Summary
I am physically based at Simon Fraser University in Vancouver, Canada, where I lead the MAGPIE research group: MAthematics, Genomics and Prediction in Infection and Evolution: MAGPIE group. I remain affiliated with Imperial College Mathematics and the Centre for Mathematics of Precision Healthcare.
My work is at the interface of mathematics and the epidemiology and evolution of pathogens. I recently held an EPSRC Fellowship with the broad aim to develop the mathematical tools to connect sequence data for pathogens to pathogen ecology. I 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? How can genomic data for diverse infections be used to design better interventions, controlling resistance or vaccine strain replacement?
To answer these questions, my group is building new approaches to analysing pathogen sequence data, studying tree space and branching processes, and doing ecological and epidemiological modelling.
Teaching
I have varied teaching responsibilities including matlab, dynamical systems, project supervision and working with summer undergraduate reseachers.
Links
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
Publications
Journals
Walter KS, Colijn C, Cohen T, et al., 2020, Genomic variant-identification methods may alter Mycobacterium tuberculosis transmission inferences, Microbial Genomics, Vol:6, ISSN:2057-5858
Tindale LC, Stockdale JE, Coombe M, et al., 2020, Evidence for transmission of COVID-19 prior to symptom onset, Elife, Vol:9, ISSN:2050-084X
Mulberry N, Rutherford A, Colijn C, 2020, Systematic comparison of coexistence in models of drug-sensitive and drug-resistant pathogen strains, Theoretical Population Biology, Vol:133, ISSN:0040-5809, Pages:150-158
Metzig C, Gould M, Noronha R, et al., 2020, Classification of origin with feature selection and network construction for folk tunes, Pattern Recognition Letters, Vol:133, ISSN:0167-8655, Pages:356-364