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.
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
Hall M, Colijn C, 2019, Transmission trees on a known pathogen phylogeny: enumeration and sampling., Mol Biol Evol
et al., 2019, Beyond the SNP Threshold: Identifying Outbreak Clusters Using Inferred Transmissions, Molecular Biology and Evolution, Vol:36, ISSN:0737-4038, Pages:587-603
et al., 2019, Correction: Evaluating strategies for control of tuberculosis in prisons and prevention of spillover into communities: An observational and modeling study from Brazil., Plos Med, Vol:16
et al., 2019, Phylogenies from dynamic networks, Plos Computational Biology, Vol:15
et al., 2019, Evaluating strategies for control of tuberculosis in prisons and prevention of spillover into communities: An observational and modeling study from Brazil, Plos Medicine, Vol:16, ISSN:1549-1676