Research Topics
| Fiona S L BrinkmanSummaryAffiliation: Simon Fraser University Country: Canada Publications
| Collaborators
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Detail Information
Publications
Curating the innate immunity interactomeDavid J Lynn
Animal and Bioscience Research Department, AGRIC, Teagasc, Grange, Dunsany, Co Meath, Ireland
BMC Syst Biol 4:117. 2010..InnateDB (http://www.innatedb.com) is a molecular interaction and pathway database developed to facilitate systems-level analyses of innate immunity...- Evidence that plant-like genes in Chlamydia species reflect an ancestral relationship between Chlamydiaceae, cyanobacteria, and the chloroplastFiona S L Brinkman
Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, British Columbia, Canada, V5A 1S6
Genome Res 12:1159-67. 2002.... - PSORTb v.2.0: expanded prediction of bacterial protein subcellular localization and insights gained from comparative proteome analysisJ L Gardy
Department of Molecular Biology and Biochemistry, Simon Fraser University Burnaby, BC, Canada V5A 1S6
Bioinformatics 21:617-23. 2005..AVAILABILITY: Web-based version: http://www.psort.org/psortb. Standalone version: Available through the website under GNU General Public License. CONTACT: , SUPPLEMENTARY INFORMATION: http://www.psort.org/psortb/supplementaryinfo.html... - Assessing the precision of high-throughput computational and laboratory approaches for the genome-wide identification of protein subcellular localization in bacteriaSebastien Rey
Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC, V5A 1S6, Canada
BMC Genomics 6:162. 2005..There is a need to compare such computational methods with laboratory proteomics approaches to identify the most effective current approach for genome-wide localization characterization and annotation... - The Burkholderia Genome Database: facilitating flexible queries and comparative analysesGeoffrey L Winsor
Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC, Canada V5A 1S6
Bioinformatics 24:2803-4. 2008..AVAILABILITY: http://www.burkholderia.com. Source code: GNU GPL... - Pseudomonas Genome Database: facilitating user-friendly, comprehensive comparisons of microbial genomesGeoffrey L Winsor
Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC V5A 1S6, Canada
Nucleic Acids Res 37:D483-8. 2009..This database aims to continue to provide a high quality, annotated genome resource for the research community and is available under an open source license... - Pseudomonas Genome Database: improved comparative analysis and population genomics capability for Pseudomonas genomesGeoffrey L Winsor
Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC V5A 1S6, Canada
Nucleic Acids Res 39:D596-600. 2011.... - ProbeLynx: a tool for updating the association of microarray probes to genesFiona M Roche
Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC, V5A 1S6, Canada
Nucleic Acids Res 32:W471-4. 2004..By also including the latest gene function annotation information in the output, ProbeLynx provides the critical first step in updating microarray data annotation... - PSORTb 3.0: improved protein subcellular localization prediction with refined localization subcategories and predictive capabilities for all prokaryotesNancy Y Yu
Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC V5A 1S6, Canada
Bioinformatics 26:1608-15. 2010..Such improvements should preferably be encompassed in a freely available web-based predictor that can also be used as a standalone program... - PSORTdb--an expanded, auto-updated, user-friendly protein subcellular localization database for Bacteria and ArchaeaNancy Y Yu
Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC V5A 1S6, Canada
Nucleic Acids Res 39:D241-4. 2011..This identification of membrane structure permits appropriate SCL prediction in an auto-updated fashion and allows PSORTdb to serve as a practical resource for genome annotation and prokaryotic research... - The association of virulence factors with genomic islandsShannan J Ho Sui
Department of Molecular Biology, Simon Fraser University, Burnaby, British Columbia, Canada
PLoS ONE 4:e8094. 2009..Furthermore, we examined the relationship between GIs and clustered regularly interspaced palindromic repeats (CRISPRs) proposed to confer resistance to phage... - Genome-wide identification of Pseudomonas aeruginosa exported proteins using a consensus computational strategy combined with a laboratory-based PhoA fusion screenShawn Lewenza
Department of Microbiology and Immunology, University of British Columbia, Vancouver, British Columbia, V6T 1Z4, Canada
Genome Res 15:321-9. 2005.... - IslandViewer: an integrated interface for computational identification and visualization of genomic islandsMorgan G I Langille
Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC, Canada
Bioinformatics 25:664-5. 2009..AVAILABILITY: The IslandViewer web service is available at http://www.pathogenomics.sfu.ca/islandviewer and the source code is freely available under the GNU GPL license... - Evidence of a large novel gene pool associated with prokaryotic genomic islandsWilliam W L Hsiao
Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, British Columbia, Canada
PLoS Genet 1:e62. 2005.... - Evaluation of genomic island predictors using a comparative genomics approachMorgan G I Langille
Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC, Canada
BMC Bioinformatics 9:329. 2008..To robustly evaluate the accuracy of such methods, we propose that a dataset of GIs be constructed using criteria that are independent of sequence composition-based analysis approaches... - Improving the specificity of high-throughput ortholog predictionDebra L Fulton
Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC, Canada
BMC Bioinformatics 7:270. 2006..In addition, there is an increasing interest in identifying orthologs most likely to have retained similar function... - Pseudomonas aeruginosa Genome Database and PseudoCAP: facilitating community-based, continually updated, genome annotationGeoffrey L Winsor
Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, B.C, Canada, V5A 1S6
Nucleic Acids Res 33:D338-43. 2005..The source code is freely available under GNU General Public Licence... - InnateDB: facilitating systems-level analyses of the mammalian innate immune responseDavid J Lynn
Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, British Columbia, Canada
Mol Syst Biol 4:218. 2008.... - PSORT-B: Improving protein subcellular localization prediction for Gram-negative bacteriaJennifer L Gardy
Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC, Canada V5A 1S6
Nucleic Acids Res 31:3613-7. 2003..This dataset, the largest of its kind, is freely available, along with the PSORT-B source code (under GNU General Public License)... - G-protein-coupled receptor independent, immunomodulatory properties of chemokine CXCL9Jiang Hong Gong
Centre for Microbial Diseases and Immunity Research, University of British Columbia, Vancouver, British Columbia, Canada
Cell Immunol 261:105-13. 2010..These results collectively demonstrate that CXCL9 has immunomodulatory functions that are not mediated through a G-protein coupled receptor and may possess additional roles in host defenses against infection... - Bovine and human cathelicidin cationic host defense peptides similarly suppress transcriptional responses to bacterial lipopolysaccharideNeeloffer Mookherjee
Department of Microbiology and Immunology, University of British Columbia, Vancouver, BC, Canada
J Leukoc Biol 80:1563-74. 2006.... - The proportional lack of archaeal pathogens: Do viruses/phages hold the key?Erin E Gill
Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, British Columbia, Canada
Bioessays 33:248-54. 2011..If phage and virus populations are indeed exclusive to their respective host Domains, this has important implications for both the evolution of pathogens and approaches to infectious disease control... - Phylogeny of Na+/Ca2+ exchanger (NCX) genes from genomic data identifies new gene duplications and a new family member in fish speciesChristian R Marshall
Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, Canada
Physiol Genomics 21:161-73. 2005..These findings present a stronger foundation for our understanding of the molecular evolution of the NCX gene family and provide a framework for further NCX phylogenetic and molecular studies... - IslandPath: aiding detection of genomic islands in prokaryotesWilliam Hsiao
Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC, Canada V5A 1S6
Bioinformatics 19:418-20. 2003..SUPPLEMENTARY INFORMATION: An online help file, which includes analyses of the utility of IslandPath, can be found at http://www.pathogenomics.sfu.ca/islandpath/current/islandhelp.html.. - Genetic and molecular analysis of GogB, a phage-encoded type III-secreted substrate in Salmonella enterica serovar typhimurium with autonomous expression from its associated phageBrian K Coombes
Michael Smith Laboratories, University of British Columbia, Vancouver, BC, V6T 1Z3, Canada
J Mol Biol 348:817-30. 2005..These data define the first autonomously expressed lysogenic conversion gene within Gifsy-1 that acts as a modular and promiscuous type III-secreted substrate of the infection process... - ArrayPipe: a flexible processing pipeline for microarray dataKarsten Hokamp
Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC, Canada
Nucleic Acids Res 32:W457-9. 2004..Additional features, such as web-based spreadsheet functionality, auto-parallelization and password protection make this a powerful tool in microarray research for individuals and large groups alike... - Whole-genome sequencing and social-network analysis of a tuberculosis outbreakJennifer L Gardy
British Columbia Centre for Disease Control, Vancouver, BC, Canada
N Engl J Med 364:730-9. 2011..Traditional contact tracing did not identify a source. We used whole-genome sequencing and social-network analysis in an effort to describe the outbreak dynamics at a higher resolution... - The complete genome of Rhodococcus sp. RHA1 provides insights into a catabolic powerhouseMichael P McLeod
Department of Microbiology and Immunology, Life Sciences Institute, University of British Columbia, Vancouver, BC, Canada V6T 1Z3
Proc Natl Acad Sci U S A 103:15582-7. 2006..In addition to establishing RHA1 as an important model for studying actinomycete physiology, this study provides critical insights that facilitate the exploitation of these industrially important microorganisms... - Methods for predicting bacterial protein subcellular localizationJennifer L Gardy
Centre for Microbial Diseases and Immunity Research, University of British Columbia, Vancouver, British Columbia, V6T 1Z4 Canada
Nat Rev Microbiol 4:741-51. 2006..These methods offer significant improvements in predictive performance over PSORT I and the accuracy of some methods now rivals that of certain high-throughput laboratory methods for protein localization identification... - Aminoglycoside efflux in Pseudomonas aeruginosa: involvement of novel outer membrane proteinsJames T H Jo
Department of Microbiology and Immunology, University of British Columbia, Vancouver, Canada V6T 1Z3
Antimicrob Agents Chemother 47:1101-11. 2003..Based on the data, we propose that OpmG is a major outer membrane efflux channel involved in aminoglycoside efflux in P. aeruginosa PAK and that OpmI, its most related paralog, may share an overlapping function... - Construction of a mini-Tn5-luxCDABE mutant library in Pseudomonas aeruginosa PAO1: a tool for identifying differentially regulated genesShawn Lewenza
Department of Microbiology and Immunology, University of British Columbia, Vancouver, British Columbia, Canada V6T 1Z4
Genome Res 15:583-9. 2005..This dual-purpose mutant library allows for functional and regulation studies and will serve as a resource for the research community to further our understanding of P. aeruginosa biology... - Molecular analyses of disease pathogenesis: application of bovine microarraysHeather L Wilson
Vaccine and Infectious Disease Organization, University of Saskatchewan, Saskatoon, Sask, Canada S7N 5E3
Vet Immunol Immunopathol 105:277-87. 2005..These limitations are discussed with an indication of future developments that will accelerate the validation of data generated when completing a molecular characterization of disease pathogenesis in cattle... - Computer-aided biotechnology: from immuno-informatics to reverse vaccinologySandro Vivona
Molecular Biology and Bioinformatics Unit, Department of Biology, University of Padua, Padua, Italy
Trends Biotechnol 26:190-200. 2008..This will herald a move to 'computer-aided biotechnology': smart projects in which time-consuming and expensive large-scale experimental approaches are progressively replaced by prediction-driven investigations... - Proteomic, microarray, and signature-tagged mutagenesis analyses of anaerobic Pseudomonas aeruginosa at pH 6.5, likely representing chronic, late-stage cystic fibrosis airway conditionsMark D Platt
Department of Chemistry, Rensselaer Polytechnic Institute, Troy, New York 12180, USA
J Bacteriol 190:2739-58. 2008..aeruginosa to limit the growth of this important CF pathogen when it is either limited or completely restricted in its oxygen supply... - Avian beta-defensin nomenclature: a community proposed updateDavid J Lynn
Immunol Lett 110:86-9. 2007 - Contribution of the PhoP-PhoQ and PmrA-PmrB two-component regulatory systems to Mg2+-induced gene regulation in Pseudomonas aeruginosaJoseph B McPhee
Department of Microbiology and Immunology and Centre for Microbial Diseases and Immunity Research, University of British Columbia, 232 2259 Lower Mall, Vancouver, BC, Canada V6T 1Z4
J Bacteriol 188:3995-4006. 2006..The number of known PmrA-regulated genes was expanded to include the PA1559-PA1560, PA4782-PA4781, and feoAB operons, in addition to the previously known PA4773-PA4775-pmrAB and pmrHFIJKLM-ugd operons... - Modulation of the TLR-mediated inflammatory response by the endogenous human host defense peptide LL-37Neeloffer Mookherjee
Centre for Microbial Diseases and Immunity Research, Department of Microbiology and Immunology, University of British Columbia, Vancouver, Canada
J Immunol 176:2455-64. 2006..We propose that the natural human host defense peptide LL-37 plays roles in the delicate balancing of inflammatory responses in homeostasis as well as in combating sepsis induced by certain TLR agonists...