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Phylogenetic Tools for Generalized HIV-1 Epidemics: Findings from the PANGEA-HIV Methods Comparison.
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.
PANGEA-HIV: phylogenetics for generalised epidemics in Africa.
Pillay D, Herbeck J, Cohen MS, de Oliveira T, Fraser C, Ratmann O, Brown AL, Kellam P; PANGEA-HIV Consortium.
Pillay D, et al.
Lancet Infect Dis. 2015 Mar;15(3):259-61. doi: 10.1016/S1473-3099(15)70036-8.
Lancet Infect Dis. 2015.
PMID: 25749217
Free PMC article.
No abstract available.
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Using nearly full-genome HIV sequence data improves phylogeny reconstruction in a simulated epidemic.
Yebra G, Hodcroft EB, Ragonnet-Cronin ML, Pillay D, Brown AJ; PANGEA_HIV Consortium; ICONIC Project.
Yebra G, et al.
Sci Rep. 2016 Dec 23;6:39489. doi: 10.1038/srep39489.
Sci Rep. 2016.
PMID: 28008945
Free PMC article.
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Longitudinal population-level HIV epidemiologic and genomic surveillance highlights growing gender disparity of HIV transmission in Uganda.
Monod M, Brizzi A, Galiwango RM, Ssekubugu R, Chen Y, Xi X, Kankaka EN, Ssempijja V, Dörner LA, Akullian A, Blenkinsop A, Bonsall D, Chang LW, Dan S, Fraser C, Golubchik T, Gray RH, Hall M, Jackson JC, Kigozi G, Laeyendecker O, Mills LA, Quinn TC, Reynolds SJ, Santelli J, Sewankambo NK, Spencer SE, Ssekasanvu J, Thomson L, Wawer MJ, Serwadda D, Godfrey-Faussett P, Kagaayi J, Grabowski MK, Ratmann O; Rakai Health Sciences Program; PANGEA-HIV consortium.
Monod M, et al.
medRxiv [Preprint]. 2023 Nov 13:2023.03.16.23287351. doi: 10.1101/2023.03.16.23287351.
medRxiv. 2023.
PMID: 36993261
Free PMC article.
Updated.
Preprint.
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Longitudinal population-level HIV epidemiologic and genomic surveillance highlights growing gender disparity of HIV transmission in Uganda.
Monod M, Brizzi A, Galiwango RM, Ssekubugu R, Chen Y, Xi X, Kankaka EN, Ssempijja V, Abeler-Dörner L, Akullian A, Blenkinsop A, Bonsall D, Chang LW, Dan S, Fraser C, Golubchik T, Gray RH, Hall M, Jackson JC, Kigozi G, Laeyendecker O, Mills LA, Quinn TC, Reynolds SJ, Santelli J, Sewankambo NK, Spencer SEF, Ssekasanvu J, Thomson L, Wawer MJ, Serwadda D, Godfrey-Faussett P, Kagaayi J, Grabowski MK, Ratmann O; Rakai Health Sciences Program; PANGEA-HIV consortium.
Monod M, et al.
Nat Microbiol. 2024 Jan;9(1):35-54. doi: 10.1038/s41564-023-01530-8. Epub 2023 Dec 5.
Nat Microbiol. 2024.
PMID: 38052974
Free PMC article.
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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.
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.
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