Biography:Mark Bender Gerstein

From HandWiki
Mark Gerstein
Born
Mark Bender Gerstein
CitizenshipUS
Alma mater
Awards
Scientific career
FieldsBioinformatics[3]
Institutions
ThesisProtein recognition: surfaces and conformational change (1993)
Doctoral advisor
Other academic advisorsMichael Levitt (postdoc)
Doctoral studentsWerner Krebs[6][7]
Website

Mark Bender Gerstein is an United States scientist working in bioinformatics. (As of 2009), he is co-director of the Yale Computational Biology and Bioinformatics program, and Albert L. Williams Professor of Biomedical Informatics, Professor of Molecular Biophysics & Biochemistry and Professor of Computer Science at Yale University.[8]

Education

After graduating from Harvard College summa cum laude with an Bachelor of Arts in Physics in 1989, Gerstein did a PhD co-supervised by Ruth Lynden-Bell[5] at the University of Cambridge and Cyrus Chothia at the Laboratory of Molecular Biology on conformational change in proteins, graduating in 1993.[9] He then went on to postdoctoral research in bioinformatics at Stanford University from 1993-1996 supervised by Nobel-laureate Michael Levitt.

Research

Gerstein does research in the field of bioinformatics.[3][10][11] 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,[12] personal genomics, cancer genomics, building tools in support of genome technologies (such as next-generation sequencing), analyzing molecular networks, and simulating macromolecular motions. Notable databases and tools that the group has developed include the Database of Macromolecular Motions,[6][7] which categorizes macromolecular conformational change; tYNA,[13] which helps analyze molecular networks; PubNet,[14] which analyzes publication networks; PeakSeq,[15] which identifies regions in the genome bound by particular transcription factors; and CNVnator,[16] 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[17] and to structuring scientific communication.[18]

Gerstein's work has been published in peer reviewed scientific journals[19][20][21] and non-scientific publications in more popular forums.[22] His work has been highly cited, with an H greater than 100.[3] 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,[23][24][25] including on the front page,[12] and in other major newspapers.[26]

Awards and honors

In addition to a W. M. Keck Foundation Distinguished Young Scholars award, Gerstein has received awards from the US Navy, IBM, Pharmaceutical Research and Manufacturers of America, and the Donaghue Foundation.[citation needed] He is a Fellow of the AAAS.[1] 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,[27] modENCODE,[28][29][30] 1000 Genomes Project, Brainspan,[citation needed] and DOE Kbase.[citation needed] He was made a Fellow of the International Society for Computational Biology in 2015.[2]

References

  1. ↑ 1.0 1.1 "Yale Scientists Awarded AAAS Fellowship". http://www.yalescientific.org/2010/09/yale-scientists-awarded-aaas-fellowship/. 
  2. ↑ 2.0 2.1 "Meet the ISCB Fellows Class of 2015". International Society for Computational Biology. Archived from the original on 2015-02-20. https://web.archive.org/web/20150220233807/http://www.iscb.org/iscb-news-items/2392-2015feb20-meet-the-iscb-fellows-class-of-2015. 
  3. ↑ 3.0 3.1 3.2 Mark Bender Gerstein publications indexed by Google Scholar
  4. ↑ 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. 
  5. ↑ 5.0 5.1 Mark Bender Gerstein at the Mathematics Genealogy Project
  6. ↑ 6.0 6.1 Krebs, Werner G. (2002). The database of macromolecular motions : a standardized system for analyzing and visualizing macromolecular motions in a database framework (PhD thesis). Yale University. OCLC 54626123.
  7. ↑ 7.0 7.1 Gerstein, M; Krebs, W (1998). "A database of macromolecular motions". Nucleic Acids Research 26 (18): 4280–90. doi:10.1093/nar/26.18.4280. PMID 9722650. 
  8. ↑ Mark Bender Gerstein's publications indexed by the Scopus bibliographic database. (Subscription content?)
  9. ↑ Gerstein, Mark (1993). Protein recognition: surfaces and conformational change (PhD thesis). University of Cambridge.
  10. ↑ Durbin, R. M.; Abecasis, G. R.; Altshuler, R. M.; Auton, G. A. R.; Brooks, D. R.; Durbin, A.; Gibbs, A. G.; Hurles, F. S. et al. (2010). "A map of human genome variation from population-scale sequencing". Nature 467 (7319): 1061–1073. doi:10.1038/nature09534. PMID 20981092. Bibcode: 2010Natur.467.1061T. 
  11. ↑ 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. PMID 19015660. 
  12. ↑ 12.0 12.1 Gina Kolata, (Sept. 5, 2012) 'Bits of Mystery DNA, Far From Junk, Play Crucial Role,' NY Times
  13. ↑ 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. 
  14. ↑ 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. PMID 16168087. 
  15. ↑ Rozowsky, J; Euskirchen, G; Auerbach, R. K.; Zhang, Z. D.; Gibson, T; Bjornson, R; Carriero, N; Snyder, M et al. (2009). "Peak Seq enables systematic scoring of ChIP-seq experiments relative to controls". Nature Biotechnology 27 (1): 66–75. doi:10.1038/nbt.1518. PMID 19122651. 
  16. ↑ 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. PMID 21324876. 
  17. ↑ 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): e1002278. doi:10.1371/journal.pcbi.1002278. PMID 22144881. Bibcode: 2011PLSCB...7E2278G. 
  18. ↑ Gerstein, M; Seringhaus, M; Fields, S (2007). "Structured digital abstract makes text mining easy". Nature 447 (7141): 142. doi:10.1038/447142a. PMID 17495904. Bibcode: 2007Natur.447..142G. 
  19. ↑ {{DBLP}} template missing ID and not present in Wikidata.
  20. ↑ List of publications from Microsoft Academic
  21. ↑ Giaever, G.; Chu, A. M.; Ni, L.; Connelly, C.; Riles, L.; Véronneau, S.; Dow, S.; Lucau-Danila, A. et al. (2002). "Functional profiling of the Saccharomyces cerevisiae genome". Nature 418 (6896): 387–391. doi:10.1038/nature00935. PMID 12140549. Bibcode: 2002Natur.418..387G. 
  22. ↑ "List of Non-technical Writing by Mark Gerstein". gersteinlab.org. Archived from the original on 2013-10-17. https://web.archive.org/web/20131017061104/http://info.gersteinlab.org/Other_Papers. 
  23. ↑ Kolata, Gina (2013-06-16). "Poking Holes in Genetic Privacy". The New York Times. ISSN 0362-4331. https://www.nytimes.com/2013/06/18/science/poking-holes-in-the-privacy-of-dna.html. 
  24. ↑ Zimmer, Carl (2014-09-01). "Tiny, Vast Windows Into Human DNA". The New York Times. ISSN 0362-4331. https://www.nytimes.com/2014/09/02/science/human-fly-worm-dna.html. 
  25. ↑ "Thoughts on Genes". The New York Times. 2008-11-10. ISSN 0362-4331. https://www.nytimes.com/2008/11/11/science/11genequotes.html. 
  26. ↑ "Scientists Unveil New Blueprint Of How The Human Genome Works". http://www.courant.com/health/connecticut/hc-genome-encode-yale-20120905-story.html. 
  27. ↑ ENCODE Project Consortium, Birney E, Stamatoyannopoulos JA, Dutta A, Guigó R, Gingeras TR, Margulies EH, Weng Z, Snyder M, Dermitzakis ET (2007). "Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project". Nature 447 (7146): 799–816. doi:10.1038/nature05874. PMID 17571346. Bibcode: 2007Natur.447..799B. 
  28. ↑ Landt, S. G.; Marinov, G. K.; Kundaje, A.; Kheradpour, P.; Pauli, F.; Batzoglou, S.; Bernstein, B. E.; Bickel, P. et al. (2012). "ChIP-seq guidelines and practices of the ENCODE and modENCODE consortia". Genome Research 22 (9): 1813–1831. doi:10.1101/gr.136184.111. PMID 22955991. 
  29. ↑ 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. PMID 21324173. 
  30. ↑ "Integrative Analysis of the Caenorhabditis elegans Genome by the modENCODE Project". Science 330 (6012): 1775–1787. 2010. doi:10.1126/science.1196914. PMID 21177976. Bibcode: 2010Sci...330.1775G. 

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