Lincoln Stein

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Lincoln Stein
Lincoln Stein with (far right) Alfonso Valencia (far left) and Sarah Teichmann (center) at the Intelligent Systems for Molecular Biology (ISMB) conference in 2016 in Orlando, Florida.
Lincoln David Stein

1960 (age 63–64)[3]
Alma materHarvard University (PhD)
Scientific career
FieldsGenome Informatics[2]
ThesisCloning of developmentally regulated genes from Schistosoma mansoni (1989)

Lincoln David Stein is a scientist and Professor in bioinformatics and computational biology at the Ontario Institute for Cancer Research.[2][4][5]


Stein completed a Doctor of Medicine at Harvard Medical School and a PhD in Cell Biology at Harvard University both in 1989[6] via the MD-PhD program. His thesis investigated gene cloning in Schistosoma mansoni.[6]


From 1992-1997 he was a director of informatics at the Massachusetts Institute of Technology (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.[citation needed]


Stein's current research projects[2][5] include Reactome,[7] WormBase,[7] BioPerl,[8] Gramene,[9] ENCODE,[10][11][12] the Generic Model Organism Database,[13] the Sequence Ontology[14] and Cloud computing.[15]

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.[16][17][18][19][20]

Awards and honours[edit]

Stein was awarded the Benjamin Franklin Award (Bioinformatics) in 2004.[21] He was elected an ISCB Fellow in 2016 by the International Society for Computational Biology.[1]


  1. ^ a b Anon (2017). "ISCB Fellows". International Society for Computational Biology. Archived from the original on 2017-03-20.
  2. ^ a b c Lincoln Stein publications indexed by Google Scholar
  3. ^ "116663444".
  4. ^ "The Ontario Institute for Cancer Research". Archived from the original on 2011-04-22.
  5. ^ a b Lincoln Stein's publications indexed by the Scopus bibliographic database. (subscription required)
  6. ^ a b Stein, Lincoln David (1989). Cloning of developmentally regulated genes from Schistosoma mansoni. (PhD thesis). Harvard University. OCLC 23368773.
  7. ^ 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 3013646. PMID 21067998.
  8. ^ 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.
  9. ^ 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.
  10. ^ 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.{{cite journal}}: CS1 maint: multiple names: authors list (link)
  11. ^ 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 3192495. PMID 21177974.{{cite journal}}: CS1 maint: multiple names: authors list (link)
  12. ^ 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.
  13. ^ 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.
  14. ^ 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.
  15. ^ 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.
  16. ^ Stein, Lincoln D. (1998). Official guide to programming with CGI. pm: [the standard for building Web scripts]. New York: Wiley. ISBN 978-0-471-24744-9.
  17. ^ Doug MacEachern; Stein, Lincoln D. (1999). Writing Apache Modules with Perl and C. Sebastopol, CA: O'Reilly. ISBN 978-1-56592-567-0.
  18. ^ Stein, Lincoln D. (2001). Network programming with Perl. Boston: Addison-Wesley. ISBN 978-0-201-61571-5.
  19. ^ Stein, Lincoln D. (1997). How to set up and maintain a Web site. Boston: Addison-Wesley. ISBN 978-0-201-63462-4.
  20. ^ Stein, Lincoln D. (1998). Web security: a step-by-step reference guide. Boston: Addison-Wesley. ISBN 978-0-201-63489-1.
  21. ^ 2004 Benjamin Franklin Award Awarded to Lincoln D. Stein