with cancer applications. Bioinformatics. 2015 May 1; 2014 Dec 17. PMID: 25524895 Wang D, Yan KK, Sisu C, Cheng C, Rozowsky J, Meyerson W, Gerstein MB: Loregic: a method to characterize the cooperative logic of regulatory factors. PLoS Comput Biol. 2015 Apr; 2015 Apr 17. PMID: 25884877 Kitchen RR, Rozowsky JS, Gerstein MB, Nairn AC: Decoding neuroproteomics: integrating the genome, translatome and functional anatomy. Nat Neurosci. 2014 Nov; 2014 Oct 28. PMID: 25349915 Sisu C, Pei B, Leng J, Frankish A, Zhang Y, Balasubramanian S, Harte R, Wang D, Rutenberg-Schoenberg M, Clark W, Diekhans M, Rozowsky J, Hubbard T, Harrow J, Gerstein MB: Comparative analysis of pseudogenes across three phyla. Proc Natl Acad Sci U S A. 2014 Sep 16; 2014 Aug 25. PMID: 25157146