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Items: 1 to 50 of 53

1.

Within-host Mycobacterium tuberculosis diversity and its utility for inferences of transmission.

Martin MA, Lee RS, Cowley LA, Gardy JL, Hanage WP.

Microb Genom. 2018 Oct;4(10). doi: 10.1099/mgen.0.000217. Epub 2018 Oct 11.

2.

Immunosignature Analysis of Myalgic Encephalomyelitis/Chronic Fatigue Syndrome (ME/CFS).

Günther OP, Gardy JL, Stafford P, Fluge Ø, Mella O, Tang P, Miller RR, Parker SM, Johnston SA, Patrick DM.

Mol Neurobiol. 2018 Oct 8. doi: 10.1007/s12035-018-1354-8. [Epub ahead of print]

PMID:
30298340
3.

A systematic method for surveying data visualizations and a resulting genomic epidemiology visualization typology: GEViT.

Crisan A, Gardy JL, Munzner T.

Bioinformatics. 2018 Sep 26. doi: 10.1093/bioinformatics/bty832. [Epub ahead of print]

PMID:
30256887
4.

TB Transmission: Closing the Gaps.

Comas I, Gardy JL.

EBioMedicine. 2018 Aug;34:4-5. doi: 10.1016/j.ebiom.2018.07.020. Epub 2018 Jul 30. No abstract available.

5.

Genotyping and Whole-Genome Sequencing to Identify Tuberculosis Transmission to Pediatric Patients in British Columbia, Canada, 2005-2014.

Guthrie JL, Delli Pizzi A, Roth D, Kong C, Jorgensen D, Rodrigues M, Tang P, Cook VJ, Johnston J, Gardy JL.

J Infect Dis. 2018 Aug 24;218(7):1155-1163. doi: 10.1093/infdis/jiy278.

6.

Universal Genotyping for Tuberculosis Prevention Programs: a 5-Year Comparison with On-Request Genotyping.

Guthrie JL, Kong C, Roth D, Jorgensen D, Rodrigues M, Tang P, Thejoe M, Elwood K, Cook VJ, Johnston J, Gardy JL.

J Clin Microbiol. 2018 Apr 25;56(5). pii: e01778-17. doi: 10.1128/JCM.01778-17. Print 2018 May.

7.

Evidence-based design and evaluation of a whole genome sequencing clinical report for the reference microbiology laboratory.

Crisan A, McKee G, Munzner T, Gardy JL.

PeerJ. 2018 Jan 10;6:e4218. doi: 10.7717/peerj.4218. eCollection 2018.

8.

Towards a genomics-informed, real-time, global pathogen surveillance system.

Gardy JL, Loman NJ.

Nat Rev Genet. 2018 Jan;19(1):9-20. doi: 10.1038/nrg.2017.88. Epub 2017 Nov 13. Review.

PMID:
29129921
9.

Genome Sequences of the Mycobacterium tuberculosis H37Rv-ptkA Deletion Mutant and Its Parental Strain.

Tsui CKM, Wong D, Narula G, Gardy JL, Hsiao WWH, Av-Gay Y.

Genome Announc. 2017 Nov 2;5(44). pii: e01156-17. doi: 10.1128/genomeA.01156-17.

10.

Molecular Epidemiology of Tuberculosis in British Columbia, Canada: A 10-Year Retrospective Study.

Guthrie JL, Kong C, Roth D, Jorgensen D, Rodrigues M, Hoang L, Tang P, Cook V, Johnston J, Gardy JL.

Clin Infect Dis. 2018 Mar 5;66(6):849-856. doi: 10.1093/cid/cix906.

11.

Complete Genome Sequence of Mycobacterium chimaera SJ42, a Nonoutbreak Strain from an Immunocompromised Patient with Pulmonary Disease.

Hasan NA, Warren RL, Epperson LE, Malecha A, Alexander DC, Turenne CY, MacMillan D, Birol I, Pleasance S, Coope R, Jones SJM, Romney MG, Ng M, Chan T, Rodrigues M, Tang P, Gardy JL, Strong M.

Genome Announc. 2017 Sep 14;5(37). pii: e00963-17. doi: 10.1128/genomeA.00963-17.

12.

Mycobacterium chimaera: unraveling a mystery through genomics.

Gardy JL.

Lancet Infect Dis. 2017 Oct;17(10):1004-1005. doi: 10.1016/S1473-3099(17)30356-0. Epub 2017 Jul 12. No abstract available.

PMID:
28711587
13.

Declaring a tuberculosis outbreak over with genomic epidemiology.

Hatherell HA, Didelot X, Pollock SL, Tang P, Crisan A, Johnston JC, Colijn C, Gardy JL.

Microb Genom. 2016 May 31;2(5):e000060. doi: 10.1099/mgen.0.000060. eCollection 2016 May.

14.

Self-rated health and reasons for non-vaccination against seasonal influenza in Canadian adults with asthma.

Guthrie JL, Fisman D, Gardy JL.

PLoS One. 2017 Feb 16;12(2):e0172117. doi: 10.1371/journal.pone.0172117. eCollection 2017.

15.

RNA-Seq Analysis of Gene Expression, Viral Pathogen, and B-Cell/T-Cell Receptor Signatures in Complex Chronic Disease.

Bouquet J, Gardy JL, Brown S, Pfeil J, Miller RR, Morshed M, Avina-Zubieta A, Shojania K, McCabe M, Parker S, Uyaguari M, Federman S, Tang P, Steiner T, Otterstater M, Holt R, Moore R, Chiu CY, Patrick DM; Complex Chronic Disease Study Group.

Clin Infect Dis. 2017 Feb 15;64(4):476-481. doi: 10.1093/cid/ciw767.

16.

A brief primer on genomic epidemiology: lessons learned from Mycobacterium tuberculosis.

Guthrie JL, Gardy JL.

Ann N Y Acad Sci. 2017 Jan;1388(1):59-77. doi: 10.1111/nyas.13273. Epub 2016 Dec 23. Review.

PMID:
28009051
17.

Metagenomic Investigation of Plasma in Individuals with ME/CFS Highlights the Importance of Technical Controls to Elucidate Contamination and Batch Effects.

Miller RR, Uyaguari-Diaz M, McCabe MN, Montoya V, Gardy JL, Parker S, Steiner T, Hsiao W, Nesbitt MJ, Tang P, Patrick DM; CCD Study Group.

PLoS One. 2016 Nov 2;11(11):e0165691. doi: 10.1371/journal.pone.0165691. eCollection 2016.

18.
19.

Translating phylogeny into action for HIV surveillance.

Gardy JL.

Lancet HIV. 2016 May;3(5):e196-7. doi: 10.1016/S2352-3018(16)30012-1. Epub 2016 Apr 7. No abstract available.

PMID:
27126483
20.

Accelerating tuberculosis elimination in low-incidence settings: the role of genomics.

Guthrie JL, Gardy JL.

Eur Respir J. 2015 Dec;46(6):1840-1. doi: 10.1183/13993003.00788-2015. No abstract available.

21.

Spatio-temporal analysis of tuberculous infection risk among clients of a homeless shelter during an outbreak.

Crisan A, Wong HY, Johnston JC, Tang P, Colijn C, Otterstatter M, Hiscoe L, Parker R, Pollock SL, Gardy JL.

Int J Tuberc Lung Dis. 2015 Sep;19(9):1033-8, i-iii. doi: 10.5588/ijtld.14.0957.

PMID:
26260820
22.

Whole-Genome Sequencing of Measles Virus Genotypes H1 and D8 During Outbreaks of Infection Following the 2010 Olympic Winter Games Reveals Viral Transmission Routes.

Gardy JL, Naus M, Amlani A, Chung W, Kim H, Tan M, Severini A, Krajden M, Puddicombe D, Sahni V, Hayden AS, Gustafson R, Henry B, Tang P.

J Infect Dis. 2015 Nov 15;212(10):1574-8. doi: 10.1093/infdis/jiv271. Epub 2015 Jul 6.

PMID:
26153409
23.

Towards genomic prediction of drug resistance in tuberculosis.

Gardy JL.

Lancet Infect Dis. 2015 Oct;15(10):1124-1125. doi: 10.1016/S1473-3099(15)00088-2. Epub 2015 Jun 23. No abstract available.

PMID:
26116184
24.

Lyme Disease Diagnosed by Alternative Methods: A Phenotype Similar to That of Chronic Fatigue Syndrome.

Patrick DM, Miller RR, Gardy JL, Parker SM, Morshed MG, Steiner TS, Singer J, Shojania K, Tang P; Complex Chronic Disease Study Group.

Clin Infect Dis. 2015 Oct 1;61(7):1084-91. doi: 10.1093/cid/civ470. Epub 2015 Jun 16.

PMID:
26082507
25.

A clonal outbreak of tuberculosis in a homeless population in the interior of British Columbia, Canada, 2008-2015.

Cheng JM, Hiscoe L, Pollock SL, Hasselback P, Gardy JL, Parker R.

Epidemiol Infect. 2015 Nov;143(15):3220-6. doi: 10.1017/S0950268815000825. Epub 2015 May 28.

PMID:
26018109
26.

A microbiological revolution meets an ancient disease: improving the management of tuberculosis with genomics.

Wlodarska M, Johnston JC, Gardy JL, Tang P.

Clin Microbiol Rev. 2015 Apr;28(2):523-39. doi: 10.1128/CMR.00124-14. Review.

27.

Stopping outbreaks with real-time genomic epidemiology.

Tang P, Gardy JL.

Genome Med. 2014 Nov 20;6(11):104. doi: 10.1186/s13073-014-0104-4. eCollection 2014.

28.

A metagenomic approach to investigate the microbial causes of myalgic encephalomyelitis/chronic fatigue syndrome: moving beyond XMRV.

Miller RR, Gardy JL, Tang P, Patrick DM.

Fatigue. 2013 Oct;1(4):185-189. No abstract available.

29.

Metagenomics for pathogen detection in public health.

Miller RR, Montoya V, Gardy JL, Patrick DM, Tang P.

Genome Med. 2013 Sep 20;5(9):81. doi: 10.1186/gm485. eCollection 2013. Review.

30.

Genomic analysis identifies targets of convergent positive selection in drug-resistant Mycobacterium tuberculosis.

Farhat MR, Shapiro BJ, Kieser KJ, Sultana R, Jacobson KR, Victor TC, Warren RM, Streicher EM, Calver A, Sloutsky A, Kaur D, Posey JE, Plikaytis B, Oggioni MR, Gardy JL, Johnston JC, Rodrigues M, Tang PK, Kato-Maeda M, Borowsky ML, Muddukrishna B, Kreiswirth BN, Kurepina N, Galagan J, Gagneux S, Birren B, Rubin EJ, Lander ES, Sabeti PC, Murray M.

Nat Genet. 2013 Oct;45(10):1183-9. doi: 10.1038/ng.2747. Epub 2013 Sep 1.

31.

Investigation of disease outbreaks with genome sequencing.

Gardy JL.

Lancet Infect Dis. 2013 Feb;13(2):101-2. doi: 10.1016/S1473-3099(12)70295-5. Epub 2012 Nov 15. No abstract available.

PMID:
23158498
32.

Cross-reactive and vaccine-induced antibody to an emerging swine-origin variant of influenza A virus subtype H3N2 (H3N2v).

Skowronski DM, Janjua NZ, De Serres G, Purych D, Gilca V, Scheifele DW, Dionne M, Sabaiduc S, Gardy JL, Li G, Bastien N, Petric M, Boivin G, Li Y.

J Infect Dis. 2012 Dec 15;206(12):1852-61. doi: 10.1093/infdis/jis500. Epub 2012 Aug 7.

PMID:
22872731
33.

Cross-lineage influenza B and heterologous influenza A antibody responses in vaccinated mice: immunologic interactions and B/Yamagata dominance.

Skowronski DM, Hamelin ME, Janjua NZ, De Serres G, Gardy JL, Rhéaume C, Bouhy X, Boivin G.

PLoS One. 2012;7(6):e38929. doi: 10.1371/journal.pone.0038929. Epub 2012 Jun 22.

34.

A sentinel platform to evaluate influenza vaccine effectiveness and new variant circulation, Canada 2010-2011 season.

Skowronski DM, Janjua NZ, De Serres G, Winter AL, Dickinson JA, Gardy JL, Gubbay J, Fonseca K, Charest H, Crowcroft NS, Fradet MD, Bastien N, Li Y, Krajden M, Sabaiduc S, Petric M.

Clin Infect Dis. 2012 Aug;55(3):332-42. doi: 10.1093/cid/cis431. Epub 2012 Apr 26.

PMID:
22539661
35.

Estimates of influenza vaccine effectiveness for 2007-2008 from Canada's sentinel surveillance system: cross-protection against major and minor variants.

Janjua NZ, Skowronski DM, De Serres G, Dickinson J, Crowcroft NS, Taylor M, Winter AL, Hottes TS, Fonseca K, Charest H, Drews SJ, Sabaiduc S, Bastien N, Li Y, Gardy JL, Petric M.

J Infect Dis. 2012 Jun 15;205(12):1858-68. doi: 10.1093/infdis/jis283. Epub 2012 Apr 9.

PMID:
22492921
36.

Cross-reactive antibody to swine influenza A(H3N2) subtype virus in children and adults before and after immunisation with 2010/11 trivalent inactivated influenza vaccine in Canada, August to November 2010.

Skowronski DM, De Serres G, Janjua NZ, Gardy JL, Gilca V, Dionne M, Hamelin ME, Rhéaume C, Boivin G.

Euro Surveill. 2012 Jan 26;17(4). pii: 20066.

37.

Whole-genome sequencing and social-network analysis of a tuberculosis outbreak.

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.

N Engl J Med. 2011 Feb 24;364(8):730-9. doi: 10.1056/NEJMoa1003176. Erratum in: N Engl J Med. 2011 Jun 2;364(22):2174.

38.

Systems-level comparison of host responses induced by pandemic and seasonal influenza A H1N1 viruses in primary human type I-like alveolar epithelial cells in vitro.

Lee SM, Chan RW, Gardy JL, Lo CK, Sihoe AD, Kang SS, Cheung TK, Guan YI, Chan MC, Hancock RE, Peiris MJ.

Respir Res. 2010 Oct 28;11:147. doi: 10.1186/1465-9921-11-147.

39.

Association between the 2008-09 seasonal influenza vaccine and pandemic H1N1 illness during Spring-Summer 2009: four observational studies from Canada.

Skowronski DM, De Serres G, Crowcroft NS, Janjua NZ, Boulianne N, Hottes TS, Rosella LC, Dickinson JA, Gilca R, Sethi P, Ouhoummane N, Willison DJ, Rouleau I, Petric M, Fonseca K, Drews SJ, Rebbapragada A, Charest H, Hamelin ME, Boivin G, Gardy JL, Li Y, Kwindt TL, Patrick DM, Brunham RC; Canadian SAVOIR Team.

PLoS Med. 2010 Apr 6;7(4):e1000258. doi: 10.1371/journal.pmed.1000258.

40.

Robust TLR4-induced gene expression patterns are not an accurate indicator of human immunity.

Brown KL, Falsafi R, Kum W, Hamill P, Gardy JL, Davidson DJ, Turvey S, Finlay BB, Speert DP, Hancock RE.

J Transl Med. 2010 Jan 27;8:6. doi: 10.1186/1479-5876-8-6.

41.

Systems-level comparison of host-responses elicited by avian H5N1 and seasonal H1N1 influenza viruses in primary human macrophages.

Lee SM, Gardy JL, Cheung CY, Cheung TK, Hui KP, Ip NY, Guan Y, Hancock RE, Peiris JS.

PLoS One. 2009 Dec 14;4(12):e8072. doi: 10.1371/journal.pone.0008072.

42.

Enabling a systems biology approach to immunology: focus on innate immunity.

Gardy JL, Lynn DJ, Brinkman FS, Hancock RE.

Trends Immunol. 2009 Jun;30(6):249-62. doi: 10.1016/j.it.2009.03.009. Epub 2009 May 8. Review.

PMID:
19428301
43.

InnateDB: facilitating systems-level analyses of the mammalian innate immune response.

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, Tulpan D, Whiteside MD, Chikatamarla A, Mah B, Munzner T, Hokamp K, Hancock RE, Brinkman FS.

Mol Syst Biol. 2008;4:218. doi: 10.1038/msb.2008.55. Epub 2008 Sep 2.

44.

The commensal Streptococcus salivarius K12 downregulates the innate immune responses of human epithelial cells and promotes host-microbe homeostasis.

Cosseau C, Devine DA, Dullaghan E, Gardy JL, Chikatamarla A, Gellatly S, Yu LL, Pistolic J, Falsafi R, Tagg J, Hancock RE.

Infect Immun. 2008 Sep;76(9):4163-75. doi: 10.1128/IAI.00188-08. Epub 2008 Jul 14.

45.

Computer-aided biotechnology: from immuno-informatics to reverse vaccinology.

Vivona S, Gardy JL, Ramachandran S, Brinkman FS, Raghava GP, Flower DR, Filippini F.

Trends Biotechnol. 2008 Apr;26(4):190-200. doi: 10.1016/j.tibtech.2007.12.006. Epub 2008 Feb 21. Review.

PMID:
18291542
46.

Complexities of targeting innate immunity to treat infection.

Brown KL, Cosseau C, Gardy JL, Hancock RE.

Trends Immunol. 2007 Jun;28(6):260-6. Epub 2007 Apr 30. Review.

PMID:
17468048
47.

Cerebral: a Cytoscape plugin for layout of and interaction with biological networks using subcellular localization annotation.

Barsky A, Gardy JL, Hancock RE, Munzner T.

Bioinformatics. 2007 Apr 15;23(8):1040-2. Epub 2007 Feb 19.

PMID:
17309895
48.

Methods for predicting bacterial protein subcellular localization.

Gardy JL, Brinkman FS.

Nat Rev Microbiol. 2006 Oct;4(10):741-51. Epub 2006 Sep 11. Review. Erratum in: Nat Rev Microbiol. 2006 Nov;4(11):1 p following 865.

PMID:
16964270

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