|Patients’, clinicians’ and the research communities’ priorities for treatment research: there is an important mismatch|
S Crowe, M Fenton, M Hall, K Cowan, I Chalmers
Research involvement and engagement 1 (1), 1-10, 2015
|PHYLOSCANNER: inferring transmission from within-and between-host pathogen genetic diversity|
C Wymant, M Hall, O Ratmann, D Bonsall, T Golubchik, M de Cesare, ...
Molecular biology and evolution 35 (3), 719-733, 2018
|Epidemic Reconstruction in a Phylogenetics Framework: Transmission Trees as Partitions of the Node Set|
M Hall, M Woolhouse, A Rambaut
PLOS Computational Biology 11 (12), e1004613, 2015
|Phylogenetic tools for generalized HIV-1 epidemics: findings from the PANGEA-HIV methods comparison|
O Ratmann, EB Hodcroft, M Pickles, A Cori, M Hall, S Lycett, C Colijn, ...
Molecular biology and evolution 34 (1), 185-203, 2017
|Revealing the micro-scale signature of endemic zoonotic disease transmission in an African urban setting|
H Bourhy, E Nakouné, M Hall, Nouvellet, Pierre, A Lepelletier, C Talbi, ...
PLOS Pathogens 12 (4), e1005525, 2016
|The effects of sampling strategy on the quality of reconstruction of viral population dynamics using Bayesian skyline family coalescent methods: A simulation study|
MD Hall, MEJ Woolhouse, A Rambaut
Virus Evolution 2 (1), vew003, 2016
|Reconstructing geographical movements and host species transitions of foot-and-mouth disease virus serotype SAT 2|
MD Hall, NJ Knowles, J Wadsworth, A Rambaut, MEJ Woolhouse
MBio 4 (5), 2013
|Viral genetic variation accounts for a third of variability in HIV-1 set-point viral load in Europe|
F Blanquart, C Wymant, M Cornelissen, A Gall, M Bakker, D Bezemer, ...
PLoS biology 15 (6), e2001855, 2017
|Easy and accurate reconstruction of whole HIV genomes from short-read sequence data with shiver|
C Wymant, F Blanquart, T Golubchik, A Gall, M Bakker, D Bezemer, ...
Virus evolution 4 (1), vey007, 2018
|Phylogeography of Rift Valley Fever virus in Africa and the Arabian Peninsula|
S Abdallah M, A Townsend Peterson, M Hall
PLOS Neglected Tropical Diseases 11 (1), e0005226, 2017
|Inferring HIV-1 transmission networks and sources of epidemic spread in Africa with deep-sequence phylogenetic analysis|
O Ratmann, MK Grabowski, M Hall, T Golubchik, C Wymant, ...
Nature communications 10 (1), 1-13, 2019
|Spatiotemporal analysis of the genetic diversity of seal influenza A (H10N7) virus, northwestern Europe|
R Bodewes, S Zohari, JS Krog, MD Hall, TC Harder, TM Bestebroer, ...
Journal of virology 90 (9), 4269-4277, 2016
|Phylogenetic methods inconsistently predict the direction of HIV transmission among heterosexual pairs in the HPTN 052 cohort|
R Rose, M Hall, AD Redd, S Lamers, AE Barbier, SF Porcella, ...
The Journal of infectious diseases 220 (9), 1406-1413, 2019
|Using genomics data to reconstruct transmission trees during disease outbreaks|
MD Hall, MEJ Woolhouse, A Rambaut
Revue scientifique et technique (International Office of Epizootics) 35 (1), 287, 2016
|Modelling the impact of co-circulating low pathogenic avian influenza viruses on epidemics of highly pathogenic avian influenza in poultry|
S Nickbakhsh, MD Hall, I Dorigatti, SJ Lycett, P Mulatti, I Monne, A Fusaro, ...
Epidemics 17, 27-34, 2016
|Quantifying HIV transmission flow between high-prevalence hotspots and surrounding communities: a population-based study in Rakai, Uganda|
O Ratmann, J Kagaayi, M Hall, T Golubchick, G Kigozi, X Xi, C Wymant, ...
The Lancet HIV 7 (3), e173-e183, 2020
|Transmission trees on a known pathogen phylogeny: Enumeration and sampling|
MD Hall, C Colijn
Molecular biology and evolution 36 (6), 1333-1343, 2019
|The evolution and phylodynamics of serotype A and SAT2 foot-and-mouth disease viruses in endemic regions of Africa|
S Lycett, VN Tanya, M Hall, DP King, S Mazeri, V Mioulet, NJ Knowles, ...
Scientific reports 9 (1), 1-11, 2019
|A Comprehensive Genomics Solution for HIV Surveillance and Clinical Monitoring in Low-Income Settings|
D Bonsall, T Golubchik, M de Cesare, M Limbada, B Kosloff, ...
Journal of clinical microbiology 58 (10), 2020
|Improved characterisation of MRSA transmission using within-host bacterial sequence diversity|
MD Hall, MTG Holden, P Srisomang, W Mahavanakul, V Wuthiekanun, ...
Elife 8, e46402, 2019