Horizontal DNA transfer mechanisms of bacteria as weapons of intragenomic conflict by Croucher, N, Mostowy, R, Wymant, C, Turner, P, Bentley, S, Fraser, C

Link between the numbers of particles and variants founding new HIV-1 infections depends on the timing of transmission by Thompson, R, Wymant, C, Spriggs, R, Raghwani, J, Fraser, C, Lythgoe, K

Learning patterns of HIV-1 resistance to broadly neutralizing antibodies with reduced subtype bias using multi-task learning by Igiraneza, AB, Zacharopoulou, P, Hinch, R, Wymant, C, Abeler-Dörner, L, Frater, J, Fraser, C

PHYLOSCANNER: Inferring transmission from within- and petween-host pathogen genetic diversity. by Wymant, C, Hall, M, Ratmann, O, Bonsall, D, Golubchik, T, de Cesare, M, Gall, A, Cornelissen, M, Fraser, C

Quantifying SARS-CoV-2 transmission suggests epidemic control with digital contact tracing by Ferretti, L, Wymant, C, Kendall, M, Zhao, L, Nurtay, A, Parker, M, Abeler-Dörner, L, Bonsall, D, Fraser, C

Epidemiological changes on the Isle of Wight after the launch of the NHS Test and Trace programme: a preliminary analysis by Kendall, M, Milsom, L, Abeler-Dörner, L, Wymant, C, Ferretti, L, Briers, M, Holmes, C, Bonsall, D, Abeler, J, Fraser, C

Estimating SARS-CoV-2 variant fitness and the impact of interventions in England using statistical and geo-spatial agent-based models by Hinch, R, Panovska-Griffiths, J, Probert, WJM, Ferretti, L, Wymant, C, Di Lauro, F, Baya, N, Ghafari, M, Abeler-Dörner, L, Fraser, C

The evolution of subtype B HIV-1 tat in the Netherlands during 1985-2012 by van der Kuyl, A, Vink, M, Zorgdrager, F, Bakker, M, Wymant, C, Hall, M, Gall, A, Blanquart, F, Berkhout, B, Fraser, C, Cornelissen, M

Time to evaluate COVID-19 contact-tracing apps by Colizza, V, Grill, E, Mikolajczyk, R, Cattuto, C, Kucharski, A, Riley, S, Kendall, M, Lythgoe, K, Bonsall, D, Wymant, C, Abeler-Dörner, L, Ferretti, L, Fraser, C

Digital measurement of SARS-CoV-2 transmission risk from 7 million contacts by Ferretti, L, Wymant, C, Petrie, J, Tsallis, D, Kendall, M, Ledda, A, Di Lauro, F, Fowler, A, Di Francia, A, Abeler-Dörner, L, Charalambides, M, Briers, M, Fraser, C

High prevalence fishing communities are not a major sourceof new HIV infections to the inland populations in RakaiDistrict, Uganda: implications for geo-spatially targeted HIVpreve... by Ratmann, O, Grabowski, MK, Hall, M, Golubchik, T, Wymant, C, Kagaayi, J, Kigozi, G, Quinn, T, Wawer, M, Laeyendecker, O, Serwadda, D, Gray, R, Fraser, C, PANGEA-HIV Consortium, Rakai Health Sciences Program

HIV genotyping and phylogenetics in the HPTN 071 (PopART) study: validation of a high-throughput sequencing assay for viral load quantification, genotyping, resistance testing and... by Bonsall, D, Golubchik, T, Kosloff, B, Limbada, M, De Cesare, M, Schaap, A, Hall, M, Wymant, C, Macintyre-Cockett, G, Brown, A, Ansari, MA, Floyd, S, Hayes, R, Ayles, H, Fidler, S, Fraser, C, Grp, HPTNPS

Viral and immune dynamics of genital human papillomavirus infections in young women with high temporal resolution by Tessandier, N, Elie, B, Boué, V, Selinger, C, Rahmoun, M, Bernat, C, Grasset, S, Groc, S, Bedin, A, Beneteau, T, Bonneau, M, Graf, C, Jacobs, N, Kamiya, T, Kerioui, M, Lajoie, J, Melki, I, Prétet, J, Reyné, B, Schlecht-Louf, G, Sofonea, MT, Supplisson, O, Wymant, C, Foulongne, V

Inferring HIV-1 transmission networks and sources of epidemic spread in Africa with deep-sequence phylogenetic analysis by Ratmann, O, Grabowski, M, Hall, M, Golubchik, T, Wymant, C, Abeler-Dörner, L, Bonsall, D, Hoppe, A, Brown, A, De Oliveira, T, Gall, A, Kellam, P, Pillay, D, Kagaayi, J, Kigozi, G, Quinn, T, Wawer, M, Laeyendecker, O, Serwadda, D, Gray, R, Fraser, C, Pangea Consortium And Rakai Health Sciences Program

A comprehensive genomics solution for HIV surveillance and clinical monitoring in low income settings by Bonsall, D, Golubchik, T, de Cesare, M, Limbada, M, Kosloff, B, MacIntyre-Cockett, G, Hall, M, Wymant, C, Ansari, MA, Abeler-Dörner, L, Schaap, A, Brown, A, Barnes, E, Piwowar-Manning, E, Eshleman, S, Wilson, E, Emel, L, Hayes, R, Fidler, S, Ayles, H, Bowden, R, Fraser, C, HPTN 071 (PopART) team

OpenABM-Covid19—An agent-based model for non-pharmaceutical interventions against COVID-19 including contact tracing by Hinch, R, Probert, WJM, Nurtay, A, Kendall, M, Wymant, C, Hall, M, Lythgoe, K, Bulas Cruz, A, Zhao, L, Stewart, A, Ferretti, L, Montero, D, Warren, J, Mather, N, Abueg, M, Wu, N, Legat, O, Bentley, K, Mead, T, Van-Vuuren, K, Feldner-Busztin, D, Ristori, T, Finkelstein, A, Bonsall, DG, Abeler-Dörner, L, Fraser, C

HIV-1 full-genome phylogenetics of generalized epidemics in sub-Saharan Africa: impact of missing nucleotide characters in next-generation sequences. by Ratmann, O, Wymant, C, Colijn, C, Danaviah, S, Essex, M, Frost, S, Gall, A, Gaiseitsiwe, S, Grabowski, M, Gray, R, Guindon, S, von Haeseler, A, Kaleebu, P, Kendall, M, Kozlov, A, Manasa, J, Minh, B, Moyo, S, Novitsky, V, Nsubuga, R, Pillay, S, Quinn, T, Serwadda, D, Ssemwanga, D, Stamatakis, A, Trifinopoulos, J, Wawer, M, Leigh Brown, A, de Oliveira, T, Kellam, P, Pillay, D, Fraser, C

Viral genetic variation accounts for a third of variability in HIV-1 set-point viral load in Europe by Blanquart, F, Wymant, C, Cornelissen, M, Gall, A, Bakker, M, Bezemer, D, Hall, M, Hillebregt, M, Ong, S, Albert, J, Bannert, N, Fellay, J, Fransen, K, Gourlay, A, Grabowski, M, Gunsenheimer-Bartmeyer, B, Günthard, H, Kivelä, P, Kouyos, R, Laeyendecker, O, Liitsola, K, Meyer, L, Porter, K, Ristola, M, van Sighem, A, Vanham, G, Berkhout, B, Kellam, P, Reiss, P, Fraser, C, BEEHIVE collaboration

Easy and accurate reconstruction of whole HIV genomes from short-read sequence data with shiver by Wymant, C, Blanquart, F, Golubchik, T, Gall, A, Bakker, M, Bezemer, D, Croucher, N, Hall, M, Hillebregt, M, Ong, S, Ratmann, O, Albert, J, Bannert, N, Fellay, J, Fransen, K, Gourlay, A, Grabowski, M, Gunsenheimer-Bartmeyer, B, Günthard, H, 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