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)
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, (2018), Journal of the international aids society, 21, 58 - 59
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, (2018), Journal of the international aids society, 21, 70 - 71
The evolution of subtype B HIV-1 tat in the Netherlands during 1985-2012.
van der Kuyl AC. et al, (2018), Virus research, 250, 51 - 64
Easy and accurate reconstruction of whole HIV genomes from short-read sequence data with shiver.
Wymant C. et al, (2018), Virus evolution, 4
PHYLOSCANNER: Inferring Transmission from Within- and Between-Host Pathogen Genetic Diversity.
Wymant C. et al, (2017), Molecular biology and evolution