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Chris Wymant

Introduction to Phylogenetics

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Christophe Fraser

How to interpret a viral phylogeny

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Matthew Hall

Introduction to Phylodynamics

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Brian Foley

Multiple sequence alignment for HIV

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Brian Foley

Recombination in HIV

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Steven Kemp

Introduction to whole genome sequence analysis - part 1

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Steven Kemp

Introduction to whole genome sequence analysis - part 2

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David Bonsall

Using NGS data to identify HIV drug resistance mutations

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Diego Cuadros

Geographical models in epidemiology

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Oliver Ratmann

Are high prevalence fishing communities on Lake Victoria

the predominant source of new HIV infections in Rakai, Uganda?

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Nicholas Bbosa

Using phylogenetics and modeling to understand HIV-1

transmission dynamics in Ugandan fishing communities

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Sarah Fidler

Results of the HPTN 071 (PopART) HIV UTT trial

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Myron Cohen

HIV Prevention in 2020

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Janet Seeley

The lives behind the phylogenetic trees - Social Science in PANGEA

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Tanya Golubchik

The inner workings of the PANGEA database

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Oliver Ratmann

Transmissions from different age and gender groups in Rakai

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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 (2020). Lancet HIV pii: S2352-3018(19)30378-9

PANGEA-HIV 2: Phylogenetics And Networks for Generalised Epidemics in Africa.

Abeler-Dörner L, Grabowski KM, Rambaut A, Pillay D, Fraser C (2019). Curr Opin HIV AIDS 14, 173–180

Inferring HIV-1 transmission networks and sources of epidemic spread in Africa with deep-sequence phylogenetic analysis.

Ratmann O, Groabowski KM, Hall M, Golubchik T, Wymant C, Abeler-Dörner L, Bonsall D, Hoppe A, Leigh Brown A, de Oliveria T, Gall A, Kellam P, Pillay D, Kagaayi J, Kigozi G, Quinn TC, Wawer MJ, Laeyendecker O, Serwadda D, Gray RH, Fraser C on behalf of the PANGEA consortium and the Rakai Health Sciences Program (2019). Nat Commun 10, 1411

Phylogeography of HIV-1 suggests that Ugandan fishing communities are a sink for, not a source of, virus from general populations.

Bbosa N, Ssemwanga D, Nsubuga RN, Salazar-Gonzalez JF, Salazar MG, Nanyonjo M, Kuteesa M, Seeley J, Kiwanuka N, Bagaya BS, Yebra G, Leigh-Brown A, Kaleebu P (2019). Sci Rep 9, 1051

A comprehensive genomics solution for HIV surveillance and clinical monitoring in a global health setting.

Bonsall D, Golubchik T, de Cesare M,, Limbada M, Kosloff B, MacIntyre-Cockett G, Hall M, Wymant C, Ansari A, Abeler-Dörner L, Schaap, A, Borwn A, Bares E, Piwowar-Manning E, Wilson E, Emel L, Hayes R, Fidler S, Ayles H, Bowden R, Fraser C (2018). BioRxiv, 397083

Ethical considerations in global HIV phylogenetic research.

Coltart CEM, Hoppe A, Parker M, Dawson L, Amon JJ, Simwinga M, Geller G, Henderson G, Laeyendecker O, Tucker JD, Eba P, Novitsky V, Vandamme AM, Seeley J, Dallabetta G, Harling G, Grabowski MK, Godfrey-Faussett P, Fraser C, Cohen MS, Pillay D; Ethics in HIV Phylogenetics Working Group (2018). Lancet HIV 5: e656-e666

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 (2018).
Virus Evol 4, vey007

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 (2017). Mol Biol Evol 35, 719-733

HIV-1 full-genome phylogenetics of generalized epidemics in sub-Saharan Africa: impact of missing nucleotide characters in next-generation sequences.

Ratmann O, Wymant C, Colijn C, Danaviah S, Essex M, Frost SDW, Gall A, Gaiseitsiwe S, Grabowski M, Gray R, Guindon S, von Haeseler A, Kaleebu P, Kendall M, Kozlov A, Manasa J, Minh BQ, Moyo S, Novitsky V, Nsubuga R, Pillay S, Quinn TC, Serwadda D, Ssemwanga D, Stamatakis A, Trifinopoulos J, Wawer M, Leigh Brown A, de Oliveira T, Kellam P, Pillay D, Fraser C (2017). AIDS Res Hum Retroviruses 33, 1083-1098

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 (2017). Mol Biol Evol 34, 185-3203

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 (2016). Sci Rep 23, 39489

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 (2015). Lancet Infect Dis 15, 259-6

Universal amplification, next-generation sequencing, and assembly of HIV-1 genomes.

Gall A, Ferns B, Morris C, Watson S, Cotten M, Robinson M, Berry N, Pillay D, Kellam P. (2012)
J Clin Microbiol 50, 3838-44