Below is a list of my publications, each with a short summary of the work, and links to blog posts that give a little more detail.
- "Speeding up Inference of Homologous Recombination in Bacteria" describes the use of advanced reversible-jump MCMC methods for inferring one of the most accurate models for recombination in bacteria: ClonalOrigin.
- "Sequential Monte Carlo with transformations". This work arose from a project on the sequential inference of phylogenetic trees, which is one of the applications in the paper. We also used similar methods in a sequential approach to Bayesian model comparison, which in some circumstances offers improved performance over reversible jump MCMC (RJMCMC), and also other SMC approaches. By analogy to RJMCMC, we make use of deterministic transformations to move between models. (discussed on Xi'an's Og)
- "Mobile elements drive recombination hotspots in the core genome of Staphylococcus aureus" studied the population-wide diversity of Staphylococcus aureus, with a particular focus on homologous recombination, in particular how this is affected by mobile elements. (discussed on Daniel Wilson's blog)
- "Prediction of Staphylococcus aureus antimicrobial resistance by whole-genome sequencing" examined the extent to which antimicrobial resistance can be determined from the whole genome sequences of S. aureus.
- "Within-Host Evolution of Staphylococcus aureus during Asymptomatic Carriage" studied the within-host diversity of S. aureus, when the bacteria is in asymptomatic carriage. (discussed on Daniel Wilson's blog)
- "Evolutionary dynamics of Staphylococcus aureus during progression from carriage to disease" studied the within-host diversity of S. aureus, when a strain in carriage goes on to cause disease. (discussed on Daniel Wilson's blog)