Mark Bender Gerstein

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.[17]

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[3] at the University of Cambridge and Cyrus Chothia at the Laboratory of Molecular Biology on conformational change in proteins, graduating in 1993.[18] 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[1][19][20][21][22][23][24] 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,[25] 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,[12][11] which categorizes macromolecular conformational change; tYNA,[26] which helps analyze molecular networks; PubNet,[27] which analyzes publication networks; PeakSeq,[28] which identifies regions in the genome bound by particular transcription factors; and CNVnator,[29] 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[30] and to structuring scientific communication.[14]

Gerstein's work has been published in peer reviewed scientific journals[1][31][32][33][34][35] and non-scientific publications in more popular forums.[36] 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.

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. He is a Fellow of the AAAS. 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,[37] modENCODE,[38][39][40] 1000 Genomes Project, Brainspan, and DOE Kbase. He was made a Fellow of the International Society for Computational Biology in 2015.[41]

References

  1. ↑ 1.0 1.1 1.2 1.3 Mark Bender Gerstein's publications indexed by Google Scholar, a free service provided by Google
  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. ↑ 3.0 3.1 3.2 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 3291568. 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 3129682. 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 2629784. PMID 19164758.
  10. ↑ Greenbaum, Dov (2004). Comparing mRNA expression and protein abundance via genomic and proteomic characteristics (PhD thesis). Yale University. OCLC 793540375.
  11. ↑ 11.0 11.1 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.
  12. ↑ 12.0 12.1 Gerstein, M; Krebs, W (1998). "A database of macromolecular motions". Nucleic acids research 26 (18): 4280–90. PMC 147832. 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. ↑ 14.0 14.1 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. ↑ Mark Bender Gerstein's publications indexed by the Scopus bibliographic database, a service provided by Elsevier.
  18. ↑ Gerstein, Mark (1993). Protein recognition: surfaces and conformational change (PhD thesis). University of Cambridge.
  19. ↑ 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 3042601. PMID 20981092.
  20. ↑ 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.
  21. ↑ Luscombe, N. M.; Babu, M. M.; Yu, H; Snyder, M; Teichmann, S. A.; Gerstein, M (2004). "Genomic analysis of regulatory network dynamics reveals large topological changes". Nature 431 (7006): 308–12. doi:10.1038/nature02782. PMID 15372033.
  22. ↑ Babu, M. M.; Luscombe, N. M.; Aravind, L; Gerstein, M; Teichmann, S. A. (2004). "Structure and evolution of transcriptional regulatory networks". Current Opinion in Structural Biology 14 (3): 283–91. doi:10.1016/j.sbi.2004.05.004. PMID 15193307.
  23. ↑ Qian, J; Stenger, B; Wilson, C. A.; Lin, J; Jansen, R; Teichmann, S. A.; Park, J; Krebs, W. G.; Yu, H; Alexandrov, V; Echols, N; Gerstein, M (2001). "Parts List: A web-based system for dynamically ranking protein folds based on disparate attributes, including whole-genome expression and interaction information". Nucleic acids research 29 (8): 1750–64. PMC 31319. PMID 11292848.
  24. ↑ Teichmann, Sarah A.; Chothia, Cyrus H.; Gerstein, Mark B. (1999). "Advances in structural genomics". Current Opinion in Structural Biology 9 (3): 390–9. doi:10.1016/S0959-440X(99)80053-0. PMID 10361097.
  25. ↑ Gina Kolata, (Sept. 5, 2012) 'Bits of Mystery DNA, Far From Junk, Play Crucial Role,' NY Times
  26. ↑ 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.
  27. ↑ 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.
  28. ↑ 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.
  29. ↑ 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.
  30. ↑ 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 3228779. PMID 22144881.
  31. ↑ Mark Bender Gerstein's publications indexed by the DBLP Bibliography Server at the University of Trier
  32. ↑ List of publications from Microsoft Academic Search
  33. ↑ 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.
  34. ↑ 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): 2101–2105. doi:10.1126/science.1062191. PMID 11474067.
  35. ↑ Krogan, N. J.; Cagney, G.; Yu, H.; Zhong, G.; Guo, X.; Ignatchenko, A.; Li, J.; Pu, S.; Datta, N.; Tikuisis, A. P.; Punna, T.; Peregrín-Alvarez, J. M.; Shales, M.; Zhang, X.; Davey, M.; Robinson, M. D.; Paccanaro, A.; Bray, J. E.; Sheung, A.; Beattie, B.; Richards, D. P.; Canadien, V.; Lalev, A.; Mena, F.; Wong, P.; Starostine, A.; Canete, M. M.; Vlasblom, J.; Wu, S.; Orsi, C. (2006). "Global landscape of protein complexes in the yeast Saccharomyces cerevisiae". Nature 440 (7084): 637–643. doi:10.1038/nature04670. PMID 16554755.
  36. ↑ [=https://web.archive.org/web/20131017061104/http://info.gersteinlab.org/Other_Papers "List of Non-technical Writing by Mark Gerstein"]. gersteinlab.org. Archived from the original on 2013-10-17.
  37. ↑ 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.
  38. ↑ 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.
  39. ↑ 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.
  40. ↑ 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 3142569. PMID 21177976.
  41. ↑ "Meet the ISCB Fellows Class of 2015". International Society for Computational Biology. Archived from the original on 2015-02-20.