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)
Phylogenetic methods inconsistently predict direction of HIV transmission among heterosexual pairs in the HPTN052 cohort.
Rose R. et al, (2018), The Journal of infectious diseases
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