His research interests lie in the fields of molecular epidemiology, computational biology and viral evolution. In particular, he has studied the evolutionary processes that shape viral genetic diversity, spanning from large-scale epidemic processes, such as population growth and spatial dispersal, to small-scale transmission histories and within-host evolutionary processes. Specific applications include the origin of HIV, the source-sink dynamics of seasonal influenza, rabies metapopulation dynamics, and Ebola virus patterns of spread. Philippe is the lead author of the second edition of the Phylogenetic Handbook and a two-time ERC grant awardee. His team has made important contributions to the popular BEAST software, which was acknowledged by the Mitchell prize in Bayesian statistics.