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SARS-CoV-2 Illumina GeNome Assembly Line (SIGNAL), a Snakemate workflow for rapid and bulk analysis of Illumina sequencing of SARS-CoV-2 genomes.
Nasir JA, Maguire F, Smith KM, Panousis EM, Baker SJC, Aftanas P, Raphenya AR, Alcock BP, Maan H, Knox NC, Banerjee A, Mossman K, Wang B, Simpson JT, Kozak RA, Mubareka S, McArthur AG. Nasir JA, et al. Among authors: simpson jt. NAR Genom Bioinform. 2024 Dec 18;6(4):lqae176. doi: 10.1093/nargab/lqae176. eCollection 2024 Dec. NAR Genom Bioinform. 2024. PMID: 39703420 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: simpson jt. 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.
An updated reference genome sequence and annotation reveals gene losses and gains underlying naked mole-rat biology.
Sokolowski DJ, Miclăuş M, Nater A, Faykoo-Martinez M, Hoekzema K, Zuzarte P, Monis S, Alvi SA, Erdmann J, Erdmann AL, Kumaragurubaran R, Bayerl J, Yoo D, Karimpour N, Ungerleider K, Hou H, Fergal M, Hourlier T, Clarke ZA, Lischer HE, Leordean DV, Jiang Y, Pugh TJ, Smith ESJ, Haggerty L, Laird DJ, Lilue J, Holmes MM, Eichler EE, Bruggmann R, Simpson JT, Balmus G, Wilson MD. Sokolowski DJ, et al. Among authors: simpson jt. bioRxiv [Preprint]. 2024 Nov 28:2024.11.26.625329. doi: 10.1101/2024.11.26.625329. bioRxiv. 2024. PMID: 39651266 Free PMC article. Preprint.
Inhibiting EZH2 targets atypical teratoid rhabdoid tumor by triggering viral mimicry via both RNA and DNA sensing pathways.
Feng S, Marhon SA, Sokolowski DJ, D'Costa A, Soares F, Mehdipour P, Ishak C, Loo Yau H, Ettayebi I, Patel PS, Chen R, Liu J, Zuzarte PC, Ho KC, Ho B, Ning S, Huang A, Arrowsmith CH, Wilson MD, Simpson JT, De Carvalho DD. Feng S, et al. Among authors: simpson jt. Nat Commun. 2024 Oct 29;15(1):9321. doi: 10.1038/s41467-024-53515-8. Nat Commun. 2024. PMID: 39472584 Free PMC article.
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: simpson jt. Microb Genom. 2024 Oct;10(10):001293. doi: 10.1099/mgen.0.001293. Microb Genom. 2024. PMID: 39401061 Free PMC article.
Stop the Bleed-Wait for the Ambulance or Get in the Car and Drive? A Post Hoc Analysis of an EAST Multicenter Trial.
Simpson JT, Nordham KD, Tatum D, Haut ER, Ali A, Maher Z, Goldberg AJ, Tatebe LC, Chang G, Taghavi S, Raza S, Toraih E, Mendiola Plá M, Ninokawa S, Anderson C, Maluso P, Keating J, Burruss S, Reeves M, Craugh LE, Shatz DV, Bhupathi A, Spalding MC, LaRiccia A, Bird E, Noorbakhsh MR, Babowice J, Nelson MC, Jacobson LE, Williams J, Vella M, Dellonte K, Hayward TZ 3rd, Holler E, Lieser MJ, Berne JD, Mederos DR, Askari R, Okafor B, Etchill E, Fang R, Roche SL, Whittenburg L, Bernard AC, Haan JM MD, Lightwine KL, Norwood SH, Murry J, Gamber MA, Carrick MM, Bugaev N, Tatar A. Simpson JT, et al. Am Surg. 2024 Sep 30:31348241265135. doi: 10.1177/00031348241265135. Online ahead of print. Am Surg. 2024. PMID: 39349054
151 results