Mark Gerstein
Birth nameMark Bender Gerstein
Birth dateFebruary 23
CitizenshipUS
FieldsBioinformatics[1]
Workplaces
Alma mater
Thesis urlhttp://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.282099
Thesis year1993
Doctoral advisor
Academic advisorsMichael Levitt (postdoc)
Doctoral studentsWerner Krebs[4][5]
Notable studentsJan O. Korbel
Awards
Website

Mark Bender Gerstein is an American scientist working in bioinformatics and data science. He is the Albert L. Williams Professor of Biomedical Informatics, professor of molecular biophysics & biochemistry, professor of statistics & data science, and professor of computer science at Yale University.[9] He is also co-director of the Yale Computational Biology and Bioinformatics program. In 2018, Gerstein was named co-director of the Yale Center for Biomedical Data Science.[10]

Education

After graduating from Harvard College summa cum laude with a Bachelor of Arts in physics in 1989, Gerstein did a PhD co-supervised by Ruth Lynden-Bell[3] at the University of Cambridge and Cyrus Chothia at the Laboratory of Molecular Biology on liquid simulation and macromolecular conformational change in proteins, graduating in 1993.[11] He then went on to postdoctoral research in bioinformatics at Stanford University from 1993 to 1996 supervised by Nobel-laureate Michael Levitt.

Research

Gerstein does research in the field of bioinformatics.[1][12][13] This involves applying a range of computational approaches to problems in molecular biology, including data mining and machine learning, molecular simulation, and database design. His research group has a number of foci including annotating the human genome,[14] personal genomics, cancer genomics, building AL/ML tools, analyzing molecular networks, simulating macromolecular motions, and processing biosensor and imaging data. Notable databases and tools that the group has developed include the Database of Macromolecular Motions,[4][5] which categorizes macromolecular conformational change; tYNA,[15] which helps analyze molecular networks; PubNet,[16] which analyzes publication networks; PeakSeq,[17] which identifies regions in the genome bound by particular transcription factors; and CNVnator,[18] which categorizes block variants in the genome. Gerstein has also written extensively on how general issues in data science impact on genomics—in particular, in relation to privacy[19] and to structuring scientific communication.[20]

Gerstein's work has been published in peer reviewed scientific journals[21][22] and non-scientific publications in more popular forums.[23] His work has been highly cited, with an H greater than 200.[1] He serves on a number of editorial and advisory boards, including those of PLoS Computational Biology, Genome Research, Genome Biology, and Molecular Systems Biology. He has been quoted in the New York Times,[24][25][26] including on the front page,[14] and in other major newspapers.[27]

Awards and honors

In addition to a W. M. Keck Foundation Distinguished Young Scholars award,[28] Gerstein has received awards from the US Navy, IBM, Pharmaceutical Research and Manufacturers of America, and the Donaghue Foundation.[29] He is a Fellow of the AAAS.[6] Other awards include a Herchel-Smith Scholarship supporting his doctoral work at Emmanuel College, Cambridge and a Damon Runyon Cancer Research Foundation Postdoctoral Fellowship. He is a contributor to a number of scientific consortia including ENCODE,[30] modENCODE,[31][32][33] 1000 Genomes Project, Brainspan,[34] and DOE Kbase.[citation needed] He was made a Fellow of the International Society for Computational Biology (ISCB) in 2015 [7] and also received an Accomplishments by a Senior Scientist Award from the ISCB in 2023.[8]

References

  1. ^
  2. ^ Gerstein, M. & Chothia, C. (1991). "Analysis of protein loop closure. Two types of hinges produce one motion in lactate dehydrogenase". Journal of Molecular Biology. 220 (1): 133–149. doi:10.1016/0022-2836(91)90387-L. PMID 2067013
  3. ^
  4. ^ Krebs, Werner G. (2002). The database of macromolecular motions: a standardized system for analyzing and visualizing macromolecular motions in a database framework (PhD). Yale University. OCLC 54626123
  5. ^ Gerstein, M & Krebs, W (1998). "A database of macromolecular motions". Nucleic Acids Research. 26 (18): 4280–90. doi:10.1093/nar/26.18.4280. PMC 147832. PMID 9722650
  6. ^ "Yale Scientists Awarded AAAS Fellowship"
  7. ^ "Meet the ISCB Fellows Class of 2015". International Society for Computational Biology. Archived 2015-02-20 at the Wayback Machine.
  8. ^ Fogg, C; Kovats, D; Vingron, M (2023). "2023 ISCB accomplishments by a senior scientist award". Bioinformatics. 39: i9–i10. doi:10.1093/bioinformatics/btad316. PMC 10311292
  9. ^
  10. ^ Xiong, Amy (February 9, 2018). "Yale establishes biomedical data science center". yaledailynews.com. Retrieved 2020-09-27.
  11. ^ Gerstein, Mark (1993). Protein recognition: surfaces and conformational change (PhD). University of Cambridge.
  12. ^ Durbin, R. M.; Abecasis, G. R.; Altshuler, R. M.; Auton, G. A. R.; Brooks, D. R.; Durbin, A.; Gibbs, A. G.; Hurles, F. S.; McVean, F. M.; Donnelly, P.; Egholm, M.; Flicek, P.; Gabriel, S. B.; Gibbs, R. A.; Knoppers, B. M.; Lander, E. S.; Lehrach, H.; Mardis, E. R.; McVean, G. A.; Nickerson, D. A.; Peltonen, L.; Schafer, A. J.; Sherry, S. T.; Wang, J.; Wilson, R. K.; Gibbs, R. A.; Deiros, D.; Metzker, M.; Muzny, D. et al. (2010). "A map of human genome variation from population-scale sequencing". Nature. 467 (7319): 1061–1073. Bibcode:2010Natur.467.1061T. doi:10.1038/nature09534. PMC 3042601. PMID 20981092
  13. ^ Wang, Z.; Gerstein, M.; Snyder, M. (2009). "RNA-Seq: A revolutionary tool for transcriptomics". Nature Reviews Genetics. 10 (1): 57–63. doi:10.1038/nrg2484. PMC 2949280. PMID 19015660
  14. ^ Gina Kolata, (Sept. 5, 2012) 'Bits of Mystery DNA, Far From Junk, Play Crucial Role,' NY Times
  15. ^ Yip, K. Y.; Yu, H; Kim, P. M.; Schultz, M; Gerstein, M (2006). "The tYNA platform for comparative interactomics: A web tool for managing, comparing and mining multiple networks". Bioinformatics. 22 (23): 2968–70. doi:10.1093/bioinformatics/btl488. PMID 17021160
  16. ^ Douglas, S. M.; Montelione, G. T.; Gerstein, M. (2005). "PubNet: A flexible system for visualizing literature derived networks". Genome Biology. 6 (9): R80. doi:10.1186/gb-2005-6-9-r80. PMC 1242215. PMID 16168087
  17. ^ Rozowsky, J; Euskirchen, G; Auerbach, R. K.; Zhang, Z. D.; Gibson, T; Bjornson, R; Carriero, N; Snyder, M; Gerstein, M. B. (2009). "Peak Seq enables systematic scoring of ChIP-seq experiments relative to controls". Nature Biotechnology. 27 (1): 66–75. doi:10.1038/nbt.1518. PMC 2924752. PMID 19122651
  18. ^ Abyzov, A; Urban, A. E.; Snyder, M; Gerstein, M (2011). "CNVnator: An approach to discover, genotype, and characterize typical and atypical CNVs from family and population genome sequencing". Genome Research. 21 (6): 974–84. doi:10.1101/gr.114876.110. PMC 3106330. PMID 21324876
  19. ^ Greenbaum, D; Sboner, A; Mu, X. J.; Gerstein, M (2011). "Genomics and privacy: Implications of the new reality of closed data for the field". PLOS Computational Biology. 7 (12). Bibcode:2011PLSCB...7E2278G. doi:10.1371/journal.pcbi.1002278. PMC 3228779. PMID 22144881
  20. ^ Gerstein, M; Seringhaus, M; Fields, S (2007). "Structured digital abstract makes text mining easy". Nature. 447 (7141): 142. Bibcode:2007Natur.447..142G. doi:10.1038/447142a. PMID 17495904
  21. ^
  22. ^ Giaever, G.; Chu, A. M.; Ni, L.; Connelly, C.; Riles, L.; Véronneau, S.; Dow, S.; Lucau-Danila, A.; Anderson, K.; André, B.; Arkin, A. P.; Astromoff, A.; El-Bakkoury, M.; Bangham, R.; Benito, R.; Brachat, S.; Campanaro, S.; Curtiss, M.; Davis, K.; Deutschbauer, A.; Entian, K. D.; Flaherty, P.; Foury, F.; Garfinkel, D. J.; Gerstein, M.; Gotte, D.; Güldener, U.; Hegemann, J. H.; Hempel, S.; Herman, Z. (2002). "Functional profiling of the Saccharomyces cerevisiae genome". Nature. 418 (6896): 387–391. Bibcode:2002Natur.418..387G. doi:10.1038/nature00935. PMID 12140549. S2CID 4400400
  23. ^ "List of Non-technical Writing by Mark Gerstein". gersteinlab.org. Archived 2013-10-17 at the Wayback Machine.
  24. ^ Kolata, Gina (2013-06-16). "Poking Holes in Genetic Privacy". The New York Times. ISSN 0362-4331. Retrieved 2016-01-18.
  25. ^ Zimmer, Carl (2014-09-01). "Tiny, Vast Windows Into Human DNA". The New York Times. ISSN 0362-4331. Retrieved 2016-01-18.
  26. ^ "Thoughts on Genes". The New York Times. 2008-11-10. ISSN 0362-4331. Retrieved 2016-01-18.
  27. ^ Reports, Wire. "Scientists Unveil New Blueprint Of How The Human Genome Works". courant.com. Retrieved 2016-01-18.
  28. ^ Mervis, Jeffrey (1999-07-16). "Keck Helps Five Careers With $1 Million Grants". Science. 285 (5426): 312–3. doi:10.1126/science.285.5426.312b. PMID 10438290. S2CID 33084600
  29. ^ "Donaghue Foundation selects five investigators for long-term support". medicine.yale.edu. Retrieved 2020-09-27.
  30. ^ ENCODE Project Consortium; Birney E; Stamatoyannopoulos JA; Dutta A; Guigó R; Gingeras TR; Margulies EH; Weng Z; Snyder M; Dermitzakis ET et al. (2007). "Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project". Nature. 447 (7146): 799–816. Bibcode:2007Natur.447..799B. doi:10.1038/nature05874. PMC 2212820. PMID 17571346
  31. ^ Landt, S. G.; Marinov, G. K.; Kundaje, A.; Kheradpour, P.; Pauli, F.; Batzoglou, S.; Bernstein, B. E.; Bickel, P.; Brown, J. B.; Cayting, P.; Chen, Y.; Desalvo, G.; Epstein, C.; Fisher-Aylor, K. I.; Euskirchen, G.; Gerstein, M.; Gertz, J.; Hartemink, A. J.; Hoffman, M. M.; Iyer, V. R.; Jung, Y. L.; Karmakar, S.; Kellis, M.; Kharchenko, P. V.; Li, Q.; Liu, T.; Liu, X. S.; Ma, L.; Milosavljevic, A.; Myers, R. M. (2012). "ChIP-seq guidelines and practices of the ENCODE and modENCODE consortia". Genome Research. 22 (9): 1813–1831. doi:10.1101/gr.136184.111. PMC 3431496. PMID 22955991
  32. ^ Cheng, C.; Yan, K. K.; Yip, K. Y.; Rozowsky, J.; Alexander, R.; Shou, C.; Gerstein, M. (2011). "A statistical framework for modeling gene expression using chromatin features and application to modENCODE datasets". Genome Biology. 12 (2): R15. doi:10.1186/gb-2011-12-2-r15. PMC 3188797. PMID 21324173
  33. ^ Gerstein MB, Lu ZJ, Van Nostrand EL, Cheng C, Arshinoff BI, Liu T, Yip KY, Robilotto R, Rechtsteiner A (2010). "Integrative Analysis of the Caenorhabditis elegans Genome by the modENCODE Project". Science. 330 (6012): 1775–1787. Bibcode:2010Sci...330.1775G. doi:10.1126/science.1196914. PMC 3142569. PMID 21177976
  34. ^ Li, Mingfeng; Santpere, Gabriel; Kawasawa, Yuka Imamura; Evgrafov, Oleg V.; Gulden, Forrest O.; Pochareddy, Sirisha; Sunkin, Susan M.; Li, Zhen; Shin, Yurae; Zhu, Ying; Sousa, André M. M. (2018-12-14). "Integrative functional genomic analysis of human brain development and neuropsychiatric risks". Science. 362 (6420). Bibcode:2018Sci...362.7615L. doi:10.1126/science.aat7615. ISSN 0036-8075. PMC 6413317. PMID 30545854