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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: joly y. 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.
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: joly y. Microb Genom. 2024 Oct;10(10):001293. doi: 10.1099/mgen.0.001293. Microb Genom. 2024. PMID: 39401061 Free PMC article.
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: joly y. 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.
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: joly y. 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.
The landscape of viral associations in human cancers.
Zapatka M, Borozan I, Brewer DS, Iskar M, Grundhoff A, Alawi M, Desai N, Sültmann H, Moch H; PCAWG Pathogens; Cooper CS, Eils R, Ferretti V, Lichter P; PCAWG Consortium. Zapatka M, et al. Nat Genet. 2020 Mar;52(3):320-330. doi: 10.1038/s41588-019-0558-9. Epub 2020 Feb 5. Nat Genet. 2020. PMID: 32025001 Free PMC article.
Genomic basis for RNA alterations in cancer.
PCAWG Transcriptome Core Group; Calabrese C, Davidson NR, Demircioğlu D, Fonseca NA, He Y, Kahles A, Lehmann KV, Liu F, Shiraishi Y, Soulette CM, Urban L, Greger L, Li S, Liu D, Perry MD, Xiang Q, Zhang F, Zhang J, Bailey P, Erkek S, Hoadley KA, Hou Y, Huska MR, Kilpinen H, Korbel JO, Marin MG, Markowski J, Nandi T, Pan-Hammarström Q, Pedamallu CS, Siebert R, Stark SG, Su H, Tan P, Waszak SM, Yung C, Zhu S, Awadalla P, Creighton CJ, Meyerson M, Ouellette BFF, Wu K, Yang H; PCAWG Transcriptome Working Group; Brazma A, Brooks AN, Göke J, Rätsch G, Schwarz RF, Stegle O, Zhang Z; PCAWG Consortium. PCAWG Transcriptome Core Group, et al. Nature. 2020 Feb;578(7793):129-136. doi: 10.1038/s41586-020-1970-0. Epub 2020 Feb 5. Nature. 2020. PMID: 32025019 Free PMC article.
Genomic footprints of activated telomere maintenance mechanisms in cancer.
Sieverling L, Hong C, Koser SD, Ginsbach P, Kleinheinz K, Hutter B, Braun DM, Cortés-Ciriano I, Xi R, Kabbe R, Park PJ, Eils R, Schlesner M; PCAWG-Structural Variation Working Group; Brors B, Rippe K, Jones DTW, Feuerbach L; PCAWG Consortium. Sieverling L, et al. Nat Commun. 2020 Feb 5;11(1):733. doi: 10.1038/s41467-019-13824-9. Nat Commun. 2020. PMID: 32024817 Free PMC article.
A deep learning system accurately classifies primary and metastatic cancers using passenger mutation patterns.
Jiao W, Atwal G, Polak P, Karlic R, Cuppen E; PCAWG Tumor Subtypes and Clinical Translation Working Group; Danyi A, de Ridder J, van Herpen C, Lolkema MP, Steeghs N, Getz G, Morris QD, Stein LD; PCAWG Consortium. Jiao W, et al. Nat Commun. 2020 Feb 5;11(1):728. doi: 10.1038/s41467-019-13825-8. Nat Commun. 2020. PMID: 32024849 Free PMC article.
252 results