|Geographic and temporal trends in the molecular epidemiology and genetic mechanisms of transmitted HIV-1 drug resistance: an individual-patient-and sequence-level meta-analysis|
SY Rhee, JL Blanco, MR Jordan, J Taylor, P Lemey, V Varghese, ...
PLoS Med 12 (4), e1001810, 2015
|Automated analysis of phylogenetic clusters|
M Ragonnet-Cronin, E Hodcroft, S Hué, E Fearnhill, V Delpech, ...
BMC bioinformatics 14 (1), 317, 2013
|HIV-1 modulates the tRNA pool to improve translation efficiency|
A Van Weringh, M Ragonnet-Cronin, E Pranckeviciene, M Pavon-Eternod, ...
Molecular biology and evolution 28 (6), 1827-1834, 2011
|Phylogenetic analyses reveal HIV-1 infections between men misclassified as heterosexual transmissions|
S Hué, AE Brown, M Ragonnet-Cronin, SJ Lycett, DT Dunn, E Fearnhill, ...
Aids 28 (13), 1967-1975, 2014
|Genetic diversity as a marker for timing infection in HIV-infected patients: evaluation of a 6-month window and comparison with BED|
M Ragonnet-Cronin, S Aris-Brosou, I Joanisse, H Merks, D Vallée, ...
The Journal of infectious diseases 206 (5), 756-764, 2012
|Identifying transmission clusters with cluster picker and HIV-TRACE|
R Rose, SL Lamers, JJ Dollar, MK Grabowski, EB Hodcroft, ...
AIDS research and human retroviruses 33 (3), 211-218, 2017
|Evaluating the effects of SARS-CoV-2 Spike mutation D614G on transmissibility and pathogenicity|
E Volz, V Hill, JT McCrone, A Price, D Jorgensen, Á O’Toole, J Southgate, ...
|Longitudinal phylogenetic surveillance identifies distinct patterns of cluster dynamics|
M Ragonnet-Cronin, M Ofner-Agostini, H Merks, R Pilon, M Rekart, ...
JAIDS Journal of Acquired Immune Deficiency Syndromes 55 (1), 102-108, 2010
|Transmission of non-B HIV subtypes in the United Kingdom is increasingly driven by large non-heterosexual transmission clusters|
M Ragonnet-Cronin, SJ Lycett, EB Hodcroft, S Hué, E Fearnhill, AE Brown, ...
The Journal of infectious diseases 213 (9), 1410-1418, 2016
|Recent and rapid transmission of HIV among people who inject drugs in Scotland revealed through phylogenetic analysis|
M Ragonnet-Cronin, C Jackson, A Bradley-Stewart, C Aitken, A McAuley, ...
The Journal of infectious diseases 217 (12), 1875-1882, 2018
|HIV transmission networks among transgender women in Los Angeles County, CA, USA: a phylogenetic analysis of surveillance data|
M Ragonnet-Cronin, YW Hu, SR Morris, Z Sheng, K Poortinga, ...
The Lancet HIV 6 (3), e164-e172, 2019
|Analysis of the history and spread of HIV-1 in Uganda using phylodynamics|
G Yebra, M Ragonnet-Cronin, D Ssemwanga, CM Parry, CH Logue, ...
The Journal of general virology 96 (Pt 7), 1890, 2015
|Non-disclosed men who have sex with men in UK HIV transmission networks: phylogenetic analysis of surveillance data|
M Ragonnet-Cronin, S Hué, EB Hodcroft, A Tostevin, D Dunn, T Fawcett, ...
The lancet HIV 5 (6), e309-e316, 2018
|Comparison of molecular testing strategies for COVID-19 control: a mathematical modelling study|
NC Grassly, M Pons-Salort, EPK Parker, PJ White, NM Ferguson, ...
The Lancet Infectious Diseases 20 (12), 1381-1389, 2020
|Using nearly full-genome HIV sequence data improves phylogeny reconstruction in a simulated epidemic|
G Yebra, EB Hodcroft, ML Ragonnet-Cronin, D Pillay, AJL Brown, ...
Scientific reports 6, 39489, 2016
|FAVITES: simultaneous simulation of transmission networks, phylogenetic trees, and sequences|
N Moshiri, M Ragonnet-Cronin, J Wertheim, S Mirarab
|Report 16: Role of testing in COVID-19 control|
N Grassly, M Pons Salort, E Parker, P White, K Ainslie, M Baguelin, ...
|Lack of effectiveness of antiretroviral therapy in preventing HIV infection in serodiscordant couples in Uganda: an observational study|
J Birungi, JE Min, KA Muldoon, P Kaleebu, R King, S Khanakwa, ...
PloS one 10 (7), e0132182, 2015
|Report 26: Reduction in mobility and COVID-19 transmission|
P Nouvellet, S Bhatia, A Cori, K Ainslie, M Baguelin, S Bhatt, A Boonyasiri, ...
|Sequencing identifies multiple early introductions of SARS-CoV-2 to the New York City region|
MT Maurano, S Ramaswami, P Zappile, D Dimartino, L Boytard, ...
Genome research 30 (12), 1781-1788, 2020