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Items: 1 to 20 of 104

1.

Improved genomic island predictions with IslandPath-DIMOB.

Bertelli C, Brinkman FSL.

Bioinformatics. 2018 Jul 1;34(13):2161-2167. doi: 10.1093/bioinformatics/bty095.

2.

Genomic characterisation of an international Pseudomonas aeruginosa reference panel indicates that the two major groups draw upon distinct mobile gene pools.

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 FSL, Levesque RC, Winstanley C.

FEMS Microbiol Lett. 2018 Jul 1;365(14). doi: 10.1093/femsle/fny120.

PMID:
29897457
3.

Microbial genomic island discovery, visualization and analysis.

Bertelli C, Tilley KE, Brinkman FSL.

Brief Bioinform. 2018 Jun 3. doi: 10.1093/bib/bby042. [Epub ahead of print]

PMID:
29868902
4.

High-throughput detection of RNA processing in bacteria.

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.

BMC Genomics. 2018 Mar 27;19(1):223. doi: 10.1186/s12864-018-4538-8.

5.

Disruption of the Gut Microbiota With Antibiotics Exacerbates Acute Vascular Rejection.

Rey K, Manku S, Enns W, Van Rossum T, Bushell K, Morin RD, Brinkman FSL, Choy JC.

Transplantation. 2018 Jul;102(7):1085-1095. doi: 10.1097/TP.0000000000002169.

PMID:
29538261
6.

The OxyR-regulated phnW gene encoding 2-aminoethylphosphonate:pyruvate aminotransferase helps protect Pseudomonas aeruginosa from tert-butyl hydroperoxide.

Panmanee W, Charoenlap N, Atichartpongkul S, Mahavihakanont A, Whiteside MD, Winsor G, Brinkman FSL, Mongkolsuk S, Hassett DJ.

PLoS One. 2017 Dec 7;12(12):e0189066. doi: 10.1371/journal.pone.0189066. eCollection 2017.

7.

SNVPhyl: a single nucleotide variant phylogenomics pipeline for microbial genomic epidemiology.

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 F, Graham M, Van Domselaar G.

Microb Genom. 2017 Jun 8;3(6):e000116. doi: 10.1099/mgen.0.000116. eCollection 2017 Jun 30.

8.

Characterization of Legionella Species from Watersheds in British Columbia, Canada.

Peabody MA, Caravas JA, Morrison SS, Mercante JW, Prystajecky NA, Raphael BH, Brinkman FSL.

mSphere. 2017 Aug 2;2(4). pii: e00246-17. doi: 10.1128/mSphere.00246-17. eCollection 2017 Jul-Aug.

9.

Context Is Everything: Harmonization of Critical Food Microbiology Descriptors and Metadata for Improved Food Safety and Surveillance.

Griffiths E, Dooley D, Graham M, Van Domselaar G, Brinkman FSL, Hsiao WWL.

Front Microbiol. 2017 Jun 26;8:1068. doi: 10.3389/fmicb.2017.01068. eCollection 2017.

10.

IslandViewer 4: expanded prediction of genomic islands for larger-scale datasets.

Bertelli C, Laird MR, Williams KP; Simon Fraser University Research Computing Group, Lau BY, Hoad G, Winsor GL, Brinkman FSL.

Nucleic Acids Res. 2017 Jul 3;45(W1):W30-W35. doi: 10.1093/nar/gkx343.

11.

Genotypes Associated with Listeria monocytogenes Isolates Displaying Impaired or Enhanced Tolerances to Cold, Salt, Acid, or Desiccation Stress.

Hingston P, Chen J, Dhillon BK, Laing C, Bertelli C, Gannon V, Tasara T, Allen K, Brinkman FS, Truelstrup Hansen L, Wang S.

Front Microbiol. 2017 Mar 8;8:369. doi: 10.3389/fmicb.2017.00369. eCollection 2017.

12.

From bugs to brains: The microbiome in neurological health.

McKay KA, Kowalec K, Brinkman F, Finlay BB, Horwitz M, Manges AR, Osborne L, Tremlett H.

Mult Scler Relat Disord. 2017 Feb;12:1-3. doi: 10.1016/j.msard.2016.12.007. Epub 2016 Dec 18.

PMID:
28283098
13.

Baseline Practices for the Application of Genomic Data Supporting Regulatory Food Safety.

Lambert D, Pightling A, Griffiths E, Van Domselaar G, Evans P, Berthelet S, Craig D, Chandry PS, Stones R, Brinkman F, Angers-Loustau A, Kreysa J, Tong W, Blais B.

J AOAC Int. 2017 May 1;100(3):721-731. doi: 10.5740/jaoacint.16-0269. Epub 2017 Jan 19.

PMID:
28105974
14.

CARD 2017: expansion and model-centric curation of the comprehensive antibiotic resistance database.

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, Wright GD, McArthur AG.

Nucleic Acids Res. 2017 Jan 4;45(D1):D566-D573. doi: 10.1093/nar/gkw1004. Epub 2016 Oct 26.

15.

A comprehensive method for amplicon-based and metagenomic characterization of viruses, bacteria, and eukaryotes in freshwater samples.

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.

Microbiome. 2016 Jul 19;4(1):20. doi: 10.1186/s40168-016-0166-1.

16.

Genomic Analysis of a Serotype 5 Streptococcus pneumoniae Outbreak in British Columbia, Canada, 2005-2009.

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.

Can J Infect Dis Med Microbiol. 2016;2016:5381871. doi: 10.1155/2016/5381871. Epub 2016 Apr 14.

17.

Time course of hepatic gene expression and plasma vitellogenin protein concentrations in estrone-exposed juvenile rainbow trout (Oncorhynchus mykiss).

Osachoff HL, Brown LLY, Tirrul L, van Aggelen GC, Brinkman FSL, Kennedy CJ.

Comp Biochem Physiol Part D Genomics Proteomics. 2016 Sep;19:112-119. doi: 10.1016/j.cbd.2016.02.002. Epub 2016 Feb 26.

PMID:
26996967
18.

Year-Long Metagenomic Study of River Microbiomes Across Land Use and Water Quality.

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.

Front Microbiol. 2015 Dec 16;6:1405. doi: 10.3389/fmicb.2015.01405. eCollection 2015.

19.

PSORTdb: expanding the bacteria and archaea protein subcellular localization database to better reflect diversity in cell envelope structures.

Peabody MA, Laird MR, Vlasschaert C, Lo R, Brinkman FS.

Nucleic Acids Res. 2016 Jan 4;44(D1):D663-8. doi: 10.1093/nar/gkv1271. Epub 2015 Nov 23.

20.

Enhanced annotations and features for comparing thousands of Pseudomonas genomes in the Pseudomonas genome database.

Winsor GL, Griffiths EJ, Lo R, Dhillon BK, Shay JA, Brinkman FS.

Nucleic Acids Res. 2016 Jan 4;44(D1):D646-53. doi: 10.1093/nar/gkv1227. Epub 2015 Nov 17.

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