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

Oliver Ratmann, M. Kate Grabowski, Matthew Hall, Tanya Golubchik, Chris Wymant, Lucie Abeler-Dıfmmode\ddoto\elseö\firner, David Bonsall, Anne Hoppe, Andrew Leigh Brown, Tulio de Oliveira, Astrid Gall, Paul Kellam, Deenan Pillay, Joseph Kagaayi, Godfrey Kigozi, Thomas C. Quinn, Maria J. Wawer, Oliver Laeyendecker, David Serwadda, Ronald H. Gray, Christophe Fraser, Helen Ayles, Rory Bowden, Vincent Calvez, Myron Cohen, Ann Dennis, Max Essex, Sarah Fidler, Daniel Frampton, Richard Hayes, Joshua T. Herbeck, Pontiano Kaleebu, Cissy Kityo, Jairam Lingappa, Vladimir Novitsky, Nick Paton, Andrew Rambaut, Janet Seeley, Deogratius Ssemwanga, Frank Tanser, Gertrude Nakigozi, Robert Ssekubugu, Fred Nalugoda, Tom Lutalo, Ronald Galiwango, Fred Makumbi, Nelson K. Sewankambo, Aaron A. R. Tobian, Steven J. Reynolds, Larry W. Chang, Dorean Nabukalu, Anthony Ndyanabo, Joseph Ssekasanvu, Hadijja Nakawooya, Jessica Nakukumba, Grace N. Kigozi, Betty S. Nantume, Nampijja Resty, Jedidah Kambasu, Margaret Nalugemwa, Regina Nakabuye, Lawrence Ssebanobe, Justine Nankinga, Adrian Kayiira, Gorreth Nanfuka, Ruth Ahimbisibwe, Stephen Tomusange, Ronald M. Galiwango, Sarah Kalibbali, Margaret Nakalanzi, Joseph Ouma Otobi, Denis Ankunda, Joseph Lister Ssembatya, John Baptist Ssemanda, Robert Kairania, Emmanuel Kato, Alice Kisakye, James Batte, James Ludigo, Abisagi Nampijja, Steven Watya, Kighoma Nehemia, Margaret Anyokot, Joshua Mwinike, George Kibumba, Paschal Ssebowa, George Mondo, Francis Wasswa, Agnes Nantongo, Rebecca Kakembo, Josephine Galiwango, Geoffrey Ssemango, Andrew D. Redd, John Santelli, Caitlin E. Kennedy, Jennifer Wagman, PANGEA Consortium, Rakai Health Sciences Program
March 2019
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Type
Journal article
Publication
Nat. Commun.
Oliver Ratmann
Oliver Ratmann
Reader in Statistics and Machine Learning for Public Good

I develop bespoke statistical methods for public good. My group and I are particularly interested in novel Bayesian methods that harness information in viral deep sequence data, mobile phone mobility data, and time-resolved patient data to characterise the spread of infectious diseases, and to guide public health interventions.