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)
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
Inferring HIV-1 transmission networks and sources of epidemic spread in Africa with deep-sequence phylogenetic analysis.
Ratmann O. et al, (2019), Nature communications, 10
High prevalence fishing communities are not a major source of new HIV infections to the inland populations in Rakai District, Uganda: implications for geo-spatially targeted HIV prevention interventions
Ratmann O. et al, (2019), JOURNAL OF THE INTERNATIONAL AIDS SOCIETY, 21, 70 - 71
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 high-resolution transmission networking
Bonsall D. et al, (2019), 21, 58 - 59