Fiona S. L. Brinkman - Publications

Affiliations: 
Molecular Biology and Biochemistry Simon Fraser University, Burnaby, British Columbia, Canada 
Area:
Bioinformatics Biology, Genetics, Evolution and Development Biology

74 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2020 Patrick DM, Sbihi H, Dai DLY, Al Mamun A, Rasali D, Rose C, Marra F, Boutin RCT, Petersen C, Stiemsma LT, Winsor GL, Brinkman FSL, Kozyrskyj AL, Azad MB, Becker AB, et al. Decreasing antibiotic use, the gut microbiota, and asthma incidence in children: evidence from population-based and prospective cohort studies. The Lancet. Respiratory Medicine. PMID 32220282 DOI: 10.1016/S2213-2600(20)30052-7  0.48
2020 McDaniel CT, Panmanee W, Winsor GL, Gill E, Bertelli C, Schurr MJ, Dongare P, Paul AT, Ko SB, Lau GW, Dasgupta N, Bogue AL, Miller WE, Mortensen JE, Haslam DB, ... ... Brinkman FSL, et al. AB569, a nontoxic chemical tandem that kills major human pathogenic bacteria. Proceedings of the National Academy of Sciences of the United States of America. PMID 32071223 DOI: 10.1073/pnas.1911927117  0.48
2019 Alcock BP, Raphenya AR, Lau TTY, Tsang KK, Bouchard M, Edalatmand A, Huynh W, Nguyen AV, Cheng AA, Liu S, Min SY, Miroshnichenko A, Tran HK, Werfalli RE, Nasir JA, ... ... Brinkman FSL, et al. CARD 2020: antibiotic resistome surveillance with the comprehensive antibiotic resistance database. Nucleic Acids Research. PMID 31665441 DOI: 10.1093/nar/gkz935  0.48
2018 Dooley DM, Griffiths EJ, Gosal GS, Buttigieg PL, Hoehndorf R, Lange MC, Schriml LM, Brinkman FSL, Hsiao WWL. FoodOn: a harmonized food ontology to increase global food traceability, quality control and data integration. Npj Science of Food. 2: 23. PMID 31304272 DOI: 10.1038/s41538-018-0032-6  0.4
2018 Gill EE, Chan LS, Winsor GL, Dobson N, Lo R, Ho Sui SJ, Dhillon BK, Taylor PK, Shrestha R, Spencer C, Hancock REW, Unrau PJ, Brinkman FSL. High-throughput detection of RNA processing in bacteria. Bmc Genomics. 19: 223. PMID 29587634 DOI: 10.1186/s12864-018-4538-8  0.48
2018 Rey K, Manku S, Enns W, Van Rossum T, Bushell K, Morin RD, Brinkman FSL, Choy JC. Disruption of the Gut Microbiota With Antibiotics Exacerbates Acute Vascular Rejection. Transplantation. PMID 29538261 DOI: 10.1097/TP.0000000000002169  0.48
2017 Panmanee W, Charoenlap N, Atichartpongkul S, Mahavihakanont A, Whiteside MD, Winsor G, Brinkman FSL, Mongkolsuk S, Hassett DJ. The OxyR-regulated phnW gene encoding 2-aminoethylphosphonate:pyruvate aminotransferase helps protect Pseudomonas aeruginosa from tert-butyl hydroperoxide. Plos One. 12: e0189066. PMID 29216242 DOI: 10.1371/journal.pone.0189066  0.48
2017 Griffiths E, Dooley D, Graham M, Van Domselaar G, Brinkman FSL, Hsiao WWL. Context Is Everything: Harmonization of Critical Food Microbiology Descriptors and Metadata for Improved Food Safety and Surveillance. Frontiers in Microbiology. 8: 1068. PMID 28694792 DOI: 10.3389/fmicb.2017.01068  0.4
2017 Bertelli C, Laird MR, Williams KP, Lau BY, Hoad G, Winsor GL, Brinkman FS. IslandViewer 4: expanded prediction of genomic islands for larger-scale datasets. Nucleic Acids Research. PMID 28472413 DOI: 10.1093/nar/gkx343  0.56
2016 Jia B, Raphenya AR, Alcock B, Waglechner N, Guo P, Tsang KK, Lago BA, Dave BM, Pereira S, Sharma AN, Doshi S, Courtot M, Lo R, Williams LE, Frye JG, ... ... Brinkman FS, et al. CARD 2017: expansion and model-centric curation of the comprehensive antibiotic resistance database. Nucleic Acids Research. PMID 27789705 DOI: 10.1093/nar/gkw1004  0.48
2016 Uyaguari-Diaz MI, Chan M, Chaban BL, Croxen MA, Finke JF, Hill JE, Peabody MA, Van Rossum T, Suttle CA, Brinkman FS, Isaac-Renton J, Prystajecky NA, Tang P. A comprehensive method for amplicon-based and metagenomic characterization of viruses, bacteria, and eukaryotes in freshwater samples. Microbiome. 4: 20. PMID 27391119 DOI: 10.1186/s40168-016-0166-1  0.48
2016 Miller RR, Langille MG, Montoya V, Crisan A, Stefanovic A, Martin I, Hoang L, Patrick DM, Romney M, Tyrrell G, Jones SJ, Brinkman FS, Tang P. Genomic Analysis of a Serotype 5 Streptococcus pneumoniae Outbreak in British Columbia, Canada, 2005-2009. The Canadian Journal of Infectious Diseases & Medical Microbiology = Journal Canadien Des Maladies Infectieuses Et De La Microbiologie MéDicale. 2016: 5381871. PMID 27366170 DOI: 10.1155/2016/5381871  0.48
2016 Winsor GL, Griffiths EJ, Lo R, Dhillon BK, Shay JA, Brinkman FS. Enhanced annotations and features for comparing thousands of Pseudomonas genomes in the Pseudomonas genome database. Nucleic Acids Research. 44: D646-53. PMID 26578582 DOI: 10.1093/nar/gkv1227  0.48
2015 Van Rossum T, Peabody MA, Uyaguari-Diaz MI, Cronin KI, Chan M, Slobodan JR, Nesbitt MJ, Suttle CA, Hsiao WW, Tang PK, Prystajecky NA, Brinkman FS. Year-Long Metagenomic Study of River Microbiomes Across Land Use and Water Quality. Frontiers in Microbiology. 6: 1405. PMID 26733955 DOI: 10.3389/fmicb.2015.01405  0.48
2015 Peabody MA, Laird MR, Vlasschaert C, Lo R, Brinkman FS. PSORTdb: expanding the bacteria and archaea protein subcellular localization database to better reflect diversity in cell envelope structures. Nucleic Acids Research. PMID 26602691 DOI: 10.1093/nar/gkv1271  0.56
2015 Peabody MA, Van Rossum T, Lo R, Brinkman FS. Evaluation of shotgun metagenomics sequence classification methods using in silico and in vitro simulated communities. Bmc Bioinformatics. 16: 363. PMID 26537885 DOI: 10.1186/s12859-015-0788-5  0.48
2015 Freschi L, Jeukens J, Kukavica-Ibrulj I, Boyle B, Dupont MJ, Laroche J, Larose S, Maaroufi H, Fothergill JL, Moore M, Winsor GL, Aaron SD, Barbeau J, Bell SC, Burns JL, ... ... Brinkman FS, et al. Clinical utilization of genomics data produced by the international Pseudomonas aeruginosa consortium. Frontiers in Microbiology. 6: 1036. PMID 26483767 DOI: 10.3389/fmicb.2015.01036  0.48
2015 Laird MR, Langille MG, Brinkman FS. GenomeD3Plot: A library for rich, interactive visualizations of genomic data in web applications. Bioinformatics (Oxford, England). PMID 26093150 DOI: 10.1093/bioinformatics/btv376  1
2015 Dhillon BK, Laird MR, Shay JA, Winsor GL, Lo R, Nizam F, Pereira SK, Waglechner N, McArthur AG, Langille MG, Brinkman FS. IslandViewer 3: more flexible, interactive genomic island discovery, visualization and analysis. Nucleic Acids Research. 43: W104-8. PMID 25916842 DOI: 10.1093/nar/gkv401  1
2014 O'Doherty KC, Neufeld JD, Brinkman FS, Gardner H, Guttman DS, Beiko RG. Opinion: Conservation and stewardship of the human microbiome. Proceedings of the National Academy of Sciences of the United States of America. 111: 14312-3. PMID 25294925 DOI: 10.1073/pnas.1413200111  0.48
2014 Winsor GL, Brinkman FS. Mining the Pseudomonas genome. Methods in Molecular Biology (Clifton, N.J.). 1149: 417-32. PMID 24818923 DOI: 10.1007/978-1-4939-0473-0_33  0.48
2013 Frédéric MY, Lundin VF, Whiteside MD, Cueva JG, Tu DK, Kang SY, Singh H, Baillie DL, Hutter H, Goodman MB, Brinkman FS, Leroux MR. Identification of 526 conserved metazoan genetic innovations exposes a new role for cofactor E-like in neuronal microtubule homeostasis. Plos Genetics. 9: e1003804. PMID 24098140 DOI: 10.1371/journal.pgen.1003804  0.48
2013 Dhillon BK, Chiu TA, Laird MR, Langille MG, Brinkman FS. IslandViewer update: Improved genomic island discovery and visualization. Nucleic Acids Research. 41: W129-32. PMID 23677610 DOI: 10.1093/nar/gkt394  1
2013 Whiteside MD, Winsor GL, Laird MR, Brinkman FS. OrtholugeDB: a bacterial and archaeal orthology resource for improved comparative genomic analysis. Nucleic Acids Research. 41: D366-76. PMID 23203876 DOI: 10.1093/nar/gks1241  0.48
2013 Breuer K, Foroushani AK, Laird MR, Chen C, Sribnaia A, Lo R, Winsor GL, Hancock RE, Brinkman FS, Lynn DJ. InnateDB: systems biology of innate immunity and beyond--recent updates and continuing curation. Nucleic Acids Research. 41: D1228-33. PMID 23180781 DOI: 10.1093/nar/gks1147  0.56
2012 Ho Sui SJ, Lo R, Fernandes AR, Caulfield MD, Lerman JA, Xie L, Bourne PE, Baillie DL, Brinkman FS. Raloxifene attenuates Pseudomonas aeruginosa pyocyanin production and virulence. International Journal of Antimicrobial Agents. 40: 246-51. PMID 22819149 DOI: 10.1016/j.ijantimicag.2012.05.009  0.48
2012 Achtman AH, Pilat S, Law CW, Lynn DJ, Janot L, Mayer ML, Ma S, Kindrachuk J, Finlay BB, Brinkman FS, Smyth GK, Hancock RE, Schofield L. Effective adjunctive therapy by an innate defense regulatory peptide in a preclinical model of severe malaria. Science Translational Medicine. 4: 135ra64. PMID 22623740 DOI: 10.1126/scitranslmed.3003515  0.48
2012 Langille MG, Laird MR, Hsiao WW, Chiu TA, Eisen JA, Brinkman FS. MicrobeDB: a locally maintainable database of microbial genomic sequences. Bioinformatics (Oxford, England). 28: 1947-8. PMID 22576174 DOI: 10.1093/bioinformatics/bts273  0.48
2012 Bashashati A, Johnson NA, Khodabakhshi AH, Whiteside MD, Zare H, Scott DW, Lo K, Gottardo R, Brinkman FS, Connors JM, Slack GW, Gascoyne RD, Weng AP, Brinkman RR. B cells with high side scatter parameter by flow cytometry correlate with inferior survival in diffuse large B-cell lymphoma. American Journal of Clinical Pathology. 137: 805-14. PMID 22523221 DOI: 10.1309/AJCPGR8BG4JDVOWR  0.48
2012 Orchard S, Kerrien S, Abbani S, Aranda B, Bhate J, Bidwell S, Bridge A, Briganti L, Brinkman FS, Brinkman F, Cesareni G, Chatr-aryamontri A, Chautard E, Chen C, Dumousseau M, et al. Protein interaction data curation: the International Molecular Exchange (IMEx) consortium. Nature Methods. 9: 345-50. PMID 22453911 DOI: 10.1038/nmeth.1931  0.48
2012 Orchard S, Kerrien S, Abbani S, Aranda B, Bhate J, Bidwell S, Bridge A, Briganti L, Brinkman F, Cesareni G, Chatr-Aryamontri A, Chautard E, Chen C, Dumousseau M, Goll J, et al. Corrigendum: Protein interaction data curation: The International Molecular Exchange (IMEx) consortium (Nature Methods (2012) 9, (345-350)) Nature Methods. 9: 626. DOI: 10.1038/nmeth0612-626a  0.48
2011 Aranda B, Blankenburg H, Kerrien S, Brinkman FS, Ceol A, Chautard E, Dana JM, De Las Rivas J, Dumousseau M, Galeota E, Gaulton A, Goll J, Hancock RE, Isserlin R, Jimenez RC, et al. PSICQUIC and PSISCORE: accessing and scoring molecular interactions. Nature Methods. 8: 528-9. PMID 21716279 DOI: 10.1038/nmeth.1637  0.48
2011 Gardy JL, Johnston JC, Ho Sui SJ, Cook VJ, Shah L, Brodkin E, Rempel S, Moore R, Zhao Y, Holt R, Varhol R, Birol I, Lem M, Sharma MK, Elwood K, ... ... Brinkman FS, et al. Whole-genome sequencing and social-network analysis of a tuberculosis outbreak. The New England Journal of Medicine. 364: 730-9. PMID 21345102 DOI: 10.1056/NEJMoa1003176  0.48
2011 Yu NY, Laird MR, Spencer C, Brinkman FS. PSORTdb--an expanded, auto-updated, user-friendly protein subcellular localization database for Bacteria and Archaea. Nucleic Acids Research. 39: D241-4. PMID 21071402 DOI: 10.1093/nar/gkq1093  0.48
2011 Winsor GL, Lam DK, Fleming L, Lo R, Whiteside MD, Yu NY, Hancock RE, Brinkman FS. Pseudomonas Genome Database: improved comparative analysis and population genomics capability for Pseudomonas genomes. Nucleic Acids Research. 39: D596-600. PMID 20929876 DOI: 10.1093/nar/gkq869  0.48
2011 Min JE, Whiteside MD, Brinkman FSL, McNeney B, Graham J. A statistical approach to high-throughput screening of predicted orthologs Computational Statistics and Data Analysis. 55: 935-943. DOI: 10.1016/j.csda.2010.08.002  0.48
2010 Lynn DJ, Chan C, Naseer M, Yau M, Lo R, Sribnaia A, Ring G, Que J, Wee K, Winsor GL, Laird MR, Breuer K, Foroushani AK, Brinkman FS, Hancock RE. Curating the innate immunity interactome. Bmc Systems Biology. 4: 117. PMID 20727158 DOI: 10.1186/1752-0509-4-117  0.48
2010 Yu NY, Wagner JR, Laird MR, Melli G, Rey S, Lo R, Dao P, Sahinalp SC, Ester M, Foster LJ, Brinkman FS. PSORTb 3.0: improved protein subcellular localization prediction with refined localization subcategories and predictive capabilities for all prokaryotes. Bioinformatics (Oxford, England). 26: 1608-15. PMID 20472543 DOI: 10.1093/bioinformatics/btq249  0.48
2010 Langille MG, Hsiao WW, Brinkman FS. Detecting genomic islands using bioinformatics approaches. Nature Reviews. Microbiology. 8: 373-82. PMID 20395967 DOI: 10.1038/nrmicro2350  1
2010 Tomljenovic-Berube AM, Mulder DT, Whiteside MD, Brinkman FS, Coombes BK. Identification of the regulatory logic controlling Salmonella pathoadaptation by the SsrA-SsrB two-component system. Plos Genetics. 6: e1000875. PMID 20300643 DOI: 10.1371/journal.pgen.1000875  0.48
2009 Langille MG, Brinkman FS. Bioinformatic detection of horizontally transferred DNA in bacterial genomes. F1000 Biology Reports. 1: 25. PMID 20948661 DOI: 10.3410/B1-25  1
2009 Ho Sui SJ, Fedynak A, Hsiao WW, Langille MG, Brinkman FS. The association of virulence factors with genomic islands. Plos One. 4: e8094. PMID 19956607 DOI: 10.1371/journal.pone.0008094  1
2009 Langille MG, Brinkman FS. IslandViewer: an integrated interface for computational identification and visualization of genomic islands. Bioinformatics (Oxford, England). 25: 664-5. PMID 19151094 DOI: 10.1093/bioinformatics/btp030  1
2009 Winstanley C, Langille MG, Fothergill JL, Kukavica-Ibrulj I, Paradis-Bleau C, Sanschagrin F, Thomson NR, Winsor GL, Quail MA, Lennard N, Bignell A, Clarke L, Seeger K, Saunders D, Harris D, ... ... Brinkman FS, et al. 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. PMID 19047519 DOI: 10.1101/gr.086082.108  0.48
2009 Winsor GL, Van Rossum T, Lo R, Khaira B, Whiteside MD, Hancock RE, Brinkman FS. Pseudomonas Genome Database: facilitating user-friendly, comprehensive comparisons of microbial genomes. Nucleic Acids Research. 37: D483-8. PMID 18978025 DOI: 10.1093/nar/gkn861  0.48
2008 Winsor GL, Khaira B, Van Rossum T, Lo R, Whiteside MD, Brinkman FS. The Burkholderia Genome Database: facilitating flexible queries and comparative analyses. Bioinformatics (Oxford, England). 24: 2803-4. PMID 18842600 DOI: 10.1093/bioinformatics/btn524  0.48
2008 Brinkman FS, Parkhill J. Population genomics: modeling the new and a renaissance of the old. Current Opinion in Microbiology. 11: 439-41. PMID 18824130 DOI: 10.1016/j.mib.2008.09.001  0.48
2008 Lynn DJ, Winsor GL, Chan C, Richard N, Laird MR, Barsky A, Gardy JL, Roche FM, Chan TH, Shah N, Lo R, Naseer M, Que J, Yau M, Acab M, ... ... Brinkman FS, et al. InnateDB: facilitating systems-level analyses of the mammalian innate immune response. Molecular Systems Biology. 4: 218. PMID 18766178 DOI: 10.1038/msb.2008.55  0.48
2008 Langille MG, Hsiao WW, Brinkman FS. Evaluation of genomic island predictors using a comparative genomics approach. Bmc Bioinformatics. 9: 329. PMID 18680607 DOI: 10.1186/1471-2105-9-329  1
2008 Vivona S, Gardy JL, Ramachandran S, Brinkman FS, Raghava GP, Flower DR, Filippini F. Computer-aided biotechnology: from immuno-informatics to reverse vaccinology. Trends in Biotechnology. 26: 190-200. PMID 18291542 DOI: 10.1016/j.tibtech.2007.12.006  0.48
2008 Platt MD, Schurr MJ, Sauer K, Vazquez G, Kukavica-Ibrulj I, Potvin E, Levesque RC, Fedynak A, Brinkman FS, Schurr J, Hwang SH, Lau GW, Limbach PA, Rowe JJ, Lieberman MA, et al. Proteomic, microarray, and signature-tagged mutagenesis analyses of anaerobic Pseudomonas aeruginosa at pH 6.5, likely representing chronic, late-stage cystic fibrosis airway conditions. Journal of Bacteriology. 190: 2739-58. PMID 18203836 DOI: 10.1128/JB.01683-07  0.48
2006 McLeod MP, Warren RL, Hsiao WW, Araki N, Myhre M, Fernandes C, Miyazawa D, Wong W, Lillquist AL, Wang D, Dosanjh M, Hara H, Petrescu A, Morin RD, Yang G, ... ... Brinkman FS, et al. The complete genome of Rhodococcus sp. RHA1 provides insights into a catabolic powerhouse. Proceedings of the National Academy of Sciences of the United States of America. 103: 15582-7. PMID 17030794 DOI: 10.1073/pnas.0607048103  0.48
2006 Mookherjee N, Wilson HL, Doria S, Popowych Y, Falsafi R, Yu JJ, Li Y, Veatch S, Roche FM, Brown KL, Brinkman FS, Hokamp K, Potter A, Babiuk LA, Griebel PJ, et al. Bovine and human cathelicidin cationic host defense peptides similarly suppress transcriptional responses to bacterial lipopolysaccharide. Journal of Leukocyte Biology. 80: 1563-74. PMID 16943385 DOI: 10.1189/jlb.0106048  0.48
2006 Fulton DL, Li YY, Laird MR, Horsman BG, Roche FM, Brinkman FS. Improving the specificity of high-throughput ortholog prediction. Bmc Bioinformatics. 7: 270. PMID 16729895 DOI: 10.1186/1471-2105-7-270  0.48
2006 McPhee JB, Bains M, Winsor G, Lewenza S, Kwasnicka A, Brazas MD, Brinkman FS, Hancock RE. 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. PMID 16707691 DOI: 10.1128/JB.00053-06  0.48
2006 Mookherjee N, Brown KL, Bowdish DM, Doria S, Falsafi R, Hokamp K, Roche FM, Mu R, Doho GH, Pistolic J, Powers JP, Bryan J, Brinkman FS, Hancock RE. Modulation of the TLR-mediated inflammatory response by the endogenous human host defense peptide LL-37. Journal of Immunology (Baltimore, Md. : 1950). 176: 2455-64. PMID 16456005  0.48
2005 Hodgson PD, Aich P, Manuja A, Hokamp K, Roche FM, Brinkman FS, Potter A, Babiuk LA, Griebel PJ. Effect of stress on viral-bacterial synergy in bovine respiratory disease: novel mechanisms to regulate inflammation. Comparative and Functional Genomics. 6: 244-50. PMID 18629190 DOI: 10.1002/cfg.474  0.48
2005 Hsiao WW, Ung K, Aeschliman D, Bryan J, Finlay BB, Brinkman FS. Evidence of a large novel gene pool associated with prokaryotic genomic islands. Plos Genetics. 1: e62. PMID 16299586 DOI: 10.1371/journal.pgen.0010062  0.48
2005 Coombes BK, Wickham ME, Brown NF, Lemire S, Bossi L, Hsiao WW, Brinkman FS, Finlay BB. 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: 817-30. PMID 15843015 DOI: 10.1016/j.jmb.2005.03.024  0.48
2005 Wilson HL, Aich P, Roche FM, Jalal S, Hodgson PD, Brinkman FS, Potter A, Babiuk LA, Griebel PJ. Molecular analyses of disease pathogenesis: application of bovine microarrays. Veterinary Immunology and Immunopathology. 105: 277-87. PMID 15808306 DOI: 10.1016/j.vetimm.2005.02.015  0.48
2005 Lewenza S, Falsafi RK, Winsor G, Gooderham WJ, McPhee JB, Brinkman FS, Hancock RE. Construction of a mini-Tn5-luxCDABE mutant library in Pseudomonas aeruginosa PAO1: a tool for identifying differentially regulated genes. Genome Research. 15: 583-9. PMID 15805499 DOI: 10.1101/gr.3513905  0.36
2005 Marshall CR, Fox JA, Butland SL, Ouellette BF, Brinkman FS, Tibbits GF. 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: 161-73. PMID 15741504 DOI: 10.1152/physiolgenomics.00286.2004  0.48
2005 Winsor GL, Lo R, Ho Sui SJ, Ung KS, Huang S, Cheng D, Ching WK, Hancock RE, Brinkman FS. Pseudomonas aeruginosa Genome Database and PseudoCAP: facilitating community-based, continually updated, genome annotation. Nucleic Acids Research. 33: D338-43. PMID 15608211 DOI: 10.1093/nar/gki047  0.48
2005 Rey S, Acab M, Gardy JL, Laird MR, deFays K, Lambert C, Brinkman FS. PSORTdb: a protein subcellular localization database for bacteria. Nucleic Acids Research. 33: D164-8. PMID 15608169 DOI: 10.1093/nar/gki027  0.56
2005 Gardy JL, Laird MR, Chen F, Rey S, Walsh CJ, Ester M, Brinkman FS. PSORTb v.2.0: expanded prediction of bacterial protein subcellular localization and insights gained from comparative proteome analysis. Bioinformatics (Oxford, England). 21: 617-23. PMID 15501914 DOI: 10.1093/bioinformatics/bti057  0.48
2004 Warren R, Hsiao WW, Kudo H, Myhre M, Dosanjh M, Petrescu A, Kobayashi H, Shimizu S, Miyauchi K, Masai E, Yang G, Stott JM, Schein JE, Shin H, Khattra J, ... ... Brinkman FS, et al. Functional characterization of a catabolic plasmid from polychlorinated- biphenyl-degrading Rhodococcus sp. strain RHA1. Journal of Bacteriology. 186: 7783-95. PMID 15516593 DOI: 10.1128/JB.186.22.7783-7795.2004  0.48
2004 Hokamp K, Roche FM, Acab M, Rousseau ME, Kuo B, Goode D, Aeschliman D, Bryan J, Babiuk LA, Hancock RE, Brinkman FS. ArrayPipe: a flexible processing pipeline for microarray data. Nucleic Acids Research. 32: W457-9. PMID 15215429 DOI: 10.1093/nar/gkh446  0.48
2003 Gardy JL, Spencer C, Wang K, Ester M, Tusnády GE, Simon I, Hua S, deFays K, Lambert C, Nakai K, Brinkman FS. PSORT-B: Improving protein subcellular localization prediction for Gram-negative bacteria. Nucleic Acids Research. 31: 3613-7. PMID 12824378 DOI: 10.1093/nar/gkg602  0.48
2003 She R, Chen F, Wang K, Ester M, Gardy JL, Brinkman FSL. Frequent-subsequence-based prediction of outer membrane proteins Proceedings of the Acm Sigkdd International Conference On Knowledge Discovery and Data Mining. 436-445. DOI: 10.1145/956750.956800  0.48
2002 Brinkman FS, Blanchard JL, Cherkasov A, Av-Gay Y, Brunham RC, Fernandez RC, Finlay BB, Otto SP, Ouellette BF, Keeling PJ, Rose AM, Hancock RE, Jones SJ, Greberg H. Evidence that plant-like genes in Chlamydia species reflect an ancestral relationship between Chlamydiaceae, cyanobacteria, and the chloroplast. Genome Research. 12: 1159-67. PMID 12176923 DOI: 10.1101/gr.341802  0.48
2001 Brinkman FS, Wan I, Hancock RE, Rose AM, Jones SJ. PhyloBLAST: facilitating phylogenetic analysis of BLAST results. Bioinformatics (Oxford, England). 17: 385-7. PMID 11301315  0.48
2000 De Koning AP, Brinkman FSL, Jones SJM, Keeling PJ. Lateral gene transfer and metabolic adaptation in the human parasite trichomonas vaginalis Molecular Biology and Evolution. 17: 1769-1773. PMID 11070064  0.48
2000 Stover CK, Pham XQ, Erwin AL, Mizoguchi SD, Warrener P, Hickey MJ, Brinkman FS, Hufnagle WO, Kowalik DJ, Lagrou M, Garber RL, Goltry L, Tolentino E, Westbrock-Wadman S, Yuan Y, et al. Complete genome sequence of Pseudomonas aeruginosa PAO1, an opportunistic pathogen. Nature. 406: 959-64. PMID 10984043 DOI: 10.1038/35023079  0.48
2000 Brinkman FSL, Bains M, Hancock REW. The amino terminus of Pseudomonas aeruginosa outer membrane protein OprF forms channels in lipid bilayer membranes: Correlation with a three-dimensional model Journal of Bacteriology. 182: 5251-5255. PMID 10960112 DOI: 10.1128/JB.182.18.5251-5255.2000  0.48
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