Research Associate, 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)
TTsampler (an R package for enumeration and uniform sampling of transmission trees for a fixed phylogeny)
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
PHYLOSCANNER: Inferring Transmission from Within- and Between-Host Pathogen Genetic Diversity.
Wymant C. et al, (2017), Molecular biology and evolution
Phylogenetics between and within hosts along the genome reveals transmission, dual infections, recombination and contamination
Wymant CM. et al, (2017)
Viral genetic variation accounts for a third of variability in HIV-1 set-point viral load in Europe.
Blanquart F. et al, (2017), PLoS biology, 15
Phylogenetic Tools for Generalized HIV-1 Epidemics: Findings from the PANGEA-HIV Methods Comparison.
Ratmann O. et al, (2017), Molecular biology and evolution, 34, 185 - 203