Mark Gerstein
Williams Professor of Biomedical Informatics, Yale
Short CV as of 31 July 2019
Harvard College AB 1989 Physics (& History of Science)
Cambridge University PhD 1993 Biophysics/Chemistry
Stanford University post-doc 1993-1996 Bioinformatics
2006 - AL Williams Prof. Biomedical Informatics, Yale U.
2002 - co-director Yale Computational Biology & Bioinformatics Program
2017 - co-director Yale Center for Biomedical Data Science
2006 - Prof. Molecular Biophysics & Biochemistry, Yale U.
2006 - Prof. Computer Science, Yale U.
2018 - Prof. Statistics & Data Science, Yale U.
2001 - 2006 Assoc. Prof. Molecular Biophysics & Biochemistry and Computer Science, Yale U
1997 - 2001 Asst. Prof. Molecular Biophysics & Biochemistry, Yale U.
2015 ISCB (Intl. Society of Computational Biology) Fellow
2009 AAAS Fellow
1997 - 2001 Young Investigator Awards from Navy & IBM, and PhRMA, Donaghue, & Keck foundations
1993 - 1996 Damon Runyon-Walter Winchell post-doctoral Fellowship
1989 - 1993 Herchel-Smith Scholarship funded PhD at Cambridge
1989 Graduated college summa cum laude & phi beta kappa
Analysis Working Group co-chair: NHGRI ModENCODE Project ('07-'14),
Brainspan Project ('09-),
1000 Genomes Functional Interpretation Group ('11-‘15), exRNA consortium ('13-),
ENCODE ('17)
CMG [Centers for Mendelian Genomics] ('13-), PsychENCODE ('14-), ENCODE &
cancer ('13-'16)
PCAWG-2 [PanCancer Analysis Working Group, non-coding drivers] ('14-),
D Wang, S Liu... PsychENCODE Consortium... JA Knowles, MB Gerstein (2018). "Comprehensive functional genomic resource and integrative model for the human brain." Science 362.
P Muir, S Li, S Lou, D Wang, DJ Spakowicz, L Salichos, J Zhang, GM Weinstock, F Isaacs, J Rozowsky, M Gerstein (2016). "The real cost of sequencing: scaling computation to keep pace with data generation." Genome Biol 17: 53.
D Wang, KK Yan, J Rozowsky, E Pan, M Gerstein (2016). "Temporal Dynamics of Collaborative Networks in Large Scientific Consortia." Trends Genet 32: 251-253.
A Harmanci, M Gerstein (2016). "Quantification of private information leakage from phenotype-genotype data: linking attacks." Nat Methods 13: 251-6.
D Greenbaum & M Gerstein (2016). "Going beyond geek chic -- CeBIT", SF Chronicle, March 10 (Opinion)
MB Gerstein... SE Brenner, BR Graveley, SE Celniker, TR Gingeras, R Waterston (2014). "Comparative analysis of the transcriptome across distant species." Nature 512: 445-8.
C Sisu, B Pei, J Leng, A Frankish, Y Zhang, S Balasubramanian, R Harte, D Wang, M Rutenberg-Schoenberg, W Clark, M Diekhans, J Rozowsky, T Hubbard, J Harrow, MB Gerstein (2014). "Comparative analysis of pseudogenes across three phyla." Proc Natl Acad Sci U S A 111: 13361-6.
E Khurana, Y Fu, V Colonna... H Yu, MA Rubin, C Tyler-Smith, M Gerstein (2013). "Integrative annotation of variants from 1092 humans: application to cancer genomics." Science 342: 1235587
MB Gerstein, A Kundaje, M Hariharan... PJ Farnham, RM Myers, SM Weissman, M Snyder (2012). "Architecture of the human regulatory network derived from ENCODE data." Nature 489: 91-100.
D Greenbaum & M Gerstein (2012). "The Age of Genetically Optimized Sports", Wall Street Journal, July 24, Page A13 (Opinion)
D Greenbaum, A Sboner, XJ Mu, M Gerstein (2011). "Genomics and privacy: implications of the new reality of closed data for the field." PLoS Comput Biol 7: e1002278.
MB Gerstein, ZJ Lu... M Snyder, L Stein, JD Lieb, RH Waterston (2010). "Integrative analysis of the Caenorhabditis elegans genome by the modENCODE project." Science 330: 1775-87.
KK Yan, G Fang, N Bhardwaj, RP Alexander, M Gerstein (2010). "Comparing genomes to computer operating systems in terms of the topology and evolution of their regulatory control networks." Proc Natl Acad Sci U S A 107: 9186-91.
J Rozowsky, G Euskirchen, RK Auerbach, ZD Zhang, T Gibson, R Bjornson, N Carriero, M Snyder, MB Gerstein (2009). "PeakSeq enables systematic scoring of ChIP-seq experiments relative to controls." Nat Biotechnol 27: 66-75.
M Gerstein, M Seringhaus, S Fields (2007). "Structured digital abstract makes text mining easy." Nature 447: 142.
PM Kim, LJ Lu, Y Xia, MB Gerstein (2006). "Relating three-dimensional structures to protein networks provides evolutionary insights." Science 314: 1938-41.
H Yu, M Gerstein (2006). "Genomic analysis of the hierarchical structure of regulatory networks." Proc Natl Acad Sci U S A 103: 14724-31.
M Gerstein, D Zheng (2006). "The real life of pseudogenes." Sci Am 295: 48-55.
NR Voss, M Gerstein (2005). "Calculation of standard atomic volumes for RNA and comparison with proteins: RNA is packed more tightly." J Mol Biol 346: 477-92.
NM Luscombe, MM Babu, H Yu, M Snyder, SA Teichmann, M Gerstein (2004). "Genomic analysis of regulatory network dynamics reveals large topological changes." Nature 431: 308-12.
R Jansen, H Yu, D Greenbaum, Y Kluger, NJ Krogan, S Chung, A Emili, M Snyder, JF Greenblatt, M Gerstein (2003). "A Bayesian networks approach for predicting protein-protein interactions from genomic data." Science 302: 449-53.
N Echols, D Milburn, M Gerstein (2003). "MolMovDB: analysis and visualization of conformational change and structural flexibility." Nucleic Acids Res 31: 478-82.
M Gerstein, M Levitt (1998). "Simulating water and the molecules of life." Sci Am 279: 100-5.
M Levitt, M Gerstein (1998). "A unified statistical framework for sequence comparison and structure comparison." Proc Natl Acad Sci U S A 95: 5913-20.