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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: alcock bp. 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.
Exploring the mobilome and resistome of Enterococcus faecium in a One Health context across two continents.
Sanderson H, Gray KL, Manuele A, Maguire F, Khan A, Liu C, Navanekere Rudrappa C, Nash JHE, Robertson J, Bessonov K, Oloni M, Alcock BP, Raphenya AR, McAllister TA, Peacock SJ, Raven KE, Gouliouris T, McArthur AG, Brinkman FSL, Fink RC, Zaheer R, Beiko RG. Sanderson H, et al. Among authors: alcock bp. Microb Genom. 2022 Sep;8(9):mgen000880. doi: 10.1099/mgen.0.000880. Microb Genom. 2022. PMID: 36129737 Free PMC article.
CARD 2020: antibiotic resistome surveillance with the comprehensive antibiotic resistance database.
Alcock BP, Raphenya AR, Lau TTY, Tsang KK, Bouchard M, Edalatmand A, Huynh W, Nguyen AV, Cheng AA, Liu S, Min SY, Miroshnichenko A, Tran HK, Werfalli RE, Nasir JA, Oloni M, Speicher DJ, Florescu A, Singh B, Faltyn M, Hernandez-Koutoucheva A, Sharma AN, Bordeleau E, Pawlowski AC, Zubyk HL, Dooley D, Griffiths E, Maguire F, Winsor GL, Beiko RG, Brinkman FSL, Hsiao WWL, Domselaar GV, McArthur AG. Alcock BP, et al. Nucleic Acids Res. 2020 Jan 8;48(D1):D517-D525. doi: 10.1093/nar/gkz935. Nucleic Acids Res. 2020. PMID: 31665441 Free PMC article.
CARD 2023: expanded curation, support for machine learning, and resistome prediction at the Comprehensive Antibiotic Resistance Database.
Alcock BP, Huynh W, Chalil R, Smith KW, Raphenya AR, Wlodarski MA, Edalatmand A, Petkau A, Syed SA, Tsang KK, Baker SJC, Dave M, McCarthy MC, Mukiri KM, Nasir JA, Golbon B, Imtiaz H, Jiang X, Kaur K, Kwong M, Liang ZC, Niu KC, Shan P, Yang JYJ, Gray KL, Hoad GR, Jia B, Bhando T, Carfrae LA, Farha MA, French S, Gordzevich R, Rachwalski K, Tu MM, Bordeleau E, Dooley D, Griffiths E, Zubyk HL, Brown ED, Maguire F, Beiko RG, Hsiao WWL, Brinkman FSL, Van Domselaar G, McArthur AG. Alcock BP, et al. Nucleic Acids Res. 2023 Jan 6;51(D1):D690-D699. doi: 10.1093/nar/gkac920. Nucleic Acids Res. 2023. PMID: 36263822 Free PMC article.
Future-proofing and maximizing the utility of metadata: The PHA4GE SARS-CoV-2 contextual data specification package.
Griffiths EJ, Timme RE, Mendes CI, Page AJ, Alikhan NF, Fornika D, Maguire F, Campos J, Park D, Olawoye IB, Oluniyi PE, Anderson D, Christoffels A, da Silva AG, Cameron R, Dooley D, Katz LS, Black A, Karsch-Mizrachi I, Barrett T, Johnston A, Connor TR, Nicholls SM, Witney AA, Tyson GH, Tausch SH, Raphenya AR, Alcock B, Aanensen DM, Hodcroft E, Hsiao WWL, Vasconcelos ATR, MacCannell DR. Griffiths EJ, et al. Gigascience. 2022 Feb 16;11:giac003. doi: 10.1093/gigascience/giac003. Gigascience. 2022. PMID: 35169842 Free PMC article.
Simultaneous detection of pathogens and antimicrobial resistance genes with the open source, cloud-based, CZ ID pipeline.
Lu D, Kalantar KL, Chu VT, Glascock AL, Guerrero ES, Bernick N, Butcher X, Ewing K, Fahsbender E, Holmes O, Hoops E, Jones AE, Lim R, McCanny S, Reynoso L, Rosario K, Tang J, Valenzuela O, Mourani PM, Pickering AJ, Raphenya AR, Alcock BP, McArthur AG, Langelier CR. Lu D, et al. Among authors: alcock bp. bioRxiv [Preprint]. 2024 Apr 18:2024.04.12.589250. doi: 10.1101/2024.04.12.589250. bioRxiv. 2024. PMID: 38645206 Free PMC article. Preprint.
CARD 2017: expansion and model-centric curation of the comprehensive antibiotic resistance database.
Jia B, Raphenya AR, Alcock B, Waglechner N, Guo P, Tsang KK, Lago BA, Dave BM, Pereira S, Sharma AN, Doshi S, Courtot M, Lo R, Williams LE, Frye JG, Elsayegh T, Sardar D, Westman EL, Pawlowski AC, Johnson TA, Brinkman FS, Wright GD, McArthur AG. Jia B, et al. Nucleic Acids Res. 2017 Jan 4;45(D1):D566-D573. doi: 10.1093/nar/gkw1004. Epub 2016 Oct 26. Nucleic Acids Res. 2017. PMID: 27789705 Free PMC article.
13 results