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

Key Professional Experience (beyond Yale, but not including “for profits”)

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-),

Representative Publications (selected from >550 in total)
(H-index of 157, Thomson/Clarivate Highly Cited Researchers list '14 to '18)


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.