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Advances in nano-catalysts based biodiesel production from non-food feedstocks.

Gardy J, Rehan M, Hassanpour A, Lai X, Nizami AS.

J Environ Manage. 2019 Nov 1;249:109316. doi: 10.1016/j.jenvman.2019.109316. Epub 2019 Aug 29.


Whole genome sequencing for improved understanding of Mycobacterium tuberculosis transmission in a remote circumpolar region.

Guthrie JL, Strudwick L, Roberts B, Allen M, McFadzen J, Roth D, Jorgensen D, Rodrigues M, Tang P, Hanley B, Johnston J, Cook VJ, Gardy JL.

Epidemiol Infect. 2019 Jan;147:e188. doi: 10.1017/S0950268819000670.


Trust and the ethical challenges in the use of whole genome sequencing for tuberculosis surveillance: a qualitative study of stakeholder perspectives.

Jackson C, Gardy JL, Shadiloo HC, Silva DS.

BMC Med Ethics. 2019 Jul 4;20(1):43. doi: 10.1186/s12910-019-0380-z.


Whole genome sequencing of Mycobacterium tuberculosis: current standards and open issues.

Meehan CJ, Goig GA, Kohl TA, Verboven L, Dippenaar A, Ezewudo M, Farhat MR, Guthrie JL, Laukens K, Miotto P, Ofori-Anyinam B, Dreyer V, Supply P, Suresh A, Utpatel C, van Soolingen D, Zhou Y, Ashton PM, Brites D, Cabibbe AM, de Jong BC, de Vos M, Menardo F, Gagneux S, Gao Q, Heupink TH, Liu Q, Loiseau C, Rigouts L, Rodwell TC, Tagliani E, Walker TM, Warren RM, Zhao Y, Zignol M, Schito M, Gardy J, Cirillo DM, Niemann S, Comas I, Van Rie A.

Nat Rev Microbiol. 2019 Sep;17(9):533-545. doi: 10.1038/s41579-019-0214-5. Review.


Digestive and genitourinary sequelae in rectal cancer survivors and their impact on health-related quality of life: Outcome of a high-resolution population-based study.

Eid Y, Bouvier V, Menahem B, Thobie A, Dolet N, Finochi M, Renier M, Gardy J, Launoy G, Dejardin O, Morello R, Alves A; Rectqol Group.

Surgery. 2019 Sep;166(3):327-335. doi: 10.1016/j.surg.2019.04.007. Epub 2019 Jun 14.


The problem with defining foreign birth as a risk factor in tuberculosis epidemiology studies.

Guthrie JL, Ronald LA, Cook VJ, Johnston J, Gardy JL.

PLoS One. 2019 Apr 30;14(4):e0216271. doi: 10.1371/journal.pone.0216271. eCollection 2019.


Universal genotyping reveals province-level differences in the molecular epidemiology of tuberculosis.

Guthrie JL, Marchand-Austin A, Cronin K, Lam K, Pyskir D, Kong C, Jorgensen D, Rodrigues M, Roth D, Tang P, Cook VJ, Johnston J, Jamieson FB, Gardy JL.

PLoS One. 2019 Apr 3;14(4):e0214870. doi: 10.1371/journal.pone.0214870. eCollection 2019.


Whole blood human transcriptome and virome analysis of ME/CFS patients experiencing post-exertional malaise following cardiopulmonary exercise testing.

Bouquet J, Li T, Gardy JL, Kang X, Stevens S, Stevens J, VanNess M, Snell C, Potts J, Miller RR, Morshed M, McCabe M, Parker S, Uyaguari M, Tang P, Steiner T, Chan WS, De Souza AM, Mattman A, Patrick DM, Chiu CY.

PLoS One. 2019 Mar 21;14(3):e0212193. doi: 10.1371/journal.pone.0212193. eCollection 2019.


Building the Framework for Standardized Clinical Laboratory Reporting of Next-generation Sequencing Data for Resistance-associated Mutations in Mycobacterium tuberculosis Complex.

Tornheim JA, Starks AM, Rodwell TC, Gardy JL, Walker TM, Cirillo DM, Jayashankar L, Miotto P, Zignol M, Schito M.

Clin Infect Dis. 2019 Oct 15;69(9):1631-1633. doi: 10.1093/cid/ciz219.


Adjutant: an R-based tool to support topic discovery for systematic and literature reviews.

Crisan A, Munzner T, Gardy JL.

Bioinformatics. 2019 Mar 15;35(6):1070-1072. doi: 10.1093/bioinformatics/bty722.


Impact of socioeconomic status on survival in patients with ovarian cancer.

Gardy J, Dejardin O, Thobie A, Eid Y, Guizard AV, Launoy G.

Int J Gynecol Cancer. 2019 May;29(4):792-801. doi: 10.1136/ijgc-2018-000097. Epub 2019 Feb 1.


Beyond the SNP Threshold: Identifying Outbreak Clusters Using Inferred Transmissions.

Stimson J, Gardy J, Mathema B, Crudu V, Cohen T, Colijn C.

Mol Biol Evol. 2019 Mar 1;36(3):587-603. doi: 10.1093/molbev/msy242.


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.


An investigation on the capability of magnetically separable Fe3O4/mordenite zeolite for refinery oily wastewater purification.

Hesas RH, Baei MS, Rostami H, Gardy J, Hassanpour A.

J Environ Manage. 2019 Jul 1;241:525-534. doi: 10.1016/j.jenvman.2018.09.005. Epub 2018 Oct 6.


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. 2019 Jun;56(6):4249-4257. doi: 10.1007/s12035-018-1354-8. Epub 2018 Oct 8.


Prediction of Susceptibility to First-Line Tuberculosis Drugs by DNA Sequencing.

CRyPTIC Consortium and the 100,000 Genomes Project, Allix-Béguec C, Arandjelovic I, Bi L, Beckert P, Bonnet M, Bradley P, Cabibbe AM, Cancino-Muñoz I, Caulfield MJ, Chaiprasert A, Cirillo DM, Clifton DA, Comas I, Crook DW, De Filippo MR, de Neeling H, Diel R, Drobniewski FA, Faksri K, Farhat MR, Fleming J, Fowler P, Fowler TA, Gao Q, Gardy J, Gascoyne-Binzi D, Gibertoni-Cruz AL, Gil-Brusola A, Golubchik T, Gonzalo X, Grandjean L, He G, Guthrie JL, Hoosdally S, Hunt M, Iqbal Z, Ismail N, Johnston J, Khanzada FM, Khor CC, Kohl TA, Kong C, Lipworth S, Liu Q, Maphalala G, Martinez E, Mathys V, Merker M, Miotto P, Mistry N, Moore DAJ, Murray M, Niemann S, Omar SV, Ong RT, Peto TEA, Posey JE, Prammananan T, Pym A, Rodrigues C, Rodrigues M, Rodwell T, Rossolini GM, Sánchez Padilla E, Schito M, Shen X, Shendure J, Sintchenko V, Sloutsky A, Smith EG, Snyder M, Soetaert K, Starks AM, Supply P, Suriyapol P, Tahseen S, Tang P, Teo YY, Thuong TNT, Thwaites G, Tortoli E, van Soolingen D, Walker AS, Walker TM, Wilcox M, Wilson DJ, Wyllie D, Yang Y, Zhang H, Zhao Y, Zhu B.

N Engl J Med. 2018 Oct 11;379(15):1403-1415. doi: 10.1056/NEJMoa1800474. Epub 2018 Sep 26.


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

Crisan A, Gardy JL, Munzner T.

Bioinformatics. 2019 May 15;35(10):1668-1676. doi: 10.1093/bioinformatics/bty832.


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.


Introducing the JMBE Themed Issue on Science Communication.

Mangan DF, Cloyd ET, Romo JA, Wessner DR, Westenberg DJ, Adukwu E, Menninger H, Gardy J.

J Microbiol Biol Educ. 2018 Mar 30;19(1). pii: 19.1.9. doi: 10.1128/jmbe.v19i1.1601. eCollection 2018. No abstract available.


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.


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.


Exogenous mineralization of hard tissues using photo-absorptive minerals and femto-second lasers; the case of dental enamel.

Anastasiou AD, Strafford S, Thomson CL, Gardy J, Edwards TJ, Malinowski M, Hussain SA, Metzger NK, Hassanpour A, Brown CTA, Brown AP, Duggal MS, Jha A.

Acta Biomater. 2018 Apr 15;71:86-95. doi: 10.1016/j.actbio.2018.02.012. Epub 2018 Feb 17.


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.


MentaLiST - A fast MLST caller for large MLST schemes.

Feijao P, Yao HT, Fornika D, Gardy J, Hsiao W, Chauve C, Chindelevitch L.

Microb Genom. 2018 Feb;4(2). doi: 10.1099/mgen.0.000146. Epub 2018 Jan 10.


Waste to biodiesel: A preliminary assessment for Saudi Arabia.

Rehan M, Gardy J, Demirbas A, Rashid U, Budzianowski WM, Pant D, Nizami AS.

Bioresour Technol. 2018 Feb;250:17-25. doi: 10.1016/j.biortech.2017.11.024. Epub 2017 Nov 10.


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.


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.


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.


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.


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.


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.


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.


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.


Genomic Infectious Disease Epidemiology in Partially Sampled and Ongoing Outbreaks.

Didelot X, Fraser C, Gardy J, Colijn C.

Mol Biol Evol. 2017 Apr 1;34(4):997-1007. doi: 10.1093/molbev/msw275.


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.


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.


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.


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.


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.


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.


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.


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.


Genetic determinants of cocaine-associated agranulocytosis.

Buxton JA, Omura J, Kuo M, Ross C, Tzemis D, Purssell R, Gardy J, Carleton B.

BMC Res Notes. 2015 Jun 13;8:240. doi: 10.1186/s13104-015-1219-4.


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.


Submaximal exercise testing with near-infrared spectroscopy in Myalgic Encephalomyelitis/Chronic Fatigue Syndrome patients compared to healthy controls: a case-control study.

Miller RR, Reid WD, Mattman A, Yamabayashi C, Steiner T, Parker S, Gardy J, Tang P, Patrick DM.

J Transl Med. 2015 May 20;13:159. doi: 10.1186/s12967-015-0527-8.


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.


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.


Real-time digital pathogen surveillance - the time is now.

Gardy J, Loman NJ, Rambaut A.

Genome Biol. 2015 Jul 30;16(1):155. doi: 10.1186/s13059-015-0726-x.


Phylogenetic tree shapes resolve disease transmission patterns.

Colijn C, Gardy J.

Evol Med Public Health. 2014 Jun 9;2014(1):96-108. doi: 10.1093/emph/eou018.

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