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Fiona Brinkman

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Brinkman in 2013

Fiona Brinkman (née Lawson) is a Professor in Bioinformatics and Genomics in the Department of Molecular Biology and Biochemistry at Simon Fraser University in British Columbia, Canada, and is a leader in the area of microbial bioinformatics. She is interested in developing "more sustainable, holistic approaches for infectious disease control and conservation of microbiomes".[1]

Education

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Brinkman received her B.Sc. in Biochemistry from the University of Waterloo in 1990 and earned her Ph.D. under the supervision of Dr. Jo-Anne Dillon at the University of Ottawa in 1996. She completed two post-doctorate fellowships at the University of British Columbia under the guidance of Drs Robert (Bob) Hancock and Ann Rose. Though originally trained as a microbiologist, she developed an interest in bioinformatics throughout her graduate and postdoctoral studies, combining the fields when she started her own group focused on pathogen/microbial bioinformatics at Simon Fraser University in 2001.

Research

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Brinkman's current research interests center around improving understanding of how microbes evolve and improving computational methods that aid the analysis of microbes and the development of new vaccines, drugs and diagnostics for infectious diseases. Increasingly her methods have been applied for more environmental applications. She is noted for developing PSORTb,[2][3] the most precise method available for computational protein subcellular localization prediction and the first computational method that exceeded the accuracy of some common high-throughput laboratory methods for such subcellular localization analysis.[4][5] This method aids the prediction of cell surface and secreted proteins in a bacterial cell that may be suitable drug targets, vaccine components or diagnostics. She has also developed bioinformatics methods that aid the more accurate identification of genomic islands (i.e. IslandViewer) and orthologs (i.e. OrtholugeDB). Her research has provided new insights into the evolution of pathogens and the role that horizontal gene transfer and genomic islands play.[6][7][8] She confirmed the anecdotal assumption that virulence factors (disease-causing genes in pathogens) are disproportionately associated with genomic islands.[9] She was among the first researchers to use whole genome sequencing to aid infectious disease outbreak investigations ("genomic epidemiology"), integrating genome sequence data with social network analysis.[10] She was involved in the Pseudomonas Genome Project[11][12] and is the coordinator of the Pseudomonas genome database, a database of Pseudomonas species genomic data and associated annotations that is continually updated. She has also developed databases (i.e. InnateDB and the Allergy and Asthma Portal) to aid more systems-based analysis of immune disorders and the immune response to infections in humans and other animals - databases that have aided the identification of new immune-modulating therapeutics.[13][14][15] She has a growing interest in applying her methods to environmental applications as part of a broader interest in developing approaches for more holistic, sustainable infectious disease control and microbiome conservation - developing approaches that may select less for antimicrobial resistance, improve the tracking of pathogens and their origins, and better factor in the important role of societal changes and the environment in shaping microbiomes.[16][17][8][10]

Awards

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Professional service

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Brinkman has a long-standing interest in bioinformatics training, improving the curation of biological/bioinformatics data, and developing effective bioinformatics data standards and databases[31][32][33][34][35][36] including the Pseudomonas aeruginosa Community Annotation Project[37] and Pseudomonas Genome Database.

She chairs the Scientific Advisory Board for The European Nucleotide Archive (EMBL-EBI) and serves as a member of several other boards, including the Genome Canada Board of Directors[38] and the Scientific Advisory Board for REACTOME. Brinkman also co-leads the Integrated Rapid Infectious Disease Analysis (IRIDA) Project and Consortium[39] and is a founding member of the Genomic Epidemiology Ontology (GenEpiO) Consortium[40] and the Food Ontology (FoodOn)[41] Group.

In the Vancouver academic community, Brinkman currently serves as the Co-Director of the Bioinformatics Graduate Training Program run through Simon Fraser University, the University of British Columbia, and the BC Cancer Agency and as the SFU representative for the Canadian Society of Microbiologists. She is a Core Faculty Member for the Canadian Bioinformatics Workshops.

Notable graduates from her lab include Jennifer Gardy.

Personal biography

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The daughter of Scottish parents, Brinkman was born in Melbourne, Australia, in 1967. She immigrated to Canada as a child where she grew up primarily in Mississauga, Ontario. Brinkman lives in Coquitlam with her family, including a son and a daughter.

See also

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References

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  1. ^ "Fiona Brinkman Laboratory - Microbe-loving bioinformatics and genomics research lab, aiming to better control infectious diseases in a sustainable way". Brinkman.mbb.sfu.ca. Retrieved 2 November 2017.
  2. ^ Gardy, J.L., C. Spencer, et al. (2003). PSORT-B: Improving protein subcellular localization prediction for Gram-negative bacteria. Nucleic Acids Res 31:3613-7.
  3. ^ Gardy, J.L., M. Laird, F. Chen, S. Rey, C.J. Walsh, G.E. Tusnády, M. Ester, F.S.L. Brinkman (2005). PSORTb v.2.0: Expanded prediction of bacterial protein subcellular localization and insights gained from comparative proteome analysis. Bioinformatics. 21:617-623.
  4. ^ Gardy, J.L., and F.S.L. Brinkman (2006). Methods for predicting bacterial protein subcellular localization. Nature Reviews Microbiology 4:741-751.
  5. ^ Rey, S., J.L. Gardy, and F.S.L. Brinkman (2005). Assessing the precision of high-throughput computational and laboratory approaches for the genome-wide identification of protein subcellular localization in bacteria. BMC Genomics 6:162
  6. ^ Hsiao, W.W.L., K. Ung, D. Aeschliman, J. Bryan, B.B. Finlay and F.S.L. Brinkman (2005). Evidence of a large novel gene pool associated with prokaryotic genomic islands. PLoS Genetics 1:e62.
  7. ^ Brinkman F.S.L., Blanchard J.L., Cherkasov A., Greberg H., Av-Gay Y., Brunham R.C., Fernandez R.C., Finlay B.B., Otto S.P., Ouellette B.F.F., Keeling P.J., Rose A.M., Hancock R.E.W., Jones S.J. (2002). Evidence that plant-like genes in Chlamydia species reflect an ancestral relationship between Chlamydiaceae, cyanobacteria, and the chloroplast. Genome Research. 12:1159-1167.
  8. ^ a b Gill, E., and F.S.L. Brinkman (2011). The proportional lack of archaeal pathogens: do phages hold the key? BioEssays 33:248-254.
  9. ^ Ho Sui, S.J., Fedynak, A., Langille, M.G.I., Hsiao, W.W., and F.S.L. Brinkman (2009). The association of virulence factors with genomic islands. PLoS ONE 4:e8094.
  10. ^ a b Gardy, J.L.*, J.C. Johnston*, S.J. Ho Sui*, S.J. Jones, V.J. Cook, L. Shah, E. Brodkin, S. Rempel, M. Lem, M.K. Sharma, K. Elwood, F.S.L. Brinkman, R.C. Brunham, and P. Tang (2011). Genomic Epidemiology of a Tuberculosis Outbreak: Whole Genome Sequencing and Social Network Analysis Reveal Transmission Dynamics (*these authors contributed equally) The New England Journal of Medicine 364:730-739.
  11. ^ Brinkman, F.S.L., C.K. Stover, and R.E.W. Hancock (2000). Sequencing solution: use volunteer annotators organized via Internet. Nature.406:933.
  12. ^ Stover, K.C., X.Q. Pham, A.L. Erwin, S.D. Mizoguchi, P. Warrener, M.J. Hickey, F.S.L. Brinkman, W. O. Hufnagle, D.J. Kowalik, M. Lagrou, R.L. Garber, L. Goltry, E. Tolentino, S. Westbrock-Wadman, Y. Yuan, L.L. Brody, S.N. Coulter, K.R. Folger, A. Kas, K. Larbig, R. Lim, K. Smith, D. Spencer, G.K.-S. Wong, Z. Wu, I. Paulsen, J. Reizer, M.H. Saier, R.E.W. Hancock, S. Lory, and M.V. Olson (2000). Complete genome sequence of Pseudomonas aeruginosa PAO1: an opportunistic pathogen. Nature. 406: 959-964.
  13. ^ Achtman, A.H. S. Pilat, C.W. Law, D.J. Lynn, L. Janot, M. Mayer, S. Ma, J. Kindrachuk, B.B. Finlay, F.S.L. Brinkman, G.K. Smyth, R.E.W. Hancock, L. Schofield (2012). Effective adjunctive therapy by an innate defense regulatory peptide in a pre-clinical model of severe malaria. Science Translational Medicine 4:135ra64.
  14. ^ The Bovine Genome Sequencing and Analysis Consortium, C.G. Elsik, R.L. Tellam, K.C. Worley (2009). The Genome Sequence of Taurine Cattle: A window to ruminant biology and evolution. Science. 24:522-528.
  15. ^ Lynn, D.J., G.L. Winsor, C. Chan, N. Richard, M.R. Laird, A. Barsky, J.L. Gardy, F.M. Roche, T.H.W. Chan, N. Shah, R. Lo, M. Naseer, J. Que, M. Yau, M. Acab, D. Tulpan, M. Whiteside, A. Chikatamarla, B. Mah, T.M. Munzner, K. Hokamp, R.E.W. Hancock, and F.S.L. Brinkman (2008). Facilitating Systems Level Analyses of the Mammalian Innate Immune Response. Molecular Systems Biology. 4:218.
  16. ^ O’Doherty KC, Neufeld JD, Brinkman FSL, Gardner H, Guttman DS, and Beiko RG (2014), Opinion: Conservation and stewardship of the human microbiome. Proceedings of the National Academy of Sciences USA 111:14312-14313.
  17. ^ Ho Sui, S.J., R. Lo, A.R. Fernandes, M.D.G. Caulfield, J.A. Lerman, L. Xie, P.E. Bourne, D.L. Baillie and F.S.L. Brinkman (2012). The estrogen receptor modulator Raloxifene attenuates Pseudomonas aeruginosa virulence. International Journal of Antimicrobial Agents 2012 40:246-251.
  18. ^ "Five SFU faculty members named to Royal Society of Canada Fellowship and College - SFU News - Simon Fraser University". www.sfu.ca. Retrieved 2018-11-29.
  19. ^ "Thomson Reuters Announces the World's Most Influential Scientific Minds 2014". Thomson Reuters. Archived from the original on March 27, 2015.
  20. ^ "HCR Clarivate Analytics". Highlycited.com. Retrieved 2 November 2017.
  21. ^ "HCR Clarivate Analytics". Thomsonreuters.com. Retrieved 2 November 2017.
  22. ^ "Canada's Most Powerful Women: Top 100". Wxnetwork.com. WXN - Women's Executive Network. Retrieved November 2, 2017.
  23. ^ "Canadian Society of Microbiologists - Past Winners". Csm-scm.org. Retrieved 2 November 2017.
  24. ^ a b "Fiona SL Brinkman - Michael Smith Foundation for Health Research". Msfhr.org. 2012-12-18. Retrieved 2 November 2017.
  25. ^ "Pathogen bioinformatics and the evolution of microbial virulence - Michael Smith Foundation for Health Research". Msfhr.org. 2007-01-02. Retrieved 2 November 2017.
  26. ^ "Federal funding bolsters health-related research at SFU - Canadian University Press Releases". Canadian-universities.net. Retrieved 2 November 2017.
  27. ^ "Canadian Who's Who". Canadian Who's Who. Retrieved 2 November 2017.
  28. ^ "Canada's Top 40 Under 40 Award Program - Caldwell Partners". Caldwellpartners.com. Retrieved 2 November 2017.
  29. ^ Sloot, Corrie (7 November 2003). "Annex Business Media - Canada - Publishing - Printing - Magazine - B2B". Labcanada.com. Retrieved 2 November 2017.
  30. ^ "2002 Young Innovators Under 35: Fiona Brinkman, 34". Technology Review. 2002. Retrieved August 14, 2011.
  31. ^ Brinkman, F.S.L., C.K. Stover, and R.E.W. Hancock (2000). Sequencing solution: use volunteer annotators organized via Internet. Nature. 406:933.
  32. ^ Winsor, G., R. Lo, S.J. Ho Sui, K.S.E. Ung, S. Huang, D. Cheng, W.-K. Ho Ching, R.E.W. Hancock, and F.S.L. Brinkman (2005). Pseudomonas aeruginosa Genome Database and PseudoCAP: Facilitating community-based, continually updated, genome annotation. Nucleic Acids Research. 33:D338-343.
  33. ^ Lynn, D.J., C. Chan, M. Naseer, M. Yau, R. Lo, A. Sribnaia, G. Ring, J. Que, K. Wee, G.L. Winsor, M.R. Laird, K. Breuer, A.K. Foroushani, F.S.L. Brinkman, R.E.W. Hancock (2010). Curating the Innate Immunity Interactome. BMC Systems Biology 4:117.
  34. ^ Orchard, S., Kerrien, S., Abbani, S., Aranda, B., Bhate, J., Bidwell, S., Bridge, A., Briganti, L., Brinkman, F.S.L., Cesareni, G., Chatr-aryamontri, A., Chautard, E., Chen, C., Dumousseau, M., Eisenberg, D., Goll, J., Hancock, R.E.W., Hannick, L.I., Jurisica, I., Khadake, J., Lynn, D.J., Mahadevan, U., Perfetto, L., Raghunath, A., Ricard-Blum, S., Roechert, B., Salwinski, L., Stümpflen, V., Tyers, M., Uetz, P., Xenarios, I., Hermjakob, H. (2012). Protein Interaction Data Curation - The International Molecular Exchange Consortium (IMEx). Nature Methods 9:345-350.
  35. ^ B. Aranda, H. Blankenburg, S. Kerrien, F.S.L. Brinkman, A. Ceol, E. Chautard, J.M. Dana, J. De Las Rivas, M. Dumousseau, E. Galeota, A. Gaulton, J. Goll, R.E.W. Hancock, R. Isserlin, R.C. Jimenez, J.. Kerssemakers, J. Khadake, D.J. Lynn, M. Michaut, G. O’Kelly, K. Ono, S. Orchard, C. Prieto, S. Razick, O. Rigina, L. Salwinski, M. Simonovic, S. Velankar, A. Winter, G. Wu, G.D. Bader, G. Cesareni, I.M. Donaldson, D. Eisenberg, G.J. Kleywegt, J. Overington, S. Ricard-Blum, M. Tyers, M. Albrecht, H. Hermjakob (2011). PSICQUIC and PSISCORE – Accessing and Scoring Molecular Interactions. Nature Methods. 8:528-529.
  36. ^ Breuer, K., Foroushani, A, Laird, M.R., Chen, C., Sribnaia, A., Lo, R., Winsor, G.L., Hancock, R.E.W, Brinkman, F.S.L., and Lynn, D. (2013) InnateDB: systems biology of innate immunity and beyond - recent updates and continuing curation. Nucleic Acids Research. (Database issue) 41: D1228-D1233.
  37. ^ "The Pseudomonas Community Annotation Project". www.pseudomonas.com. Retrieved 2018-11-29.
  38. ^ "Fiona Brinkman | Genome Canada". www.genomecanada.ca. Retrieved 2018-11-29.
  39. ^ "IRIDA – Integrated Rapid Infectious Disease Analysis Project". www.irida.ca. Retrieved 2018-11-29.
  40. ^ "Genomic Epidemiology Ontology". Genomic Epidemiology Ontology. Retrieved 2018-11-29.
  41. ^ "FoodOn by FoodOntology". foodontology.github.io. Retrieved 2018-11-29.
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