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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: bujold d. Microb Genom. 2024 Oct;10(10):001293. doi: 10.1099/mgen.0.001293. Microb Genom. 2024. PMID: 39401061 Free PMC article.
The Canadian VirusSeq Data Portal & 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, Joly Y, Alturmessov Y, Consortium C, Consortium C; 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: bujold d. ArXiv [Preprint]. 2024 May 8:arXiv:2405.04734v1. ArXiv. 2024. Update in: Microb Genom. 2024 Oct;10(10). doi: 10.1099/mgen.0.001293 PMID: 38764594 Free PMC article. Updated. Preprint.
Epigenetic variation impacts individual differences in the transcriptional response to influenza infection.
Aracena KA, Lin YL, Luo K, Pacis A, Gona S, Mu Z, Yotova V, Sindeaux R, Pramatarova A, Simon MM, Chen X, Groza C, Lougheed D, Gregoire R, Brownlee D, Boye C, Pique-Regi R, Li Y, He X, Bujold D, Pastinen T, Bourque G, Barreiro LB. Aracena KA, et al. Among authors: bujold d. Nat Genet. 2024 Mar;56(3):408-419. doi: 10.1038/s41588-024-01668-z. Epub 2024 Feb 29. Nat Genet. 2024. PMID: 38424460
EpiVar Browser: advanced exploration of epigenomics data under controlled access.
Lougheed DR, Liu H, Aracena KA, Grégoire R, Pacis A, Pastinen T, Barreiro LB, Joly Y, Bujold D, Bourque G. Lougheed DR, et al. Among authors: bujold d. bioRxiv [Preprint]. 2023 Aug 5:2023.08.03.551309. doi: 10.1101/2023.08.03.551309. bioRxiv. 2023. Update in: Bioinformatics. 2024 Mar 4;40(3):btae136. doi: 10.1093/bioinformatics/btae136 PMID: 37577719 Free PMC article. Updated. Preprint.
Data and Tools Integration in the Canadian Open Neuroscience Platform.
Poline JB, Das S, Glatard T, Madjar C, Dickie EW, Lecours X, Beaudry T, Beck N, Behan B, Brown ST, Bujold D, Beauvais M, Caron B, Czech C, Dharsee M, Dugré M, Evans K, Gee T, Ippoliti G, Kiar G, Knoppers BM, Kuehn T, Le D, Lo D, Mazaheri M, MacFarlane D, Muja N, O'Brien EA, O'Callaghan L, Paiva S, Park P, Quesnel D, Rabelais H, Rioux P, Legault M, Tremblay-Mercier J, Rotenberg D, Stone J, Strauss T, Zaytseva K, Zhou J, Duchesne S, Khan AR, Hill S, Evans AC. Poline JB, et al. Among authors: bujold d. Sci Data. 2023 Apr 6;10(1):189. doi: 10.1038/s41597-023-01946-1. Sci Data. 2023. PMID: 37024500 Free PMC article.
RNAget: an API to securely retrieve RNA quantifications.
Upchurch S, Palumbo E, Adams J, Bujold D, Bourque G, Nedzel J, Graham K, Kagda MS, Assis P, Hitz B, Righi E, Guigó R, Wold BJ; GA4GH RNA-Seq Task Team. Upchurch S, et al. Among authors: bujold d. Bioinformatics. 2023 Apr 3;39(4):btad126. doi: 10.1093/bioinformatics/btad126. Bioinformatics. 2023. PMID: 36897015 Free PMC article.
GA4GH: International policies and standards for data sharing across genomic research and healthcare.
Rehm HL, Page AJH, Smith L, Adams JB, Alterovitz G, Babb LJ, Barkley MP, Baudis M, Beauvais MJS, Beck T, Beckmann JS, Beltran S, Bernick D, Bernier A, Bonfield JK, Boughtwood TF, Bourque G, Bowers SR, Brookes AJ, Brudno M, Brush MH, Bujold D, Burdett T, Buske OJ, Cabili MN, Cameron DL, Carroll RJ, Casas-Silva E, Chakravarty D, Chaudhari BP, Chen SH, Cherry JM, Chung J, Cline M, Clissold HL, Cook-Deegan RM, Courtot M, Cunningham F, Cupak M, Davies RM, Denisko D, Doerr MJ, Dolman LI, Dove ES, Dursi LJ, Dyke SOM, Eddy JA, Eilbeck K, Ellrott KP, Fairley S, Fakhro KA, Firth HV, Fitzsimons MS, Fiume M, Flicek P, Fore IM, Freeberg MA, Freimuth RR, Fromont LA, Fuerth J, Gaff CL, Gan W, Ghanaim EM, Glazer D, Green RC, Griffith M, Griffith OL, Grossman RL, Groza T, Auvil JMG, Guigó R, Gupta D, Haendel MA, Hamosh A, Hansen DP, Hart RK, Hartley DM, Haussler D, Hendricks-Sturrup RM, Ho CWL, Hobb AE, Hoffman MM, Hofmann OM, Holub P, Hsu JS, Hubaux JP, Hunt SE, Husami A, Jacobsen JO, Jamuar SS, Janes EL, Jeanson F, Jené A, Johns AL, Joly Y, Jones SJM, Kanitz A, Kato K, Keane TM, Kekesi-Lafrance K, Kelleher J, Kerry G, Khor SS, Knoppers BM, Konopko MA, Kosaki K, Kuba M, Lawson J, Leinonen … See abstract for full author list ➔ Rehm HL, et al. Among authors: bujold d. Cell Genom. 2021 Nov 10;1(2):100029. doi: 10.1016/j.xgen.2021.100029. Cell Genom. 2021. PMID: 35072136 Free PMC article.
CanDIG: Federated network across Canada for multi-omic and health data discovery and analysis.
Dursi LJ, Bozoky Z, de Borja R, Li H, Bujold D, Lipski A, Rashid SF, Sethi A, Memon N, Naidoo D, Coral-Sasso F, Wong M, Quirion PO, Lu Z, Agarwal S, Pavlov Y, Ponomarev A, Husic M, Pace K, Palmer S, Grover SA, Hakgor S, Siu LL, Malkin D, Virtanen C, Pugh TJ, Jacques PÉ, Joly Y, Jones SJM, Bourque G, Brudno M. Dursi LJ, et al. Among authors: bujold d. Cell Genom. 2021 Nov 10;1(2):100033. doi: 10.1016/j.xgen.2021.100033. eCollection 2021 Nov 10. Cell Genom. 2021. PMID: 36778585 Free PMC article.
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