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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. 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.
Phylogenetic Tools for Generalized HIV-1 Epidemics: Findings from the PANGEA-HIV Methods Comparison.
Ratmann O, Hodcroft EB, Pickles M, Cori A, Hall M, Lycett S, Colijn C, Dearlove B, Didelot X, Frost S, Hossain AS, Joy JB, Kendall M, Kühnert D, Leventhal GE, Liang R, Plazzotta G, Poon AF, Rasmussen DA, Stadler T, Volz E, Weis C, Leigh Brown AJ, Fraser C; PANGEA-HIV Consortium. Ratmann O, et al. Among authors: hall m. Mol Biol Evol. 2017 Jan;34(1):185-203. doi: 10.1093/molbev/msw217. Epub 2016 Oct 7. Mol Biol Evol. 2017. PMID: 28053012 Free PMC article.
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: hall m. Mol Biol Evol. 2018 Mar 1;35(3):719-733. doi: 10.1093/molbev/msx304. Mol Biol Evol. 2018. PMID: 29186559 Free PMC article.
Easy and accurate reconstruction of whole HIV genomes from short-read sequence data with shiver.
Wymant C, Blanquart F, Golubchik T, Gall A, Bakker M, Bezemer D, Croucher NJ, Hall M, Hillebregt M, Ong SH, Ratmann O, Albert J, Bannert N, Fellay J, Fransen K, Gourlay A, Grabowski MK, Gunsenheimer-Bartmeyer B, Günthard HF, Kivelä P, Kouyos R, Laeyendecker O, Liitsola K, Meyer L, Porter K, Ristola M, van Sighem A, Berkhout B, Cornelissen M, Kellam P, Reiss P, Fraser C; BEEHIVE Collaboration. Wymant C, et al. Among authors: hall m. Virus Evol. 2018 May 18;4(1):vey007. doi: 10.1093/ve/vey007. eCollection 2018 Jan. Virus Evol. 2018. PMID: 29876136 Free PMC article.
Phylogenetic Methods Inconsistently Predict the Direction of HIV Transmission Among Heterosexual Pairs in the HPTN 052 Cohort.
Rose R, Hall M, Redd AD, Lamers S, Barbier AE, Porcella SF, Hudelson SE, Piwowar-Manning E, McCauley M, Gamble T, Wilson EA, Kumwenda J, Hosseinipour MC, Hakim JG, Kumarasamy N, Chariyalertsak S, Pilotto JH, Grinsztejn B, Mills LA, Makhema J, Santos BR, Chen YQ, Quinn TC, Fraser C, Cohen MS, Eshleman SH, Laeyendecker O. Rose R, et al. Among authors: hall m. J Infect Dis. 2019 Sep 26;220(9):1406-1413. doi: 10.1093/infdis/jiy734. J Infect Dis. 2019. PMID: 30590741 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: hall m. Nat Commun. 2019 Mar 29;10(1):1411. doi: 10.1038/s41467-019-09139-4. Nat Commun. 2019. PMID: 30926780 Free PMC article.
Evaluation of Phylogenetic Methods for Inferring the Direction of Human Immunodeficiency Virus (HIV) Transmission: HIV Prevention Trials Network (HPTN) 052.
Zhang Y, Wymant C, Laeyendecker O, Grabowski MK, Hall M, Hudelson S, Piwowar-Manning E, McCauley M, Gamble T, Hosseinipour MC, Kumarasamy N, Hakim JG, Kumwenda J, Mills LA, Santos BR, Grinsztejn B, Pilotto JH, Chariyalertsak S, Makhema J, Chen YQ, Cohen MS, Fraser C, Eshleman SH. Zhang Y, et al. Among authors: hall m. Clin Infect Dis. 2021 Jan 23;72(1):30-37. doi: 10.1093/cid/ciz1247. Clin Infect Dis. 2021. PMID: 31922537 Free PMC article.
Quantifying HIV transmission flow between high-prevalence hotspots and surrounding communities: a population-based study in Rakai, Uganda.
Ratmann O, Kagaayi J, Hall M, Golubchick T, Kigozi G, Xi X, Wymant C, Nakigozi G, Abeler-Dörner L, Bonsall D, Gall A, Hoppe A, Kellam P, Bazaale J, Kalibbala S, Laeyendecker O, Lessler J, Nalugoda F, Chang LW, de Oliveira T, Pillay D, Quinn TC, Reynolds SJ, Spencer SEF, Ssekubugu R, Serwadda D, Wawer MJ, Gray RH, Fraser C, Grabowski MK; Rakai Health Sciences Program and the Pangea HIV Consortium. Ratmann O, et al. Among authors: hall m. Lancet HIV. 2020 Mar;7(3):e173-e183. doi: 10.1016/S2352-3018(19)30378-9. Epub 2020 Jan 14. Lancet HIV. 2020. PMID: 31953184 Free PMC article.
7,089 results