Mark Bender Gerstein

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Mark Gerstein
Born Mark Bender Gerstein
Residence US, UK
Citizenship US
Fields Bioinformatics[1]
Institutions
Alma mater
Thesis Protein recognition: surfaces and conformational change (1993)
Doctoral advisor
Other academic advisors Michael Levitt (postdoc)
Doctoral students
Notable awards
Website

Mark Bender Gerstein is an American 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.[20]

Education[edit]

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[3] at the University of Cambridge and Cyrus Chothia at the Laboratory of Molecular Biology on conformational change in proteins, graduating in 1993.[21] He then went on to postdoctoral research in bioinformatics at Stanford University from 1993-1996 supervised by Nobel-laureate Michael Levitt.

Research[edit]

Gerstein does research in the field of bioinformatics.[1][22][23] 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,[24] 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,[11][12] which categorizes macromolecular conformational change; tYNA,[25] which helps analyze molecular networks; PubNet,[26] which analyzes publication networks; PeakSeq,[27] which identifies regions in the genome bound by particular transcription factors; and CNVnator,[28] 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[29] and to structuring scientific communication.[14]

Gerstein's work has been published in peer reviewed scientific journals[30][31][32] and non-scientific publications in more popular forums.[33] His work has been highly cited, with an H greater than 100.[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,[34][35][36] including on the front page,[24] and in other major newspapers.[37]

Awards and honors[edit]

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.[18] 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,[38] modENCODE,[39][40][41] 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.[19]

Selected publications[edit]

  • Wang, Zhong; Gerstein, Mark; Snyder, Michael (2009). "RNA-Seq: A revolutionary tool for transcriptomics". Nature Reviews Genetics. 10 (1): 57–63. doi:10.1038/nrg2484. PMC 2949280Freely accessible. PMID 19015660. 
  • Durbin, Richard M.; Altshuler, David L.; Durbin, Richard M.; Abecasis, Gonçalo R.; Bentley, David R.; Chakravarti, Aravinda; Clark, Andrew G.; Collins, Francis S.; de la Vega, Francisco M.; Donnelly, Peter; Egholm, Michael; Flicek, Paul; Gabriel, Stacey B.; Gibbs, Richard A.; Knoppers, Bartha M.; Lander, Eric S.; Lehrach, Hans; Mardis, Elaine R.; McVean, Gil A.; Nickerson, Debbie A.; Peltonen, Leena; Schafer, Alan J.; Sherry, Stephen T.; Wang, Jun; Wilson, Richard K.; Gibbs, Richard A.; Deiros, David; Metzker, Mike; Muzny, Donna; et al. (2010). "A map of human genome variation from population-scale sequencing". Nature. 467 (7319): 1061–73. doi:10.1038/nature09534. PMC 3042601Freely accessible. PMID 20981092. 
  • Birney, Ewan; Stamatoyannopoulos, John A.; Dutta, Anindya; Guigó, Roderic; Gingeras, Thomas R.; Margulies, Elliott H.; Weng, Zhiping; Snyder, Michael; Dermitzakis, Emmanouil T.; Stamatoyannopoulos, John A.; Thurman, Robert E.; Kuehn, Michael S.; Taylor, Christopher M.; Neph, Shane; Koch, Christoph M.; Asthana, Saurabh; Malhotra, Ankit; Adzhubei, Ivan; Greenbaum, Jason A.; Andrews, Robert M.; Flicek, Paul; Boyle, Patrick J.; Cao, Hua; Carter, Nigel P.; Clelland, Gayle K.; Davis, Sean; Day, Nathan; Dhami, Pawandeep; Dillon, Shane C.; 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. doi:10.1038/nature05874. PMC 2212820Freely accessible. PMID 17571346. 
  • Giaever, Guri; Chu, Angela M.; Ni, Li; Connelly, Carla; Riles, Linda; Véronneau, Steeve; Dow, Sally; Lucau-Danila, Ankuta; Anderson, Keith; André, Bruno; Arkin, Adam P.; Astromoff, Anna; El Bakkoury, Mohamed; Bangham, Rhonda; Benito, Rocio; Brachat, Sophie; Campanaro, Stefano; Curtiss, Matt; Davis, Karen; Deutschbauer, Adam; Entian, Karl-Dieter; Flaherty, Patrick; Foury, Francoise; Garfinkel, David J.; Gerstein, Mark; Gotte, Deanna; Güldener, Ulrich; Hegemann, Johannes H.; Hempel, Svenja; et al. (2002). "Functional profiling of the Saccharomyces cerevisiae genome". Nature. 418 (6896): 387–91. doi:10.1038/nature00935. PMID 12140549. 
  • Zhu, H.; Bilgin, M; Bangham, R; Hall, D; Casamayor, A; Bertone, P; Lan, N; Jansen, R; Bidlingmaier, S; Houfek, T; Mitchell, T; Miller, P; Dean, R. A.; Gerstein, M; Snyder, M (2001). "Global Analysis of Protein Activities Using Proteome Chips". Science. 293 (5537): 2101–5. doi:10.1126/science.1062191. PMID 11474067. 

References[edit]

  1. ^ a b c Mark Bender Gerstein's publications indexed by Google Scholar
  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. ^ a b c d Mark Bender Gerstein at the Mathematics Genealogy Project
  4. ^ Bertone, Paul Nicholas (2005). Microarray approaches to experimental genome annotation (PhD thesis). Yale University. OCLC 62230773. 
  5. ^ Marx, V. (2013). "The author file: Paul Bertone". Nature Methods. 10 (12): 1137. doi:10.1038/nmeth.2747. 
  6. ^ Gianoulis, Tara Ann (2009). Mining biological complexity : cross integration of large-scale metagenomics, environmental, and chemical datasets (PhD thesis). Yale University. OCLC 607864193. 
  7. ^ Gianoulis, T. A.; Griffin, M. A.; Spakowicz, D. J.; Dunican, B. F.; Alpha, C. J.; Sboner, A; Sismour, A. M.; Kodira, C; Egholm, M; Church, G. M.; Gerstein, M. B.; Strobel, S. A. (2012). "Genomic analysis of the hydrocarbon-producing, cellulolytic, endophytic fungus Ascocoryne sarcoides". PLoS Genetics. 8 (3): e1002558. doi:10.1371/journal.pgen.1002558. PMC 3291568Freely accessible. PMID 22396667. 
  8. ^ Gianoulis, T. A.; Agarwal, A; Snyder, M; Gerstein, M. B. (2011). "The CRIT framework for identifying cross patterns in systems biology and application to chemogenomics". Genome Biology. 12 (3): R32. doi:10.1186/gb-2011-12-3-r32. PMC 3129682Freely accessible. PMID 21453526. 
  9. ^ Gianoulis, T. A.; Raes, J; Patel, P. V.; Bjornson, R; Korbel, J. O.; Letunic, I; Yamada, T; Paccanaro, A; Jensen, L. J.; Snyder, M; Bork, P; Gerstein, M. B. (2009). "Quantifying environmental adaptation of metabolic pathways in metagenomics". Proceedings of the National Academy of Sciences. 106 (5): 1374–9. doi:10.1073/pnas.0808022106. PMC 2629784Freely accessible. PMID 19164758. 
  10. ^ Greenbaum, Dov (2004). Comparing mRNA expression and protein abundance via genomic and proteomic characteristics (PhD thesis). Yale University. OCLC 793540375. 
  11. ^ a b 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. 
  12. ^ a b 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 147832Freely accessible. PMID 9722650. 
  13. ^ Seringhaus, Michael Rolf (2007). Computational prediction of essential genes, and other applications of bioinformatics to genome annotation (PhD thesis). Yale University. OCLC 213261935. 
  14. ^ a b Gerstein, M; Seringhaus, M; Fields, S (2007). "Structured digital abstract makes text mining easy". Nature. 447 (7141): 142. doi:10.1038/447142a. PMID 17495904. 
  15. ^ Habegger, Lukas (2012). Computational methodologies for transcript analysis in the age of next-generation DNA sequencing (PhD thesis). Yale University. OCLC 830037658. 
  16. ^ Auerbach, Raymond Kyle (2012). Elucidating transcriptional regulation using high-throughput sequencing, data integration, and computational methods (PhD thesis). Yale University. OCLC 844003771. 
  17. ^ Chen, Jieming (2015). Variant Interpretation in Personal Genomes using Repeat Protein Sequences, Networks and Allele-specific Analyses (PhD thesis). Yale University. 
  18. ^ a b "Yale Scientists Awarded AAAS Fellowship". 
  19. ^ a b "Meet the ISCB Fellows Class of 2015". International Society for Computational Biology. Archived from the original on 2015-02-20. 
  20. ^ Mark Bender Gerstein's publications indexed by the Scopus bibliographic database, a service provided by Elsevier. (subscription required)
  21. ^ Gerstein, Mark (1993). Protein recognition: surfaces and conformational change (PhD thesis). University of Cambridge. 
  22. ^ 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.; Reid, J. (2010). "A map of human genome variation from population-scale sequencing". Nature. 467 (7319): 1061–1073. doi:10.1038/nature09534. PMC 3042601Freely accessible. PMID 20981092. 
  23. ^ 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 2949280Freely accessible. PMID 19015660. 
  24. ^ a b Gina Kolata, (Sept. 5, 2012) 'Bits of Mystery DNA, Far From Junk, Play Crucial Role,' NY Times
  25. ^ 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. 
  26. ^ 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 1242215Freely accessible. PMID 16168087. 
  27. ^ 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 2924752Freely accessible. PMID 19122651. 
  28. ^ 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 3106330Freely accessible. PMID 21324876. 
  29. ^ 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. PMC 3228779Freely accessible. PMID 22144881. 
  30. ^ Mark Gerstein at DBLP Bibliography Server
  31. ^ List of publications from Microsoft Academic Search
  32. ^ 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. doi:10.1038/nature00935. PMID 12140549. 
  33. ^ [=https://web.archive.org/web/20131017061104/http://info.gersteinlab.org/Other_Papers "List of Non-technical Writing by Mark Gerstein"] Check |archiveurl= value (help). gersteinlab.org. Archived from the original on 2013-10-17. 
  34. ^ Kolata, Gina (2013-06-16). "Poking Holes in Genetic Privacy". The New York Times. ISSN 0362-4331. Retrieved 2016-01-18. 
  35. ^ Zimmer, Carl (2014-09-01). "Tiny, Vast Windows Into Human DNA". The New York Times. ISSN 0362-4331. Retrieved 2016-01-18. 
  36. ^ "Thoughts on Genes". The New York Times. 2008-11-10. ISSN 0362-4331. Retrieved 2016-01-18. 
  37. ^ "Scientists Unveil New Blueprint Of How The Human Genome Works". courant.com. Retrieved 2016-01-18. 
  38. ^ 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 2212820Freely accessible. PMID 17571346. 
  39. ^ 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 3431496Freely accessible. PMID 22955991. 
  40. ^ 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 3188797Freely accessible. PMID 21324173. 
  41. ^ Gerstein MB, Lu ZJ, Van Nostrand EL, Cheng C, Arshinoff BI, Liu T, Yip KY, Robilotto R, Rechtsteiner A, et al. (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 3142569Freely accessible. PMID 21177976. 

External links[edit]