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The 2021 WHO catalogue of Mycobacterium tuberculosis complex mutations associated with drug resistance: A genotypic analysis.
Walker TM, Miotto P, Köser CU, Fowler PW, Knaggs J, Iqbal Z, Hunt M, Chindelevitch L, Farhat M, Cirillo DM, Comas I, Posey J, Omar SV, Peto TE, Suresh A, Uplekar S, Laurent S, Colman RE, Nathanson CM, Zignol M, Walker AS; CRyPTIC Consortium; Seq&Treat Consortium; Crook DW, Ismail N, Rodwell TC. Walker TM, et al. Among authors: knaggs j. Lancet Microbe. 2022 Apr;3(4):e265-e273. doi: 10.1016/S2666-5247(21)00301-3. Lancet Microbe. 2022. PMID: 35373160 Free PMC article.
A crowd of BashTheBug volunteers reproducibly and accurately measure the minimum inhibitory concentrations of 13 antitubercular drugs from photographs of 96-well broth microdilution plates.
Fowler PW, Wright C, Spiers H, Zhu T, Baeten EML, Hoosdally SW, Gibertoni Cruz AL, Roohi A, Kouchaki S, Walker TM, Peto TEA, Miller G, Lintott C, Clifton D, Crook DW, Walker AS; Zooniverse Volunteer Community; CRyPTIC Consortium. Fowler PW, et al. Elife. 2022 May 19;11:e75046. doi: 10.7554/eLife.75046. Elife. 2022. PMID: 35588296 Free PMC article.
High fluoroquinolone resistance proportions among multidrug-resistant tuberculosis driven by dominant L2 Mycobacterium tuberculosis clones in the Mumbai Metropolitan Region.
Dreyer V, Mandal A, Dev P, Merker M, Barilar I, Utpatel C, Nilgiriwala K, Rodrigues C, Crook DW; CRyPTIC Consortium; Rasigade JP, Wirth T, Mistry N, Niemann S. Dreyer V, et al. Genome Med. 2022 Aug 22;14(1):95. doi: 10.1186/s13073-022-01076-0. Genome Med. 2022. PMID: 35989319 Free PMC article.
Bedaquiline and clofazimine resistance in Mycobacterium tuberculosis: an in-vitro and in-silico data analysis.
Sonnenkalb L, Carter JJ, Spitaleri A, Iqbal Z, Hunt M, Malone KM, Utpatel C, Cirillo DM, Rodrigues C, Nilgiriwala KS, Fowler PW, Merker M, Niemann S; Comprehensive Resistance Prediction for Tuberculosis: an International Consortium. Sonnenkalb L, et al. Lancet Microbe. 2023 May;4(5):e358-e368. doi: 10.1016/S2666-5247(23)00002-2. Epub 2023 Mar 29. Lancet Microbe. 2023. PMID: 37003285 Free PMC article.
Performance comparison of next generation sequencing analysis pipelines for HIV-1 drug resistance testing.
Lee ER, Parkin N, Jennings C, Brumme CJ, Enns E, Casadellà M, Howison M, Coetzer M, Avila-Rios S, Capina R, Marinier E, Van Domselaar G, Noguera-Julian M, Kirkby D, Knaggs J, Harrigan R, Quiñones-Mateu M, Paredes R, Kantor R, Sandstrom P, Ji H. Lee ER, et al. Among authors: knaggs j. Sci Rep. 2020 Jan 31;10(1):1634. doi: 10.1038/s41598-020-58544-z. Sci Rep. 2020. PMID: 32005884 Free PMC article.
Formalin fixation increases deamination mutation signature but should not lead to false positive mutations in clinical practice.
Prentice LM, Miller RR, Knaggs J, Mazloomian A, Aguirre Hernandez R, Franchini P, Parsa K, Tessier-Cloutier B, Lapuk A, Huntsman D, Schaeffer DF, Sheffield BS. Prentice LM, et al. Among authors: knaggs j. PLoS One. 2018 Apr 26;13(4):e0196434. doi: 10.1371/journal.pone.0196434. eCollection 2018. PLoS One. 2018. PMID: 29698444 Free PMC article.
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