My research in a nutshell
Viruses and bacteria have DNA (or in some cases RNA) genomes which mutate rapidly. By tracking where, when and in what species particular mutations or genomic re-arrangements arise, it is possible to infer transmission patterns between groups of individuals, e.g. patterns of farm to farm transmissions for fast mutating livestock pathogens; global transmission patterns between countries (mediated by trade or travel patterns); or transmission between wild and farmed animals. Genomic sequencing is now relatively inexpensive and reasonably fast and there is a large amount of pathogen sequence data available - the challenge is to develop analysis and prediction methods. I am researching fast but robust computational bayesian and machine learning methods for transmission pattern inference, integrating sequence and other epidemiological data, for example considering avian and swine influenza, bovine tuberculous and bovine viral diarrhoea. I aim to be able to answer questions such as - what are the routes and rates of infection ? what are the rates of cross species transmissions ? and how quickly might new strains arise ?