My work is at the interface of mathematics and the epidemiology and evolution of pathogens. I hold an EPSRC Fellowship with the broad aim to develop the mathematical tools to connect sequence data for pathogens to pathogen ecology. I also have a long-standing interest on the dynamics of diverse interacting pathogens. For example, how does the interplay between co-infection, competition and selection drive the development of antimicrobial resistance? To answer these questions, my group is building new approaches to analysing phylogenetic trees derived from pathogen sequence data, studying tree space and branching processes, and doing ecological and epidemiological modelling.
I have varied teaching responsibilities including matlab, dynamical systems, project supervision and working with summer undergraduate reseachers.
Michelle Kendall and I have developed an approach to comparing phylogenetic trees (and other branching trees). It uses a novel metric on rooted trees, which can help to tease out different evolutionary stories making up a group of trees.
You can play with the tool online here using the web-based tree comparison tool that Michelle has developed.
We also have an R package: treescape
et al., 2017, Genomic infectious disease epidemiology in partially sampled and ongoing outbreaks., Mol Biol Evol
et al., 2017, Phylogenetic Tools for Generalized HIV-1 Epidemics: Findings from the PANGEA-HIV Methods Comparison., Mol Biol Evol, Vol:34, Pages:185-203
et al., 2016, Whole-Genome Sequencing for Routine Pathogen Surveillance in Public Health: a Population Snapshot of Invasive Staphylococcus aureus in Europe, Mbio, Vol:7, ISSN:2150-7511
et al., 2016, Diverse drug-resistant subpopulations of Mycobacterium tuberculosis are sustained in continuous culture, Journal of the Royal Society Interface, Vol:13, ISSN:1742-5689
et al., 2016, ClassTR: Classifying Within-Host Heterogeneity Based on Tandem Repeats with Application to Mycobacterium tuberculosis Infections, Plos Computational Biology, Vol:12, ISSN:1553-734X