Biography:Suzanna Lewis

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Suzanna Lewis
Known forBiomedical Ontologies
AwardsFellow of the AAAS[1]
Scientific career
InstitutionsLawrence Berkeley National Laboratory
Websiteberkeleybop.org/person/suzanna-lewis
bioperl.org/wiki/Suzi_Lewis

Suzanna (Suzi) E. Lewis is a scientist and Principal Investigator (PI) at the Berkeley Bioinformatics Open-source Project (BBOP) based at Lawrence Berkeley National Laboratory. Lewis leads the development of open standards and software for genome annotation and ontologies.[2][3][4]

Education

Lewis has Master of Science degrees in Biology and Computer science.[5]

Research

She led the team responsible for the systematic annotation[6] of the Drosophila melanogaster genome, which included development of the Gadfly[7] annotation pipeline and database framework, and the annotation curation tool Apollo.[8] Lewis' work in genome annotation also includes playing instrumental roles in the GASP[9] community assessment exercises to evaluate the state of the art in genome annotation, development of the Gbrowse[10] genome browser, and the data coordination center for the modENCODE project.[11] In addition to her work in genome annotation, Lewis has been a leader in the development of Open Biomedical Ontologies (OBO),[12] National Center for Biomedical Ontology (NCBO),[13][14] contributing to the Gene Ontology[15] Sequence Ontology,[16] Uberon anatomy ontologies,[17] and developing open software for editing and navigating ontologies such as AmiGO,[18] OBO-Edit[19] and Phenote.

Awards and honors

In 2005 Lewis was elected a fellow of the American Association for the Advancement of Science in recognition of her contributions to science in the fields of Information, Computing, and Communication.[1]

References

  1. ↑ 1.0 1.1 "AAAS News & Notes". http://www.aaas.org/news/newsandnotes/inside125.shtml. 
  2. ↑ "Nominations for the Benjamin Franklin Award for Open Access in the Life Sciences 2012". http://caseybergman.wordpress.com/2012/02/18/nominations-for-the-benjamin-franklin-award-for-open-access-in-the-life-sciences/. 
  3. ↑ "Suzi Lewis - BioPerl". http://www.bioperl.org/wiki/Suzi_Lewis. 
  4. ↑ "Berkeley Drosophila Genome Project BDGP: Contact Info". http://www.fruitfly.org/about/contacts.html. 
  5. ↑ "Suzanna Lewis: Berkeley Bioinformatics Open-source Projects (BBOP)". Archived from the original on 2012-10-23. https://web.archive.org/web/20121023110705/http://www.berkeleybop.org/person/suzanna-lewis. 
  6. ↑ Misra, S.; Crosby, M.; Mungall, C.; Matthews, B.; Campbell, K.; Hradecky, P.; Huang, Y.; Kaminker, J. et al. (2002). "Annotation of the Drosophila melanogaster euchromatic genome: A systematic review". Genome Biology 3 (12): research0083.research0081–83.research0081. doi:10.1186/gb-2002-3-12-research0083. PMID 12537572. 
  7. ↑ Mungall, C. J.; Misra, S.; Berman, B. P.; Carlson, J.; Frise, E.; Harris, N.; Marshall, B.; Shu, S. et al. (2002). "An integrated computational pipeline and database to support whole-genome sequence annotation". Genome Biology 3 (12): research0081.research0081–81.research0081. doi:10.1186/gb-2002-3-12-research0081. PMID 12537570. 
  8. ↑ Lewis, S. E.; Searle, S. M.; Harris, N.; Gibson, M.; Lyer, V.; Richter, J.; Wiel, C.; Bayraktaroglir, L. et al. (2002). "Apollo: A sequence annotation editor". Genome Biology 3 (12): research0082.research0081–82.research0081. doi:10.1186/gb-2002-3-12-research0082. PMID 12537571. 
  9. ↑ Reese, M. G.; Hartzell, G.; Harris, N. L.; Ohler, U.; Abril, J. F.; Lewis, S. E. (2000). "Genome annotation assessment in Drosophila melanogaster". Genome Research 10 (4): 483–501. doi:10.1101/gr.10.4.483. PMID 10779488. 
  10. ↑ Stein, L. D.; Mungall, C.; Shu, S.; Caudy, M.; Mangone, M.; Day, A.; Nickerson, E.; Stajich, J. E. et al. (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. PMID 12368253. 
  11. ↑ Washington, N. L.; Stinson, E. O.; Perry, M. D.; Ruzanov, P.; Contrino, S.; Smith, R.; Zha, Z.; Lyne, R. et al. (2011). "The modENCODE Data Coordination Center: Lessons in harvesting comprehensive experimental details". Database 2011: bar023. doi:10.1093/database/bar023. PMID 21856757. 
  12. ↑ Smith, B.; Ashburner, M.; Rosse, C.; Bard, J.; Bug, W.; Ceusters, W.; Goldberg, L. J.; Eilbeck, K. et al. (2007). "The OBO Foundry: Coordinated evolution of ontologies to support biomedical data integration". Nature Biotechnology 25 (11): 1251–1255. doi:10.1038/nbt1346. PMID 17989687.  open access
  13. ↑ Musen, M. A.; Noy, N. F.; Shah, N. H.; Whetzel, P. L.; Chute, C. G.; Story, M. -A.; Smith, B.; And The Ncbo, T. (2011). "The National Center for Biomedical Ontology". Journal of the American Medical Informatics Association 19 (2): 190–195. doi:10.1136/amiajnl-2011-000523. PMID 22081220. 
  14. ↑ Rubin, D. L.; Lewis, S. E.; Mungall, C. J.; Misra, S.; Westerfield, M.; Ashburner, M.; Sim, I.; Chute, C. G. et al. (2006). "National Center for Biomedical Ontology: Advancing Biomedicine through Structured Organization of Scientific Knowledge". OMICS: A Journal of Integrative Biology 10 (2): 185–198. doi:10.1089/omi.2006.10.185. PMID 16901225. https://digital.library.unt.edu/ark:/67531/metadc881902/m2/1/high_res_d/890649.pdf. 
  15. ↑ Botstein, D.; Cherry, J. M.; Ashburner, M.; Ball, C. A.; Blake, J. A.; Butler, H.; Davis, A. P.; Dolinski, K. et al. (2000). "Gene ontology: Tool for the unification of biology. The Gene Ontology Consortium". Nature Genetics 25 (1): 25–29. doi:10.1038/75556. PMID 10802651.  open access
  16. ↑ 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. PMID 15892872. 
  17. ↑ Mungall, C. J.; Torniai, C.; Gkoutos, G. V.; Lewis, S. E.; Haendel, M. A. (2012). "Uberon, an integrative multi-species anatomy ontology". Genome Biology 13 (1): R5. doi:10.1186/gb-2012-13-1-r5. PMID 22293552. 
  18. ↑ Carbon S, Ireland A, Mungall CJ, Shu S, Marshall B, Lewis S; AmiGO Hub; Web Presence Working Group (2008). "AmiGO: Online access to ontology and annotation data". Bioinformatics 25 (2): 288–289. doi:10.1093/bioinformatics/btn615. PMID 19033274. 
  19. ↑ Day-Richter, J.; Harris, M. A.; Haendel, M.; Lewis, S. (2007). "OBO-Edit an ontology editor for biologists". Bioinformatics 23 (16): 2198–2200. doi:10.1093/bioinformatics/btm112. PMID 17545183. 




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