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TheiaEuk: a species-agnostic bioinformatics workflow for fungal genomic characterization.
Ambrosio FJ 3rd, Scribner MR, Wright SM, Otieno JR, Doughty EL, Gorzalski A, Siao DD, Killian S, Hua C, Schneider E, Tran M, Varghese V, Libuit KG, Pandori M, Sevinsky JR, Hess D. Ambrosio FJ 3rd, et al. Among authors: sevinsky jr. Front Public Health. 2023 Aug 1;11:1198213. doi: 10.3389/fpubh.2023.1198213. eCollection 2023. Front Public Health. 2023. PMID: 37593727 Free PMC article.
Genomic surveillance of Nevada patients revealed prevalence of unique SARS-CoV-2 variants bearing mutations in the RdRp gene.
Hartley PD, Tillett RL, AuCoin DP, Sevinsky JR, Xu Y, Gorzalski A, Pandori M, Buttery E, Hansen H, Picker MA, Rossetto CC, Verma SC. Hartley PD, et al. Among authors: sevinsky jr. medRxiv [Preprint]. 2020 Oct 2:2020.08.21.20178863. doi: 10.1101/2020.08.21.20178863. medRxiv. 2020. PMID: 32869037 Free PMC article. Updated. Preprint.
Genomic evidence for reinfection with SARS-CoV-2: a case study.
Tillett RL, Sevinsky JR, Hartley PD, Kerwin H, Crawford N, Gorzalski A, Laverdure C, Verma SC, Rossetto CC, Jackson D, Farrell MJ, Van Hooser S, Pandori M. Tillett RL, et al. Among authors: sevinsky jr. Lancet Infect Dis. 2021 Jan;21(1):52-58. doi: 10.1016/S1473-3099(20)30764-7. Epub 2020 Oct 12. Lancet Infect Dis. 2021. PMID: 33058797 Free PMC article.
Rapid Lineage Assignment of Severe Acute Respiratory Syndrome Coronavirus 2 Cases through Automated Library Preparation, Sequencing, and Bioinformatic Analysis.
Gorzalski AJ, Kerwin H, Verma S, Hess DC, Sevinsky J, Libuit K, Vlasova-St Louis I, Siao D, Siao L, Buñuel D, Van Hooser S, Pandori MW. Gorzalski AJ, et al. J Mol Diagn. 2023 Apr;25(4):191-196. doi: 10.1016/j.jmoldx.2023.01.005. Epub 2023 Feb 7. J Mol Diagn. 2023. PMID: 36754279 Free PMC article.
GAMBIT (Genomic Approximation Method for Bacterial Identification and Tracking): A methodology to rapidly leverage whole genome sequencing of bacterial isolates for clinical identification.
Lumpe J, Gumbleton L, Gorzalski A, Libuit K, Varghese V, Lloyd T, Tadros F, Arsimendi T, Wagner E, Stephens C, Sevinsky J, Hess D, Pandori M. Lumpe J, et al. PLoS One. 2023 Feb 16;18(2):e0277575. doi: 10.1371/journal.pone.0277575. eCollection 2023. PLoS One. 2023. PMID: 36795668 Free PMC article.
Pathogen genomics in public health laboratories: successes, challenges, and lessons learned from California's SARS-CoV-2 Whole-Genome Sequencing Initiative, California COVIDNet.
Smith EA, Libuit KG, Kapsak CJ, Scribner MR, Wright SM, Bell J, Morales C, Crumpler M, Messenger S, Hacker JK, Ledin K, Glaser C, Jacobson K, Sevinsky JR, Wadford DA. Smith EA, et al. Among authors: sevinsky jr. Microb Genom. 2023 Jun;9(6):mgen001027. doi: 10.1099/mgen.0.001027. Microb Genom. 2023. PMID: 37267020 Free PMC article.
Development of an amplicon-based sequencing approach in response to the global emergence of mpox.
Chen NFG, Chaguza C, Gagne L, Doucette M, Smole S, Buzby E, Hall J, Ash S, Harrington R, Cofsky S, Clancy S, Kapsak CJ, Sevinsky J, Libuit K, Park DJ, Hemarajata P, Garrigues JM, Green NM, Sierra-Patev S, Carpenter-Azevedo K, Huard RC, Pearson C, Incekara K, Nishimura C, Huang JP, Gagnon E, Reever E, Razeq J, Muyombwe A, Borges V, Ferreira R, Sobral D, Duarte S, Santos D, Vieira L, Gomes JP, Aquino C, Savino IM, Felton K, Bajwa M, Hayward N, Miller H, Naumann A, Allman R, Greer N, Fall A, Mostafa HH, McHugh MP, Maloney DM, Dewar R, Kenicer J, Parker A, Mathers K, Wild J, Cotton S, Templeton KE, Churchwell G, Lee PA, Pedrosa M, McGruder B, Schmedes S, Plumb MR, Wang X, Barcellos RB, Godinho FMS, Salvato RS, Ceniseros A, Breban MI, Grubaugh ND, Gallagher GR, Vogels CBF. Chen NFG, et al. PLoS Biol. 2023 Jun 13;21(6):e3002151. doi: 10.1371/journal.pbio.3002151. eCollection 2023 Jun. PLoS Biol. 2023. PMID: 37310918 Free PMC article.
Accelerating bioinformatics implementation in public health.
Libuit KG, Doughty EL, Otieno JR, Ambrosio F, Kapsak CJ, Smith EA, Wright SM, Scribner MR, Petit Iii RA, Mendes CI, Huergo M, Legacki G, Loreth C, Park DJ, Sevinsky JR. Libuit KG, et al. Among authors: sevinsky jr. Microb Genom. 2023 Jul;9(7):mgen001051. doi: 10.1099/mgen.0.001051. Microb Genom. 2023. PMID: 37428142 Free PMC article.
26 results