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Demographics of sources of HIV-1 transmission in Zambia: a molecular epidemiology analysis in the HPTN 071 PopART study.
Hall M, Golubchik T, Bonsall D, Abeler-Dörner L, Limbada M, Kosloff B, Schaap A, de Cesare M, MacIntyre-Cockett G, Otecko N, Probert W, Ratmann O, Bulas Cruz A, Piwowar-Manning E, Burns DN, Cohen MS, Donnell DJ, Eshleman SH, Simwinga M, Fidler S, Hayes R, Ayles H, Fraser C; HPTN 071 (PopART) Phylogenetics protocol team; PANGEA consortium. Hall M, et al. Among authors: golubchik t. Lancet Microbe. 2024 Jan;5(1):e62-e71. doi: 10.1016/S2666-5247(23)00220-3. Epub 2023 Dec 8. Lancet Microbe. 2024. PMID: 38081203 Free PMC article. Clinical Trial.
Prediction of Susceptibility to First-Line Tuberculosis Drugs by DNA Sequencing.
CRyPTIC Consortium and the 100,000 Genomes Project; Allix-Béguec C, Arandjelovic I, Bi L, Beckert P, Bonnet M, Bradley P, Cabibbe AM, Cancino-Muñoz I, Caulfield MJ, Chaiprasert A, Cirillo DM, Clifton DA, Comas I, Crook DW, De Filippo MR, de Neeling H, Diel R, Drobniewski FA, Faksri K, Farhat MR, Fleming J, Fowler P, Fowler TA, Gao Q, Gardy J, Gascoyne-Binzi D, Gibertoni-Cruz AL, Gil-Brusola A, Golubchik T, Gonzalo X, Grandjean L, He G, Guthrie JL, Hoosdally S, Hunt M, Iqbal Z, Ismail N, Johnston J, Khanzada FM, Khor CC, Kohl TA, Kong C, Lipworth S, Liu Q, Maphalala G, Martinez E, Mathys V, Merker M, Miotto P, Mistry N, Moore DAJ, Murray M, Niemann S, Omar SV, Ong RT, Peto TEA, Posey JE, Prammananan T, Pym A, Rodrigues C, Rodrigues M, Rodwell T, Rossolini GM, Sánchez Padilla E, Schito M, Shen X, Shendure J, Sintchenko V, Sloutsky A, Smith EG, Snyder M, Soetaert K, Starks AM, Supply P, Suriyapol P, Tahseen S, Tang P, Teo YY, Thuong TNT, Thwaites G, Tortoli E, van Soolingen D, Walker AS, Walker TM, Wilcox M, Wilson DJ, Wyllie D, Yang Y, Zhang H, Zhao Y, Zhu B. CRyPTIC Consortium and the 100,000 Genomes Project, et al. Among authors: golubchik t. N Engl J Med. 2018 Oct 11;379(15):1403-1415. doi: 10.1056/NEJMoa1800474. Epub 2018 Sep 26. N Engl J Med. 2018. PMID: 30280646 Free PMC article.
Corrigendum: Rapid antibiotic-resistance predictions from genome sequence data for Staphylococcus aureus and Mycobacterium tuberculosis.
Bradley P, Gordon NC, Walker TM, Dunn L, Heys S, Huang B, Earle S, Pankhurst LJ, Anson L, de Cesare M, Piazza P, Votintseva AA, Golubchik T, Wilson DJ, Wyllie DH, Diel R, Niemann S, Feuerriegel S, Kohl TA, Ismail N, Omar SV, Smith EG, Buck D, McVean G, Walker AS, Peto TE, Crook DW, Iqbal Z. Bradley P, et al. Among authors: golubchik t. Nat Commun. 2016 Apr 20;7:11465. doi: 10.1038/ncomms11465. Nat Commun. 2016. PMID: 27095245 Free PMC article. No abstract available.
PHYLOSCANNER: Inferring Transmission from Within- and Between-Host Pathogen Genetic Diversity.
Wymant C, Hall M, Ratmann O, Bonsall D, Golubchik T, de Cesare M, Gall A, Cornelissen M, Fraser C; STOP-HCV Consortium, The Maela Pneumococcal Collaboration, and The BEEHIVE Collaboration. Wymant C, et al. Among authors: golubchik t. Mol Biol Evol. 2018 Mar 1;35(3):719-733. doi: 10.1093/molbev/msx304. Mol Biol Evol. 2018. PMID: 29186559 Free PMC article.
Inferring HIV-1 transmission networks and sources of epidemic spread in Africa with deep-sequence phylogenetic analysis.
Ratmann O, Grabowski MK, Hall M, Golubchik T, Wymant C, Abeler-Dörner L, Bonsall D, Hoppe A, Brown AL, de Oliveira T, Gall A, Kellam P, Pillay D, Kagaayi J, Kigozi G, Quinn TC, Wawer MJ, Laeyendecker O, Serwadda D, Gray RH, Fraser C; PANGEA Consortium and Rakai Health Sciences Program. Ratmann O, et al. Among authors: golubchik t. Nat Commun. 2019 Mar 29;10(1):1411. doi: 10.1038/s41467-019-09139-4. Nat Commun. 2019. PMID: 30926780 Free PMC article.
Illumina and Nanopore methods for whole genome sequencing of hepatitis B virus (HBV).
McNaughton AL, Roberts HE, Bonsall D, de Cesare M, Mokaya J, Lumley SF, Golubchik T, Piazza P, Martin JB, de Lara C, Brown A, Ansari MA, Bowden R, Barnes E, Matthews PC. McNaughton AL, et al. Among authors: golubchik t. Sci Rep. 2019 May 8;9(1):7081. doi: 10.1038/s41598-019-43524-9. Sci Rep. 2019. PMID: 31068626 Free PMC article.
Recombination Analysis of Near Full-Length HIV-1 Sequences and the Identification of a Potential New Circulating Recombinant Form from Rakai, Uganda.
Capoferri AA, Lamers SL, Grabowski MK, Rose R, Wawer MJ, Serwadda D, Gray RH, Quinn TC, Kigozi G, Kagaayi J, Laeyendecker O; Rakai Health Sciences Program and the PANGEA Consortium. Capoferri AA, et al. AIDS Res Hum Retroviruses. 2020 Jun;36(6):467-474. doi: 10.1089/AID.2019.0150. Epub 2020 Mar 2. AIDS Res Hum Retroviruses. 2020. PMID: 31914792 Free PMC article.
High prevalence of integrase mutation L74I in West African HIV-1 subtypes prior to integrase inhibitor treatment.
El Bouzidi K, Kemp SA, Datir RP, Murtala-Ibrahim F, Aliyu A, Kwaghe V, Frampton D, Roy S, Breuer J, Sabin CA, Ogbanufe O, Charurat ME, Bonsall D, Golubchik T, Fraser C, Dakum P, Ndembi N, Gupta RK. El Bouzidi K, et al. Among authors: golubchik t. J Antimicrob Chemother. 2020 Jun 1;75(6):1575-1579. doi: 10.1093/jac/dkaa033. J Antimicrob Chemother. 2020. PMID: 32105319 Free PMC article.
107 results