Publications

See an up-to-date list of most Brinkman Lab publications in the following resources:

  • PubMed (doesn’t include non-medical papers)
  • Google Scholar (includes more publications but not those before my surname changed from Lawson to Brinkman in 1997)

Selected Publications:

  • 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. 2016 Jul 19;4(1):20. doi: 10.1186/s40168-016-0166-1.PMID: 27391119
  • 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. Can J Infect Dis Med Microbiol. 2016;2016:5381871. doi: 10.1155/2016/5381871. Epub 2016 Apr 14.PMID: 27366170
  • Osachoff HL, Brown LL, Tirrul L, van Aggelen GC, Brinkman FS, Kennedy CJ. Time course of hepatic gene expression and plasma vitellogenin protein concentrations in estrone-exposed juvenile rainbow trout (Oncorhynchus mykiss). Comp Biochem Physiol Part D Genomics Proteomics. 2016 Sep;19:112-9. doi: 10.1016/j.cbd.2016.02.002. Epub 2016 Feb 26.PMID: 26996967
  • Van Rossum T, Pylatuk MM, Osachoff HL, Griffiths EJ, Lo R, Quach M, Palmer R, Lower N, Brinkman FSL, Kennedy CJ. Microbiome Analysis Across a Natural Copper Gradient at a Proposed Northern Canadian Mine Site. Front. Environ. Sci., 2016 Jan 6. Frontiers in Environmental Science: Article
  • 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. Front. Microbiol. 2015 Dec 16;6:1405. PubMed PMID: 26733955.
  • 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 Res. 2016 Jan 4;44(D1):D663-8. PubMed PMID: 26602691.
  • 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 Res. 2015 Nov 17. PubMed PMID: 26578582.
  • 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. 2015 Nov 4;16:363. PubMed PMID: 26537885.
  • 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, Camara M, Cantin A, Charette SJ, Dewar K, Déziel É, Grimwood K, Hancock RE, Harrison JJ, Heeb S, Jelsbak L, Jia B, Kenna DT, Kidd TJ, Klockgether J, Lam JS, Lamont IL, Lewenza S, Loman N, Malouin F, Manos J, McArthur AG, McKeown J, Milot J, Naghra H, Nguyen D, Pereira SK, Perron GG, Pirnay JP, Rainey PB, Rousseau S, Santos PM, Stephenson A, Taylor V, Turton JF, Waglechner N, Williams P, Thrane SW, Wright GD, Brinkman FS, Tucker NP, Tümmler B, Winstanley C, Levesque RC. Clinical utilization of genomics data produced by the international Pseudomonas aeruginosa consortium. Front Microbiol. 2015 Sep 29;6:1036. PubMed PMID: 26483767.
  • Laird MR, Langille MG, Brinkman FS. GenomeD3Plot: A library for rich, interactive visualizations of genomic data in web applications. Bioinformatics. 2015 Jun 20. pii: btv376. PubMed PMID: 26093150.
  • Frias S, Bryan K, Brinkman FS, Lynn DJ. CerebralWeb: a Cytoscape.js plug-in to visualize networks stratified by subcellular localization. Database (Oxford). 2015 May 7;2015:bav041. doi: 10.1093/database/bav041. Print 2015. PubMed PMID: 25953080.
  • 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 Res. 2015 Apr 27. pii: gkv401. [Epub ahead of print] PubMed PMID: 25916842.
  • O’Doherty KC, Neufeld JD, Brinkman FS, Gardner H, Guttman DS, Beiko RG. Opinion: Conservation and stewardship of the human microbiome. Proc Natl Acad Sci U S A. 2014 Oct 7;111(40):14312-3. doi: 10.1073/pnas.1413200111. PubMed PMID: 25294925.
  • Carlsten C, Brauer M, Brinkman F, Brook J, Daley D, McNagny K, Pui M, Royce D, Takaro T, Denburg J. Genes, the environment and personalized medicine: We need to harness both environmental and genetic data to maximize personal and population health. EMBO Rep. 2014 Jul;15(7):736-9. PubMed PMID: 24907240.
  • N Prystajecky,  FSL Brinkman,  B Auk,  JL Isaac-Renton,  P Tang. Personalized genetic testing and norovirus susceptibility. Can J Infect Dis. 2014 July/Aug;25(4):222-24.
  • Winsor GL, Brinkman FS. Mining the Pseudomonas genome. Methods Mol Biol.2014;1149:417-32. PMID: 24818923.
  • Foroushani AB, Brinkman FS, Lynn DJ. Pathway-GPS and SIGORA: identifying relevant pathways based on the over-representation of their gene-pair signatures. PeerJ. 2013 Dec 19;1:e229. PMID: 24432194.
  • 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 Genet. 2013;9(10):e1003804. PMID: 24098140.
  • Dhillon BK, Chiu TA, Laird MR, Langille MG, Brinkman FS. IslandViewer update: Improved genomic island discovery and visualization. Nucleic Acids Res. 2013 Jul;41(Web Server issue):W129-32. PMID: 23677610.
  • Whiteside MD, Winsor GL, Laird MR, Brinkman FS. OrtholugeDB: a bacterial and archaeal orthology resource for improved comparative genomic analysis. Nucleic Acids Res. 2013 Jan;41(Database issue):D366-76. PMID: 23203876.
  • 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 Res. 2013 Jan;41(Database issue):D1228-33.  PMID: 23180781.
  • 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. Int J Antimicrob Agents. 2012 Sep;40(3):246-51. PMID: 22819149.
  • 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. Sci Transl Med. 2012 May 23;4(135):135ra64. PMID: 22623740.
  • Langille MG, Laird MR, Hsiao WW, Chiu TA, Eisen JA, Brinkman FS. MicrobeDB: a locally maintainable database of microbial genomic sequences. Bioinformatics. 2012 Jul 15;28(14):1947-8. PMID: 22576174.
  • 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. Am J Clin Pathol. 2012 May;137(5):805-14. PMID: 22523221.
  • Orchard S, Kerrien S, Abbani S, Aranda B, Bhate J, Bidwell S, Bridge A, Briganti L, Brinkman FS, Cesareni G, Chatr-aryamontri A, Chautard E, Chen C,Dumousseau M, Goll J, Hancock RE, Hannick LI, Jurisica I, Khadake J, Lynn DJ, Mahadevan U, Perfetto L, Raghunath A, Ricard-Blum S, Roechert B, Salwinski L, Stümpflen V, Tyers M, Uetz P, Xenarios I, Hermjakob H. Protein interaction data curation: the International Molecular Exchange (IMEx) consortium. Nat Methods. 2012 Apr;9(4):345-50. PMID: 22453911.
  • Schreiber F, Lynn DJ, Houston A, Peters J, Mwafulirwa G, Finlay BB, Brinkman FS, Hancock RE, Heyderman RS, Dougan G, Gordon MA. The human transcriptome during nontyphoid Salmonella and HIV coinfection reveals attenuated NFkappaB-mediated inflammation and persistent cell cycle disruption. J Infect Dis. 2011 Oct 15;204(8):1237-45. PMID: 21917897.
  • 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, Kerssemakers J, Khadake J, Lynn DJ, Michaut M, O’Kelly G, Ono K, Orchard S, Prieto C, Razick S, Rigina O, Salwinski L, Simonovic M, Velankar S, Winter A, Wu G, Bader GD, Cesareni G, Donaldson IM, Eisenberg D, Kleywegt GJ, Overington J, Ricard-Blum S, Tyers M, Albrecht M, Hermjakob H. PSICQUIC and PSISCORE: accessing and scoring molecular interactions. Nat Methods. 2011 Jun29;8(7):528-9.  PMID: 21716279.
  • 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, Jones SJ, Brinkman FS, Brunham RC, Tang P. Whole-genome sequencing and social-network analysis of a tuberculosis outbreak. N Engl J Med. 2011 Feb 24;364(8):730-9. PMID: 21345102.
  • Gill EE, Brinkman FS. The proportional lack of archaeal pathogens: Doviruses/phages hold the key? Bioessays. 2011 Apr;33(4):248-54. Epub 2011 Feb 15. PMID: 21328413.
  • 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 Res. 2011 Jan;39(Database issue):D241-4. PMID: 21071402.
  • 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 Res. 2011 Jan;39(Database issue):D596-600. PMID: 20929876.
  • 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 Syst Biol. 2010 Aug 20;4:117. PMID: 20727158.
  • Yu NY, Wagner JR, Laird MR, Melli G, Rey S, Lo R, Dao P, Sahinalp SC, EsterM, Foster LJ, Brinkman FS. PSORTb 3.0: improved protein subcellular localization prediction with refined localization subcategories and predictive capabilities for all prokaryotes. Bioinformatics. 2010 Jul 1;26(13):1608-15. PMID: 20472543.