I have expertise in genomic laboratory methods and bioinformatic analysis of pathogen genomes, and work with viral, fungal and bacterial human pathogens. I try to synergise approaches from different fields, e.g. applying well established tools and techniques from eukaryotic genomics to the study of pathogen genomes; this uses a combination of established tools and de novo scripted analyses methods.
My current research in the Thomson group at WTSI focuses on Sexually Transmitted (STIs) and Neglected Diseases (NTDs), with a particular focus on Syphilis and Treponemas. I use genome sequencing and population genomics to address questions of inter- and intra-host evolutionary dynamics and population structure, host adaptation and acquisition of virulence, and patient-to-patient transmission.
Genotypic Diversity Is Associated with Clinical Outcome and Phenotype in Cryptococcal Meningitis across Southern Africa.
PLoS neglected tropical diseases 2015;9;6;e0003847
Clinical and biological insights from viral genome sequencing.
Nature reviews. Microbiology 2017;15;3;183-192
Genomic epidemiology of Cryptococcus yeasts identifies adaptation to environmental niches underpinning infection across an African HIV/AIDS cohort.
Molecular ecology 2017;26;7;1991-2005
A Population Genomics Approach to Assessing the Genetic Basis of Within-Host Microevolution Underlying Recurrent Cryptococcal Meningitis Infection.
G3 (Bethesda, Md.) 2017;7;4;1165-1176
Tracing Genetic Exchange and Biogeography of <i>Cryptococcus neoformans</i> var. <i>grubii</i> at the Global Population Level.