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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: aftanas p. 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.
Genomic and transcriptomic characterization of delta SARS-CoV-2 infection in free-ranging white-tailed deer (Odocoileus virginianus).
Kotwa JD, Lobb B, Massé A, Gagnier M, Aftanas P, Banerjee A, Banete A, Blais-Savoie J, Bowman J, Buchanan T, Chee HY, Kruczkiewicz P, Nirmalarajah K, Soos C, Vernygora O, Yip L, Lindsay LR, McGeer AJ, Maguire F, Lung O, Doxey AC, Pickering B, Mubareka S. Kotwa JD, et al. Among authors: aftanas p. iScience. 2023 Oct 24;26(11):108319. doi: 10.1016/j.isci.2023.108319. eCollection 2023 Nov 17. iScience. 2023. PMID: 38026171 Free PMC article.
Publisher Correction: Divergent SARS-CoV-2 variant emerges in white-tailed deer with deer-to-human transmission.
Pickering B, Lung O, Maguire F, Kruczkiewicz P, Kotwa JD, Buchanan T, Gagnier M, Guthrie JL, Jardine CM, Marchand-Austin A, Massé A, McClinchey H, Nirmalarajah K, Aftanas P, Blais-Savoie J, Chee HY, Chien E, Yim W, Banete A, Griffin BD, Yip L, Goolia M, Suderman M, Pinette M, Smith G, Sullivan D, Rudar J, Vernygora O, Adey E, Nebroski M, Goyette G, Finzi A, Laroche G, Ariana A, Vahkal B, Côté M, McGeer AJ, Nituch L, Mubareka S, Bowman J. Pickering B, et al. Among authors: aftanas p. Nat Microbiol. 2023 Jan;8(1):188. doi: 10.1038/s41564-022-01298-3. Nat Microbiol. 2023. PMID: 36509933 Free PMC article. No abstract available.
Divergent SARS-CoV-2 variant emerges in white-tailed deer with deer-to-human transmission.
Pickering B, Lung O, Maguire F, Kruczkiewicz P, Kotwa JD, Buchanan T, Gagnier M, Guthrie JL, Jardine CM, Marchand-Austin A, Massé A, McClinchey H, Nirmalarajah K, Aftanas P, Blais-Savoie J, Chee HY, Chien E, Yim W, Banete A, Griffin BD, Yip L, Goolia M, Suderman M, Pinette M, Smith G, Sullivan D, Rudar J, Vernygora O, Adey E, Nebroski M, Goyette G, Finzi A, Laroche G, Ariana A, Vahkal B, Côté M, McGeer AJ, Nituch L, Mubareka S, Bowman J. Pickering B, et al. Among authors: aftanas p. Nat Microbiol. 2022 Dec;7(12):2011-2024. doi: 10.1038/s41564-022-01268-9. Epub 2022 Nov 10. Nat Microbiol. 2022. PMID: 36357713 Free PMC article.
Immunogenicity of convalescent and vaccinated sera against clinical isolates of ancestral SARS-CoV-2, Beta, Delta, and Omicron variants.
Banerjee A, Lew J, Kroeker A, Baid K, Aftanas P, Nirmalarajah K, Maguire F, Kozak R, McDonald R, Lang A, Gerdts V, Straus SE, Gilbert L, Li AX, Mozafarihashjin M, Walmsley S, Gingras AC, Wrana JL, Mazzulli T, Colwill K, McGeer AJ, Mubareka S, Falzarano D. Banerjee A, et al. Among authors: aftanas p. Med. 2022 Jun 10;3(6):422-432.e3. doi: 10.1016/j.medj.2022.04.002. Epub 2022 Apr 14. Med. 2022. PMID: 35437520 Free PMC article.
Surface and Air Contamination With Severe Acute Respiratory Syndrome Coronavirus 2 From Hospitalized Coronavirus Disease 2019 Patients in Toronto, Canada, March-May 2020.
Kotwa JD, Jamal AJ, Mbareche H, Yip L, Aftanas P, Barati S, Bell NG, Bryce E, Coomes E, Crowl G, Duchaine C, Faheem A, Farooqi L, Hiebert R, Katz K, Khan S, Kozak R, Li AX, Mistry HP, Mozafarihashjin M, Nasir JA, Nirmalarajah K, Panousis EM, Paterson A, Plenderleith S, Powis J, Prost K, Schryer R, Taylor M, Veillette M, Wong T, Zoe Zhong X, McArthur AG, McGeer AJ, Mubareka S. Kotwa JD, et al. Among authors: aftanas p. J Infect Dis. 2022 Mar 2;225(5):768-776. doi: 10.1093/infdis/jiab578. J Infect Dis. 2022. PMID: 34850051 Free PMC article.
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