Lincoln Stein

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Lincoln Stein
Born Lincoln David Stein
1960 (age 55–56)[1]
Fields Genome Informatics[2]
Alma mater Harvard University
Thesis Cloning of developmentally regulated genes from Schistosoma mansoni (1989)
Notable awards Ben Franklin Award (2004)

Professor Lincoln David Stein is a scientist and leader in bioinformatics and computational biology at the Ontario Institute for Cancer Research.[2][3][4]


Stein completed a Doctor of Medicine at Harvard Medical School and a PhD in Cell Biology at Harvard University both in 1989[5] via the MD-PhD program. His thesis investigated gene cloning in Schistosoma mansoni.[5]


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.


Stein's current research projects[2][4] include Reactome,[6] WormBase,[6] BioPerl,[7] Gramene,[8] ENCODE,[9][10][11] the Generic Model Organism Database,[12] the Sequence Ontology[13] and Cloud computing.[14]

Stein is also the original developer of 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.[15][16][17][18][19]

Awards and honours[edit]

Stein was awarded the Benjamin Franklin Award (Bioinformatics) in 2004.[20]


  1. ^
  2. ^ a b c Lincoln Stein's publications indexed by Google Scholar
  3. ^ The Ontario Institute for Cancer Research
  4. ^ a b Lincoln Stein's publications indexed by the Scopus bibliographic database, a service provided by Elsevier. (subscription required)
  5. ^ a b Stein, Lincoln (1989). Cloning of developmentally regulated genes from Schistosoma mansoni (PhD thesis). Harvard University. 
  6. ^ a b 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 3013646free to read. PMID 21067998. 
  7. ^ 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 187536free to read. PMID 12368254. 
  8. ^ 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 1540266free to read. PMID 12481044. 
  9. ^ 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 3142569free to read. PMID 21177976. 
  10. ^ 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. PMC 3192495free to read. PMID 21177974. 
  11. ^ 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 3245176free to read. PMID 22080565. 
  12. ^ 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 187535free to read. PMID 12368253. 
  13. ^ 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 1175956free to read. PMID 15892872. 
  14. ^ 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 2898083free to read. PMID 20441614. 
  15. ^ 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. 
  16. ^ Doug MacEachern; Stein, Lincoln D. (1999). Writing Apache Modules with Perl and C. Sebastopol, CA: O'Reilly. ISBN 1-56592-567-X. 
  17. ^ Stein, Lincoln D. (2001). Network programming with Perl. Boston: Addison-Wesley. ISBN 0-201-61571-1. 
  18. ^ Stein, Lincoln D. (1997). How to set up and maintain a Web site. Boston: Addison-Wesley. ISBN 0-201-63462-7. 
  19. ^ Stein, Lincoln D. (1998). Web security: a step-by-step reference guide. Boston: Addison-Wesley. ISBN 0-201-63489-9. 
  20. ^ 2004 Benjamin Franklin Award Awarded to Lincoln D. Stein