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. She completed her B.Sc. in Biochemistry at the University of Waterloo in 1990 and her Ph.D. under the supervision of Dr. Jo-Anne Dillon at the University of Ottawa in 1996. She completed two postdoctorates at the University of British Columbia under the guidance of Drs Robert (Bob) Hancock and Ann Rose. Originally trained as a microbiologist, she developed an interest in bioinformatics through her graduate and postdoctoral studies, leading her to develop a career in pathogen bioinformatics as a professor starting in 2001.
Brinkman's current research interests center around improving understanding of how pathogens and pathogenicity evolve and improving computational methods that aid the development of new vaccines, drugs and diagnostics for infectious diseases. She is noted for developing , 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. 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 and orthologs. Her research has provided new insights into the evolution of pathogens and the role that horizontal gene transfer and genomic islands play. She was involved in the Pseudomonas Genome Project  and is the coordinator of the , a database of Pseudomonas species genomic data and associated annotations that is continually updated. She is the Research Director, Bioinformatics, of the Genome Canada Pathogenomics Project, and she is co-lead of the Bioinformatics for Combating Infectious Diseases (BCID) project.
Brinkman is married and has a son and a daughter.
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- Canadian Society of Microbiologists Fisher Award (2007)
- Michael Smith Foundation for Health Research Senior Scholar (2007-2012)
- Canadian Institutes of Health Research New Investigator (2005-2010)
- Canadian Who's Who (2005)
- Canada's Top 40 Under 40 (2003)
- Innovation and Science Council of British Columbia (now the BC Innovation Council) Young Innovator Award (2003)
- MIT Technology Review TR100 (2002) as one of the top 100 innovators in the world under the age of 35
- Michael Smith Foundation for Health Research Scholar (2001-2006)
- 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.
- 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.
- Gardy, J.L., and F.S.L. Brinkman (2006). Methods for predicting bacterial protein subcellular localization. Nature Reviews Microbiology 4:741-751.
- 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
- 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.
- 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.
- Brinkman, F.S.L., C.K. Stover, and R.E.W. Hancock (2000). Sequencing solution: use volunteer annotators organized via Internet. Nature.406:933.
- 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.
- "2002 Young Innovators Under 35: Fiona Brinkman, 34". Technology Review. 2002. Retrieved August 14, 2011.