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The Canadian VirusSeq Data Portal and Duotang: open resources for SARS-CoV-2 viral sequences and genomic epidemiology.
Gill EE, Jia B, Murall CL, Poujol R, Anwar MZ, John NS, Richardsson J, Hobb A, Olabode AS, Lepsa A, Duggan AT, Tyler AD, N'Guessan A, Kachru A, Chan B, Yoshida C, Yung CK, Bujold D, Andric D, Su E, Griffiths EJ, Van Domselaar G, Jolly GW, Ward HKE, Feher H, Baker J, Simpson JT, Uddin J, Ragoussis J, Eubank J, Fritz JH, Gálvez JH, Fang K, Cullion K, Rivera L, Xiang L, Croxen MA, Shiell M, Prystajecky N, Quirion PO, Bajari R, Rich S, Mubareka S, Moreira S, Cain S, Sutcliffe SG, Kraemer SA, Alturmessov Y, Joly Y, Cphln Consortium, CanCOGeN Consortium, VirusSeq Data Portal Academic And Health Network, Fiume M, Snutch TP, Bell C, Lopez-Correa C, Hussin JG, Joy JB, Colijn C, Gordon PMK, Hsiao WWL, Poon AFY, Knox NC, Courtot M, Stein L, Otto SP, Bourque G, Shapiro BJ, Brinkman FSL. Gill EE, et al. Among authors: joy jb. Microb Genom. 2024 Oct;10(10):001293. doi: 10.1099/mgen.0.001293. Microb Genom. 2024. PMID: 39401061 Free PMC article.
Genomic epidemiology of the first two waves of SARS-CoV-2 in Canada.
McLaughlin A, Montoya V, Miller RL, Mordecai GJ; Canadian COVID-19 Genomics Network (CanCOGen) Consortium; Worobey M, Poon AFY, Joy JB. McLaughlin A, et al. Among authors: joy jb. Elife. 2022 Aug 2;11:e73896. doi: 10.7554/eLife.73896. Elife. 2022. PMID: 35916373 Free PMC article.
Ancestral Reconstruction.
Joy JB, Liang RH, McCloskey RM, Nguyen T, Poon AF. Joy JB, et al. PLoS Comput Biol. 2016 Jul 12;12(7):e1004763. doi: 10.1371/journal.pcbi.1004763. eCollection 2016 Jul. PLoS Comput Biol. 2016. PMID: 27404731 Free PMC article. No abstract available.
Phylogenetic approach to recover integration dates of latent HIV sequences within-host.
Jones BR, Kinloch NN, Horacsek J, Ganase B, Harris M, Harrigan PR, Jones RB, Brockman MA, Joy JB, Poon AFY, Brumme ZL. Jones BR, et al. Among authors: joy jb. Proc Natl Acad Sci U S A. 2018 Sep 18;115(38):E8958-E8967. doi: 10.1073/pnas.1802028115. Epub 2018 Sep 5. Proc Natl Acad Sci U S A. 2018. PMID: 30185556 Free PMC article.
Phylogenetic Tools for Generalized HIV-1 Epidemics: Findings from the PANGEA-HIV Methods Comparison.
Ratmann O, Hodcroft EB, Pickles M, Cori A, Hall M, Lycett S, Colijn C, Dearlove B, Didelot X, Frost S, Hossain AS, Joy JB, Kendall M, Kühnert D, Leventhal GE, Liang R, Plazzotta G, Poon AF, Rasmussen DA, Stadler T, Volz E, Weis C, Leigh Brown AJ, Fraser C; PANGEA-HIV Consortium. Ratmann O, et al. Among authors: joy jb. Mol Biol Evol. 2017 Jan;34(1):185-203. doi: 10.1093/molbev/msw217. Epub 2016 Oct 7. Mol Biol Evol. 2017. PMID: 28053012 Free PMC article.
A systematic, deep sequencing-based methodology for identification of mixed-genotype hepatitis C virus infections.
Olmstead AD, Montoya V, Chui CK, Dong W, Joy JB, Tai V, Poon AFY, Nguyen T, Brumme CJ, Martinello M, Matthews GV, Richard Harrigan P, Dore GJ, Applegate TL, Grebely J, Howe AYM. Olmstead AD, et al. Among authors: joy jb. Infect Genet Evol. 2019 Apr;69:76-84. doi: 10.1016/j.meegid.2019.01.016. Epub 2019 Jan 14. Infect Genet Evol. 2019. PMID: 30654177
The emergence of SARS-CoV-2 in Europe and North America.
Worobey M, Pekar J, Larsen BB, Nelson MI, Hill V, Joy JB, Rambaut A, Suchard MA, Wertheim JO, Lemey P. Worobey M, et al. Among authors: joy jb. Science. 2020 Oct 30;370(6516):564-570. doi: 10.1126/science.abc8169. Epub 2020 Sep 10. Science. 2020. PMID: 32912998 Free PMC article.
67 results