Mark Bender Gerstein

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.^[3]

Education

After graduating from Harvard College summa cum laude with an Bachelor of Arts in Physics in 1989, Gerstein studied under Ruth Lynden-Bell^[2] in the chemistry department of the University of Cambridge and Cyrus Chothia of the British Medical Research Council, earning a PhD in 1993.^[4] He then went on to postdoctoral research in bioinformatics at Stanford University from 1993-1996 under Nobel-laureate Michael Levitt.

Publications and editorial positions

Gerstein has a number of scientific publications^{[5][6][7][8][9][10][11][12]} and non-scientific publications in more popular forums.^[13] His work has been highly cited, with an H greater than 100.^[5] 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 memberships

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,^[14] modENCODE,^[15][16][17] 1000 Genomes Project, Brainspan, and the DOE Kbase

Research

Gerstein does research in the field of bioinformatics and data science. 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,^[18] personal 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, which categorizes macromolecular conformational change; tYNA,^[19] which helps analyze molecular networks; PubNet,^[20] which analyzes publication networks; PeakSeq,^[21] which identifies regions in the genome bound by particular transcription factors; and CNVnator,^[22] 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^[23] and how to structure scientific communication.

Notes and references

1. ↑ 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. 
2. ↑ 2.0 2.1 2.2 Mark Bender Gerstein at the Mathematics Genealogy Project
3. ↑ Mark Bender Gerstein from the Scopus bibliographic database
4. ↑ Gerstein, Mark (1993). Protein recognition: surfaces and conformational change (PhD thesis). University of Cambridge. 
5. ↑ 5.0 5.1 List of publications from Google Scholar
6. ↑ List of publications from the DBLP Bibliography Server
7. ↑ List of publications from Microsoft Academic Search
8. ↑ List of Scientific Papers from the Gerstein Lab
9. ↑ 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. 
10. ↑ 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. 
11. ↑ 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. 
12. ↑ http://www.ncbi.nlm.nih.gov/pubmed?term=mark%20gerstein%5Bau%5D Mark Gerstein publications in PubMed
13. ↑ List of Non-technical Writing by Mark Gerstein
14. ↑ 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. 
15. ↑ 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. 
16. ↑ 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. 
17. ↑ 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. PMID 21177976. 
18. ↑ Gina Kolata, (Sept. 5, 2012) 'Bits of Mystery DNA, Far From Junk, Play Crucial Role,' NY Times
19. ↑ tYNA network analysis program
20. ↑ PubNet publication network analysis program
21. ↑ PeakSeq program for identifying binding sites in chipseq experiments
22. ↑ CNVnator package for identifying structural variants in the genome
23. ↑ 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.