American bioinformatician
Mark Bender Gerstein is an American scientist working in
bioinformatics and
Data Science . As of 2009
[update] , he is co-director of the
Yale
Computational Biology and Bioinformatics program.
Mark Gerstein is
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 .
[8] In 2018, Gerstein was named co-director of the
Yale Center for Biomedical Data Science.
[9]
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
[5] at the
University of Cambridge and
Cyrus Chothia at the
Laboratory of Molecular Biology on
conformational change in proteins, graduating in 1993.
[10] 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 .
[3]
[11]
[12] 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,
[13]
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,
[14] which helps analyze molecular networks; PubNet,
[15] which analyzes publication networks; PeakSeq,
[16] which identifies regions in the genome bound by particular transcription factors; and CNVnator,
[17] 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
[18] and to structuring scientific communication.
[19]
Gerstein's work has been published in
peer reviewed
scientific journals
[20]
[21]
[22] and non-scientific publications in more popular forums.
[23] 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,
[24]
[25]
[26] including on the front page,
[13] 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 .
[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 ,
[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 in 2015.
[2]
References
^
a
b
"Yale Scientists Awarded AAAS Fellowship" .
^
a
b
"Meet the ISCB Fellows Class of 2015" .
International Society for Computational Biology . Archived from
the original on 2015-02-20.
^
a
b
c
Mark B. Gerstein publications indexed by
Google Scholar
^
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 .
^
a
b
Mark B. Gerstein at the
Mathematics Genealogy Project
^
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 .
^
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
147832 .
PMID
9722650 .
^
Mark B. Gerstein's publications indexed by the
Scopus bibliographic database. (subscription required)
^ Xiong, Amy (February 9, 2018).
"Yale establishes biomedical data science center" . yaledailynews.com . Retrieved 2020-09-27 .
^
Gerstein, Mark (1993).
Protein recognition: surfaces and conformational change (PhD thesis). University of Cambridge.
^
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 .
^ 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 .
^
a
b Gina Kolata, (Sept. 5, 2012) '
Bits of Mystery DNA, Far From Junk, Play Crucial Role ,' NY Times
^ 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 .
^ 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 .
^ 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 .
^ 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 .
^ 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.
Bibcode :
2011PLSCB...7E2278G .
doi :
10.1371/journal.pcbi.1002278 .
PMC
3228779 .
PMID
22144881 .
^ 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 .
^
Mark Gerstein at
DBLP Bibliography Server
^
Mark B. Gerstein publications indexed by
Microsoft Academic
^ 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 .
^
"List of Non-technical Writing by Mark Gerstein" . gersteinlab.org. Archived from
the original on 2013-10-17.
^ Kolata, Gina (2013-06-16).
"Poking Holes in Genetic Privacy" . The New York Times .
ISSN
0362-4331 . Retrieved 2016-01-18 .
^ Zimmer, Carl (2014-09-01).
"Tiny, Vast Windows Into Human DNA" . The New York Times .
ISSN
0362-4331 . Retrieved 2016-01-18 .
^
"Thoughts on Genes" . The New York Times . 2008-11-10.
ISSN
0362-4331 . Retrieved 2016-01-18 .
^
"Scientists Unveil New Blueprint Of How The Human Genome Works" . courant.com . Retrieved 2016-01-18 .
^ 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 .
^
"Donaghue Foundation selects five investigators for long-term support" . medicine.yale.edu . Retrieved 2020-09-27 .
^ 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 .
^ 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 .
^ 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 .
^ 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 .
^ 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): eaat7615.
Bibcode :
2018Sci...362.7615L .
doi :
10.1126/science.aat7615 .
ISSN
0036-8075 .
PMC
6413317 .
PMID
30545854 .
External links
2009 2010 2011 2012 2013 2014 2015 2016 2017 2018 2019 2020 2021 2022
International National Academics