Lincoln Stein

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Lincoln David Stein
Institutions Ontario Institute for Cancer Research,
Harvard Medical School,
Whitehead Institute,
Cold Spring Harbor Laboratory
Alma mater Harvard University
Thesis Cloning of developmentally regulated genes from Schistosoma mansoni (1989)
Notable awards Benjamin Franklin Award (Bioinformatics)
Website
stein.cshl.org/~lstein
www.cshl.edu/Faculty/stein-lincoln-professor.html
oicr.on.ca/person/researcher/lincoln-stein

Professor Lincoln David Stein is a scientist and leader in bioinformatics and computational biology at the Ontario Institute for Cancer Research.[1]

Education and employment[edit]

Stein completed a Doctor of Medicine at Harvard Medical School and a PhD in Cell Biology at Harvard University both in 1989[2] via the MD/PhD program. His thesis investigated gene cloning in Schistosoma mansoni.[2] From 1992-1997 he was a director of informatics at the MIT Genome Centre, Whitehead Institute of Biomedical Research. From 1998 to 2004 he was an Associate Professor at Cold Spring Harbor Laboratory. He has been working at the Ontario Institute for Cancer Research since 2007.

Research[edit]

Stein's current projects include Reactome,[3] WormBase,[4] BioPerl,[5] Gramene,[6] ENCODE,[7][8][9] the Generic Model Organism Database,[10] the Sequence Ontology[11] and Cloud computing.[12] In 2004, Lincoln was the winner of the Benjamin Franklin Award in Bioinformatics.[13]

Stein is also the original developer of CGI.pm and a contributor to mod_perl, both widely used in the Perl programming language for web applications, as well as many other Perl modules and associated books.[14][15][16][17][18]

References[edit]

  1. ^ http://www.oicr.on.ca/research/stein.htm The Ontario Institute for Cancer Research
  2. ^ a b Stein, Lincoln (1989). Cloning of developmentally regulated genes from Schistosoma mansoni (PhD thesis). Harvard University. 
  3. ^ Croft, D.; O'Kelly, G.; Wu, G.; Haw, R.; Gillespie, M.; Matthews, L.; Caudy, M.; Garapati, P.; Gopinath, G.; Jassal, B.; Jupe, S.; Kalatskaya, I.; Mahajan, S.; May, B.; Ndegwa, N.; Schmidt, E.; Shamovsky, V.; Yung, C.; Birney, E.; Hermjakob, H.; d'Eustachio, P.; Stein, L. (2010). "Reactome: A database of reactions, pathways and biological processes". Nucleic Acids Research 39 (Database issue): D691–D697. doi:10.1093/nar/gkq1018. PMC 3013646. PMID 21067998.  edit
  4. ^ Croft, D.; O'Kelly, G.; Wu, G.; Haw, R.; Gillespie, M.; Matthews, L.; Caudy, M.; Garapati, P.; Gopinath, G.; Jassal, B.; Jupe, S.; Kalatskaya, I.; Mahajan, S.; May, B.; Ndegwa, N.; Schmidt, E.; Shamovsky, V.; Yung, C.; Birney, E.; Hermjakob, H.; d'Eustachio, P.; Stein, L. (2010). "Reactome: A database of reactions, pathways and biological processes". Nucleic Acids Research 39 (Database issue): D691–D697. doi:10.1093/nar/gkq1018. PMC 3013646. PMID 21067998.  edit
  5. ^ Stajich, J. E.; Block, D.; Boulez, K.; Brenner, S.; Chervitz, S.; Dagdigian, C.; Fuellen, G.; Gilbert, J.; Korf, I.; Lapp, H.; Lehväslaiho, H.; Matsalla, C.; Mungall, C. J.; Osborne, B. I.; Pocock, M. R.; Schattner, P.; Senger, M.; Stein, L. D.; Stupka, E.; Wilkinson, M. D.; Birney, E. (2002). "The BioPerl Toolkit: Perl Modules for the Life Sciences". Genome Research 12 (10): 1611–1618. doi:10.1101/gr.361602. PMC 187536. PMID 12368254.  edit
  6. ^ Ware, D. H.; Jaiswal, P.; Ni, J.; Yap, I. V.; Pan, X.; Clark, K. Y.; Teytelman, L.; Schmidt, S. C.; Zhao, W.; Chang, K.; Cartinhour, S.; Stein, L. D.; McCouch, S. R. (2002). "Gramene, a Tool for Grass Genomics". Plant Physiology 130 (4): 1606–1613. doi:10.1104/pp.015248. PMC 1540266. PMID 12481044.  edit
  7. ^ 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.  edit
  8. ^ modENCODE Consortium, Roy S, Ernst J, Kharchenko PV, Kheradpour P, Negre N, Eaton ML, Landolin JM, Bristow CA, Ma L, et al. (2010). "Identification of Functional Elements and Regulatory Circuits by Drosophila modENCODE". Science 330 (6012): 1787–1797. Bibcode:2010Sci...330.1787R. doi:10.1126/science.1198374. PMID 21177974.  edit
  9. ^ Contrino, S.; Smith, R. N.; Butano, D.; Carr, A.; Hu, F.; Lyne, R.; Rutherford, K.; Kalderimis, A.; Sullivan, J.; Carbon, S.; Kephart, E. T.; Lloyd, P.; Stinson, E. O.; Washington, N. L.; Perry, M. D.; Ruzanov, P.; Zha, Z.; Lewis, S. E.; Stein, L. D.; Micklem, G. (2011). "ModMine: Flexible access to modENCODE data". Nucleic Acids Research 40 (Database issue): D1082–D1088. doi:10.1093/nar/gkr921. PMC 3245176. PMID 22080565.  edit
  10. ^ Stein, L. D.; Mungall, C.; Shu, S.; Caudy, M.; Mangone, M.; Day, A.; Nickerson, E.; Stajich, J. E.; Harris, T. W.; Arva, A.; Lewis, S. (2002). "The Generic Genome Browser: A Building Block for a Model Organism System Database". Genome Research 12 (10): 1599–1610. doi:10.1101/gr.403602. PMC 187535. PMID 12368253.  edit
  11. ^ Eilbeck, K.; Lewis, S. E.; Mungall, C. J.; Yandell, M.; Stein, L.; Durbin, R.; Ashburner, M. (2005). "The Sequence Ontology: A tool for the unification of genome annotations". Genome Biology 6 (5): R44. doi:10.1186/gb-2005-6-5-r44. PMC 1175956. PMID 15892872.  edit
  12. ^ Stein, L. D. (2010). "The case for cloud computing in genome informatics". Genome Biology 11 (5): 207. doi:10.1186/gb-2010-11-5-207. PMC 2898083. PMID 20441614.  edit
  13. ^ http://www.bioinformatics.org/franklin/2004/ 2004 Benjamin Franklin Award Awarded to Lincoln D. Stein
  14. ^ Stein, Lincoln D. (1998). Official guide to programming with CGI. pm: [the standard for building Web scripts]. New York: Wiley. ISBN 0-471-24744-8. 
  15. ^ Doug MacEachern; Stein, Lincoln D. (1999). Writing Apache Modules with Perl and C. Sebastopol, CA: O'Reilly. ISBN 1-56592-567-X. 
  16. ^ Stein, Lincoln D. (2001). Network programming with Perl. Boston: Addison-Wesley. ISBN 0-201-61571-1. 
  17. ^ Stein, Lincoln D. (1997). How to set up and maintain a Web site. Boston: Addison-Wesley. ISBN 0-201-63462-7. 
  18. ^ Stein, Lincoln D. (1998). Web security: a step-by-step reference guide. Boston: Addison-Wesley. ISBN 0-201-63489-9.