Senior Researcher, Nuffield Department of Medicine
I am a researcher in pathogen phylodynamics, with a particular interest in inference of who infected who. I am also interested in investigating the effects of sampling bias in molecular epidemiological studies. I obtained my PhD in 2015 at the University of Edinburgh under Professor Mark Woolhouse and Professor Andrew Rambaut. I currently work at the BDI with Professor Christophe Fraser on the PANGEA HIV project, focussing on the reconstruction of transmission patterns within a very large and rich dataset of next-generation HIV sequences.
Software in which I have a hand:
Phyloscanner (construction of phylogenies and investigation of transmission in large genetic datasets)
STraTUS (an R package for enumeration and uniform sampling of transmission trees for a fixed phylogeny)
Evaluation of phylogenetic methods for inferring the direction of HIV transmission: HPTN 052.
Zhang Y. et al, (2020), Clinical infectious diseases : an official publication of the Infectious Diseases Society of America
HIV-1 founder variant multiplicity is determined by the infection stage of the source partner
Villabona-Arenas CJ. et al, (2019)
Improved characterisation of MRSA transmission using within-host bacterial sequence diversity.
Hall MD. et al, (2019), eLife, 8
Quantifying the contribution of different aged men and women to onwards transmission of HIV-1 in generalised epidemics in sub-Saharan Africa: A modelling and phylogenetics approach from the HPTN071 (PopART) trial
Probert W. et al, (2019), JOURNAL OF THE INTERNATIONAL AIDS SOCIETY, 22, 107 - 107
Transmission Trees on a Known Pathogen Phylogeny: Enumeration and Sampling.
Hall MD. and Colijn C., (2019), Molecular biology and evolution, 36, 1333 - 1343