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Publications

Search for publications automatically through Medline/PubMed
(Plus some additional computer science-oriented publications can be viewed through a CS biblography.
Note that Dr. Brinkman's surname changed due to marriage from Lawson to Brinkman in 1997.)

Selected Publications
(since 2000)

  • Gong, J.-H. E.F. Nicholls, M.R. Elliott, K.L. Brown, K. Hokamp, F.M. Roche, C.Y Cheung, R. Falsafi, F.S.L. Brinkman, D.M Bowdish, and R.E.W. Hancock (2010). G-protein-coupled receptor independent, immunomodulatory properties of chemokine CXCL9. Cellular Immunology In Press.

  • 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.

  • J.L. Gardy*, Lynn, D.L.*, F.S.L. Brinkman and R.E.W. Hancock (2009). Enabling a systems biology approach to immunology: focus on innate immunity. Trends in Immunology 30:249-262. (*co-1st authors)
  • 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. (David Lynn of our group was one of the 13 members of the lead analysis organization)
  • Langille, M.G.I., and F.S.L. Brinkman (2009). IslandViewer: an integrated interface for computational identification and visualization of genomic islands. Bioinformatics 25:664-665.
  • Langille, M.G.I., and F.S.L. Brinkman (2009). Bioinformatic detection of horizontally transferred DNA in bacterial genomes. F1000 Biology Reports 1:25.
  • Winsor, G.L., T. Van Rossum, R. Lo, M.D. Whiteside, B. Kairha, R.E.W. Hancock and F.S.L. Brinkman (2009). Pseudomonas Genome Database: Facilitating User-Friendly, Comprehensive Comparisons of Microbial Genomes. Nucleic Acids Research. 37:D483-488.
  • C. Winstanley, M.G.I. Langille, J. Fothergill, I. Kucabic-Ibruls, C. Paradis-Bleau, F. Sanschagrin, N. Thompson, G.L. Winsor, M.A. Quail, N. Lennard, A. Bignell, L. Clarke, K. Seeger, D. Saunders, D. Harris, R.E.W. Hancock, J. Parkhill, F.S.L. Brinkman, and R.C. Levesque (2009). Newly introduced genomic prophage islands are critical determinants of in vivo competitiveness in the Liverpool Epidemic Strain of Pseudomonas aeruginosa. Genome Research. 19:12-23. (Reviewed/highlighted in Lancet ID)
  • Brinkman, F.S.L., and J. Parkhill (2008). Population genomics: Modeling the new and a renaissance of the old. Current Opinion in Microbiology. 11:439-441.
  • Winsor, G.L., B. Kairha, T. Van Rossum, R. Lo, M.D. Whiteside and F.S.L. Brinkman (2008). The Burkholderia Genome Database: Facilitating flexible queries and comparative analyses. Bioinformatics 24:2803-2804.
  • 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. (Reviewed/highlighted in Cell Host and Microbe)
  • Langille, M.G.I., W.W.L. Hsiao and F.S.L. Brinkman (2008). Evaluation of genomic island predictors using a comparative genomics approach. BMC Bioinformatics. 9:329.
  • Langille, M.G.I., F. Zhou, W.W.L. Hsiao, A. Fedynak, Y. Xu, and F.S.L. Brinkman (2008). Mobile genetic elements and their prediction. In Press. In Xing Yu and J. Peter Gogarten (eds.), Computational Methods for Understanding Bacterial and Archaeal Genomes, World Scientific Publishing, USA.
  • Platt M.D., M.J. Schurr, K. Sauer, G. Vazquez, I. Kukavia-Ibrulj, E. Potvin, R.C. Levesque, A. Fedynak, F.S.L. Brinkman, J. Schurr, S. Hwang, G.W. Lau, P.A. Limbach, J.J. Rowe, M.A. Lieberman, N. Barraud, J. Webb, S. Kjelleberg, D.F. Hunt, and D.J. Hassett (2008) Proteomic, Microarray and Signature Tagged Mutagenesis Analysis of Anaerobic Pseudomonas aeruginosa at pH 6.5, Representing Chronic Cystic Fibrosis Airway Conditions. Journal of Bacteriology 190:2739-2758.
  • S. Vivona, J.L. Gardy, S. Ramachandran, F.S.L. Brinkman, G.P.S. Raghava, D.R. Flower and F. Filippini (2008). Computer Aided Biotechnology: from Immunoinformatics to Reverse Vaccinology. Trends in Biotechnology. 26:190-200.
  • Lynn, D.J., R. Higgs, A.T. Lloyd, V. Herve-Grepinet, Y. Nys, F.S.L. Brinkman, P.-L. Yu, A. Soulier, P. Kaiser, G. Zhang, C. O'Farrelly, and R.I. Lehrer (2007). Avian Beta-Defensin Nomenclature: A Community Proposed Update. Immunology Letters. 110:86-89.
  • McLeod, M.P., R.L. Warren, W.W.L. Hsiao, N. Araki, M. Myhre, C. Fernandes, D. Miyazawa, W. Wong, A.L. Lillquist, D. Wang, M. Dosanjh, H. Hara, A. Petrescu, R.D. Morin, G. Yang, J.M. Stott, J.E. Schein, H. Shin, D. Smailus, A.S. Siddiqui, M.A. Marra, S.J.M. Jones, R. Holt, F.S.L. Brinkman, K. Miyauchi, M. Fukuda, J.E. Davies, W.W. Mohn, and L.D. Eltis. (2006). The complete genome of Rhodococcus sp. RHA1 provides insights into a catabolic powerhouse. Proceedings of the National Academy of Sciences 103:15582-15587.
  • Gardy, J.L. and F.S.L. Brinkman (2006). Methods for predicting bacterial protein subcellular localization. Nature Reviews Microbiology 4, 741-751.
  • Mookherjee, N., H.L. Wilson, S. Doria, Y. Popowych, R. Falsafi, J, Yu, Y. Li, S. Veatch, F.M. Roche, K.L. Brown, F.S.L. Brinkman, K. Hokamp, A. Potter, L.A. Babiuk, P.J. Griebel and R.E.W. Hancock (2006). Bovine and human cathelicidin cationic host defence peptides similarly suppress transcriptional responses to bacterial lipopolysaccharide. Journal of Leukocyte Biology. 80:[Advanced online publication Aug 30, 2006)
  • Fulton, D.L., Y.Y. Li, M. Laird, B.G.S. Horsman, F.M. Roche and F.S.L. Brinkman (2006). Improving the specificity of high-throughput Ortholog prediction. BMC Bioinformatics. 7:270.
    (This version of Ortholuge was also profiled in the April 11, 2006 issue of BioArray News)
  • Gardy, J.L., and F.S.L. Brinkman (2006). Methods for the computational prediction of periplasmic proteins. In Press. In M. Ehermann (ed.), The Periplasm. ASM Press, USA.
  • Brinkman, F.S.L. (2006) The Pseudomonas Genome Database. pp. 341-361 In J.L. Ramos and R.C. Levesque (ed.), Pseudomonas, Vol. 4. Springer, Dordrecht, The Netherlands.
  • McPhee, J.B., M. Bains, G. Winsor, S. Lewenza, A. Kwasnicka, M.D. Brazas, F.S.L. Brinkman, and R.E.W. Hancock (2006). Contribution of the PhoP-PhoQ and PmrA-PmrB two-component regulatory systems to Mg2+-induced gene regulation in Pseudomonas aeruginosa. Journal of Bacteriology 188:3995-4006.
  • Mookherjee, N., K. Brown, D.M. Bowdish, S. Doria, R. Falsafi, K. Hokamp, F.M. Roche, R. Mu, G. Doho, J. Pistolic, J.-P. Powers, J. Bryan, F.S.L. Brinkman and R.E.W. Hancock (2006). Modulation of the Toll-like receptor-mediated inflammatory response by the endogenous human host defence peptide LL-37. Journal of Immunology. 176:2455-2464.
  • 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.
    (This work further suggests that microbes may have access to a larger arsenal of genes for medically and environmentally important adaptations than previously appreciated. Cited in Faculty of 1000)
  • 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.
    (Demonstrates that the PSORTb method we developed is the first computational method for protein subcellular localization prediction that exceeds the precision of high-throughput laboratory/proteomic methods.)
  • Hodgson P.D., P. Aich, A. Manuja, K. Hokamp, F.M. Roche, F.S.L. Brinkman, A. Potter, L.A. Babiuk, P.J. Griebel (2005). Effect of Stress on Viral-Bacterial Synergy in Bovine Respiratory Disease: Novel Mechanisms to Regulate Inflammation. Comparative and Functional Genomics 6: 244–250.
  • Coombes, B.K., M.E. Wickham, N.F. Brown, S. Lemire, L. Bossi, W.W.L. Hsiao, F.S.L. Brinkman, B.B. Finlay (2005). Genetic and molecular analysis of GogB, a phage-encoded type III-secreted substrate in Salmonella enterica serovar Typhimurium with autonomous expression from its associated phage. Journal of Molecular Biology 348:817-830.
  • Wilson, H.L., P. Aich, F.M. Roche, S. Jalal, P.D. Hodgson, F.S.L. Brinkman, A. Potter, L.A. Babiuk, and P.J. Griebel (2005). Molecular Analyses of Disease Pathogenesis: Application of Bovine Microarrays. Veterinary Immunology and Immunopathology 105:277-287.
  • Marshall, C.R., J.A. Fox, S.L. Butland, B.F.F. Ouellette, F.S.L. Brinkman, and G.F. Tibbits (2005). Phylogeny of Na+-Ca2+ Exchanger (NCX) genes from genomic data identifies new gene duplications and a new family member in fish species. Physiological Genomics 21:161-173.
  • Lewenza, S., R.K. Falsafi, G. Winsor, W. James Gooderham, J.B. McPhee, F.S.L. Brinkman and R.E.W. Hancock (2005). Construction of a mini-Tn5-luxCDABE mutant library in Pseudomonas aeruginosa PAO1: a tool for identifying differentially regulated genes. Genome Research 15:583-589.
  • Gardy, J.L., M. Laird, F. Chen, S. Rey, C.J. Walsh, G.E. Tusnády, M. Ester, F.S.L. Brinkman (2005). PSORT-B v.2.0: Expanded prediction of bacterial protein subcellular localization and insights gained from comparative proteome analysis. Bioinformatics. 21:617-623.
    (Reports new version of PSORTb that has higher recall but is still the most precise predictor of protein subcellular localization. Noted for its high CS citation rate by Thompson Scientific Essential Science Indicators.)
  • Brinkman, F.S.L. (2005). Phylogenetic analysis of BLAST results In M. Dunn Encyclopedia of Genetics, Genomics, Proteomics and Bioinformatics. John Wiley & Sons. In Press.
  • Lewenza, S., J.L. Gardy, F.S.L. Brinkman and R.E.W. Hancock (2005). Genome-wide identification of Pseudomonas aeruginosa exported proteins using a consensus computational strategy combined with a laboratory-based PhoA fusion screen. Genome Research 15:321-329.
  • Rey, S., M. Acab, J.L. Gardy, M.R. Laird, K. deFays, C. Lambert, and F.S.L. Brinkman (2005). PSORT-DB: A Database of Subcellular Localizations for Bacteria. Nucleic Acids Research 33:D164-168. (Database issue)
  • 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. (Database issue)
  • Brinkman, F.S.L. and J.L. Fueyo (2004). Bioinformatics and Microbial Pathogenesis. In C.M. Fraser, K.E. Nelson, and T.M. Read (ed.), Microbial Genomics. Humana Press Inc., USA.
  • Brinkman, F.S.L. (2004). Phylogenetic analysis. In A.D. Baxevanis and B.F.F. Ouellette (ed.), Bioinformatics: A practical guide to the analysis of genes and proteins, 3rd Edition. John Wiley & Sons, USA.
  • Warren, R., W.W.L. Hsiao, H. Kudo, M. Myhre, M. Dosanjh, A. Petrescu, H. Kobayashi, S. Shimizu, K. Miyauchi, E. Masai, G. Yang, J.M. Stott, J.E. Schein, H. Shin, J. Khattra, D. Smailus, R. Holt, S. Jones, W.W. Mohn, F.S.L. Brinkman, M. Fukuda, J. Davies, and L.D. Eltis (2004). Functional Characterization of a Catabolic Plasmid from PCB-Degrading Rhodococcus sp. RHA1. Journal of Bacteriology. 186:7783-7795.
    (Cited by Faculty of 1000)
  • Hassett, D.J., S.V. Lymar, J.J. Rowe, M.J. Schurr, L. Passador, A.B. Herr, G.L. Winsor, F.S.L. Brinkman, S.S. Yoon, G.W. Lau, and S.H. Hwang (2004). Anaerobic Metabolism by Pseudomonas aeruginosa in Cystic Fibrosis Airway Biofilms: Role of Nitric Oxide, Quorum Sensing, and Alginate Production. In M.M. Nakano and P. Zuber (ed.), Strict and Facultative Anaerobes: Medical and Environmental Aspects. Horizon Scientific Press, Wymondham, U. K.
  • Roche, F.M. K. Hokamp, M. Acab, L.A. Babiuk, R.E.W. Hancock, and F.S.L. Brinkman (2004). ProbeLynx: A tool for updating the association of microarray probes to genes. Nucleic Acids Research. 32:W457-9.
  • Hokamp, K., F.M. Roche, M. Acab, M.-E. Rousseau, B. Kuo, D. Goode, D. Aeschliman, J. Bryan, L.A. Babiuk, R.E.W. Hancock, and F.S.L. Brinkman (2004). ArrayPipe: a flexible processing pipeline for microarray data. Nucleic Acids Research. 32:W471-4.
  • R. She, F. Chen, K. Wang, M. Ester, J.L. Gardy, and F.S.L. Brinkman (2003). Frequent-Subsequence-Based Prediction of Outer Membrane Proteins. Ninth ACM SIGKDD on Knowledge Discovery and Data Mining. 436-445.
  • Gardy, J.L., C. Spencer, K. Wang, M. Ester, G.E. Tusnády, I. Simon, S. Hua, K. deFays, C. Lambert, K. Nakai and F.S.L. Brinkman (2003). PSORT-B: Improving protein subcellular localization prediction for Gram-negative bacteria. Nucleic Acids Research. 31: 3613-3617.
    (first version of PSORTb)
  • Gardy, J.L. and F.S.L. Brinkman (2003). The Benefits of Interdisciplinary Research: Our Experiences With Pathogen Bioinformatics. Science - Next Wave. 17 January 2003.
  • Hsiao, W., I. Wan, S.J. Jones, and F.S.L. Brinkman (2003). IslandPath: Aiding detection of genomic islands in prokaryotes. Bioinformatics. 19: 418-420.
  • Jo, J.T.H., F.S.L. Brinkman and R.E.W. Hancock (2003). Aminoglycoside efflux in Pseudomonas aeruginosa: Involvement of novel outer membrane proteins. Antimicrobial Agents and Chemotherapy. 47:1101-1111.
  • 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.
    (Cited by Faculty of 1000)
  • Hancock, R.E.W. and F.S.L. Brinkman (2002). Functions of Pseudomonas Porins in Uptake and Efflux. Annual Review of Microbiology. 56:17-38.
  • Brinkman, F.S.L., E.L.A. Macfarlane, P. Warrener, and R.E.W. Hancock (2001). Evolutionary relationships amongst virulence-associated histidine kinases. Infection and Immunity. 69:5207-11. (Highlighted in the September issue of ASM News, the American Society for Microbiology Newsletter)Model of OprM, from Wong et al., 2001
     
  • Brinkman, F.S.L., I. Wan, R.E.W. Hancock, A.M. Rose and S.J. Jones (2001). PhyloBLAST: facilitating phylogenetic analysis of BLAST results. Bioinformatics. 17:385-387.
  • Wong, K.K., F.S.L. Brinkman, R.S. Benz, and R.E.W. Hancock (2001). Evaluation of a structural model of Pseudomonas aeruginosa outer membrane protein OprM, an efflux component involved in intrinsic antibiotic resistance. Journal of Bacteriology. 183:367-374. Figure from the paper, at right, illustrates the location of mutations (grey, green and black balls) on a computational model of the OprM outer membrane protein. By overlaying the location of mutations on a 3D model, insight can be gained about the function of different regions of the proteins.
  • Brinkman, F.S.L., and D.D. Leipe (2001). Phylogenetic analysis. pp. 323-358. In A.D. Baxevanis and B.F.F. Ouellette (ed.), Bioinformatics: A practical guide to the analysis of genes and proteins, 2nd Edition. John Wiley & Sons, USA. (Part of the "Methods of Biochemical Analysis" series. Paper or cloth version of this book is currently available, as well as the paperback of the former edition)
  • 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.

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  • de Koning, A., F.S.L. Brinkman, S. J. Jones, and P. Keeling (2000). Lateral gene transfer and metabolic adaptation in the human parasite Trichomonas vaginalis. Molecular Biology and Evolution. 17:1769-1773. (See also a commentary article that discusses this in Science)