Publications

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

Selected Publications

Lau WYV, Hoad GR, Jin V, Winsor GL, Madyan A, Gray KL, Laird MR, Lo R, Brinkman FSL (2021). PSORTdb 4.0: expanded and redesigned bacterial and archaeal protein subcellular localization database incorporating new secondary localizations.
Nucleic Acids Res. 49 (D1), D803-D808. doi: 10.1093/nar/gkaa1095. PMID: 33313828.
Maguire F, Jia B, Gray KL, Lau WYV, Beiko RG, Brinkman FSL (2020). Metagenome-assembled genome binning methods with short reads disproportionately fail for plasmids and genomic Islands.
Microb Genom. 2020 Oct;6(10):mgen000436. doi: 10.1099/mgen.0.000436. PMID: 33001022.
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, Mandhane PJ, Moraes TJ, Sears MR, Subbarao P, Finlay BB, Turvey SE (2020). Decreasing antibiotic use, the gut microbiota, and asthma incidence in children: evidence from population-based and prospective cohort studies.
Lancet Respir Med. 2020 Mar 24:S2213-2600(20)30052-7. doi: 10.1016/S2213-2600(20)30052-7. Epub ahead of print. PMID: 32220282
Peabody MA, Lau WYV, Hoad GR, Jia B, Maguire F, Gray KL, Beiko RG, Brinkman FSL (2020). PSORTm: a bacterial and archaeal protein subcellular localization prediction tool for metagenomics data.
Bioinformatics. 2020 May 1;36(10):3043-3048. doi: 10.1093/bioinformatics/btaa136. PMID: 32108861; PMCID: PMC7214030
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, Dexheimer P, Muruve DA, Aronow BJ, Forbes MDE, Danilczuk M, Brinkman FSL, Hancock REW, Meyer TJ, Hassett DJ (2020). AB569, a nontoxic chemical tandem that kills major human pathogenic bacteria.
Proc Natl Acad Sci U S A. 2020 Mar 3;117(9):4921-4930. doi: 10.1073/pnas.1911927117. Epub 2020 Feb 18. PMID: 32071223; PMCID: PMC7060718
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, Oloni M, Speicher DJ, Florescu A, Singh B, Faltyn M, Hernandez- Koutoucheva A, Sharma AN, Bordeleau E, Pawlowski AC, Zubyk HL, Dooley D, Griffiths E, Maguire F, Winsor GL, Beiko RG, Brinkman FSL, Hsiao WWL, Domselaar GV, McArthur AG (2020). CARD 2020: antibiotic resistome surveillance with the comprehensive antibiotic resistance database.
Nucleic Acids Res. 2020 Jan 8;48(D1):D517-D525. doi: 10.1093/nar/gkz935. PMID: 31665441; PMCID: PMC7145624
Tyson S, Peterson CL, Olson A, Tyler S, Knox N, Griffiths E, Dooley D, Hsiao W, Cabral J, Johnson RP, Laing C, Gannon V, Lynch T, Van Domselaar G, Brinkman F, Graham M (2019). Eleven High-Quality Reference Genome Sequences and 360 Draft Assemblies of Shiga Toxin-Producing Escherichia coli Isolates from Human, Food, Animal, and Environmental Sources in Canada.
Microbiol Resour Announc. 2019 Oct 10;8(41):e00625-19. doi: 10.1128/MRA.00625-19. PMID: 31601655; PMCID: PMC6787312
Dooley DM, Griffiths EJ, Gosal GS, Buttigieg PL, Hoehndorf R, Lange MC, Schriml LM, Brinkman FSL, Hsiao WWL (2018). FoodOn: a harmonized food ontology to increase global food traceability, quality control and data integration.
Nature Partner Journal:Science of Food 2:23.
Bertelli C and Brinkman FS (2018). Improved genomic island predictions withIslandPath-DIMOB.
Bioinformatics, 34(13), pp.2161-2167. doi: 10.1093/bioinformatics/bty095. Pubmed PMID: 29905770
Freschi L, Bertelli C, Jeukens J, Moore MP, Kukavica-Ibrulj I, Emond-Rheault JG, Hamel J, Fothergill JL, Tucker NP, McClean S, Klockgether J, de Soyza A, Brinkman FS, Levesque RC and Winstanley C (2018). Genomic characterisation of an international Pseudomonas aeruginosa reference panel indicates that the two major groups draw upon distinct mobile gene pools.
FEMS Microbiology Letters, 365(14). doi:10.1093/femsle/fny120. Pubmed PMID: 29897457
Rey K, Manku S, Enns W, Van Rossum T, Bushell K, Morin RD, Brinkman FS and Choy JC (2018). Disruption of the Gut Microbiota With Antibiotics Exacerbates Acute Vascular Rejection.
Transplantation, 102(7), pp.1085-1095. doi: 10.1097/TP.0000000000002169. Pubmed PMID: 29538261
Bertelli C, Tilley KE and Brinkman FS (2018). Microbial genomic island discovery, visualization and analysis.
Briefings in Bioinformatics. doi: 10.1093/bib/bby042. Pubmed PMID: 29868902
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 and Brinkman FS (2018). High-throughput detection of RNA processing in bacteria.
BMC Genomics, 19(1). doi: 10.1186/s12864-018-4538-8. Pubmed PMID: 29587634
Panmanee W, Charoenlap N, Atichartpongkul S, Mahavihakanont A, Whiteside MD, Winsor G, Brinkman FSL, Mongkolsuk S and Hassett DJ (2017). The OxyR-regulated phnW gene encoding 2-aminoethylphosphonate:pyruvate aminotransferase helps protect Pseudomonas aeruginosa from tert-butyl hydroperoxide.
PLOS ONE, 12(12), p.e0189066. doi: 10.1371/journal.pone.0189066. Pubmed PMID: 29216242
Peabody MA, Caravas JA, Morrison SS, Mercante JW, Prystajecky NA, Raphael BH and Brinkman FS (2017). Characterization of Legionella Species from Watersheds in British Columbia, Canada.
mSphere, 2(4). doi: 10.1128/mSphere.00246-17. Pubmed PMID: 28776042
Bertelli C, Laird MR, Williams KP; Simon Fraser University Research Computing Group, Lau BY, Hoad G, Winsor GL and Brinkman FS (2017). IslandViewer 4: expanded prediction of genomic islands for larger-scale datasets.
Nucleic Acids Research, 45(W1), pp.W30-W35. doi: 10.1093/nar/gkx343. Pubmed PMID: 28472413
Griffiths EJ, Dooley D, Graham M, Van Domselaar G, Brinkman FS and Hsiao WWL (2017). Context Is Everything: Harmonization of Critical Food Microbiology Descriptors and Metadata for Improved Food Safety and Surveillance.
Frontiers in Microbiology, 8. doi: 10.3389/fmicb.2017.01068. Pubmed PMID: 28694792
Petkau A, Mabon P, Sieffert C, Knox NC, Cabral J, Iskander M, Iskander M, Weedmark K, Zaheer R, Katz LS, Nadon C, Reimer A, Taboada E, Beiko RG, Hsiao W, Brinkman FS, Graham M and Van Domselaar G (2017). SNVPhyl: a single nucleotide variant phylogenomics pipeline for microbial genomic epidemiology.
Microbial Genomics, 3(6). doi: 10.1099/mgen.0.000116. Pubmed PMID: 29026651
Lambert D, Pightling A, Griffiths EJ, Van Domselaar G, Evans P, Berthelet S, Craig D, Chandry P, Stones R, Brinkman FS, Angers-Loustau A, Kreysa J, Tong W and Blais B (2017). Baseline Practices for the Application of Genomic Data Supporting Regulatory Food Safety.
Journal of AOAC International, 100(3), pp.721-731. doi: 10.5740/jaoacint.16-0269. Pubmed PMID: 28105974
Hingston P, Chen J, Dhillon BK, Laing C, Bertelli C, Gannon V, Tasara T, Allen K, Brinkman FS, Truelstrup Hansen L and Wang S (2017). Genotypes Associated with Listeria monocytogenes Isolates Displaying Impaired or Enhanced Tolerances to Cold, Salt, Acid, or Desiccation Stress.
Frontiers in Microbiology, 8. doi: 10.3389/fmicb.2017.00369. Pubmed PMID: 28337186
McKay K, Kowalec K, Brinkman FS, Finlay BB, Horwitz M, Manges AR, Osborne L and Tremlett H (2017). From bugs to brains: The microbiome in neurological health.
Multiple Sclerosis and Related Disorders, 12, pp.1-3. doi: 10.1016/j.msard.2016.12.007. Pubmed PMID: 28283098
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, Elsayegh T, Sardar D, Westman EL, Pawlowski AC, Johnson TA, Brinkman FS and Wright GD, McArthur AG. (2016). CARD 2017: expansion and model-centric curation of the comprehensive antibiotic resistance database.
Nucleic Acids Research, 45(D1), pp.D566-D573. doi:10.1093/nar/gkw1004. Pubmed PMID : 27789705
Osachoff HL, Brown LL, Tirrul L, van Aggelen GC, Brinkman FS and Kennedy CJ (2016). Time course of hepatic gene expression and plasma vitellogenin protein concentrations in estrone-exposed juvenile rainbow trout (Oncorhynchus mykiss).
Comparative Biochemistry and Physiology Part D: Genomics and Proteomics, 19, pp.112-119.doi:10.1016/j.cbd.2016.02.002. Pubmed PMID: 26996967
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
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. 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.
Prystajecky N, Brinkman FS, Auk B, Isaac-Renton JL, Tang P. Personalized genetic testing and norovirus susceptibility.
Can J Infect Dis. 2014 July/Aug;25(4):222-24. PMID: 25285128
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: Do viruses/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.