Professor Oliver Pybus

Research Interests

Ancestry and diversification are processes unique to biology that shape every aspect of living systems, from individual cells to whole ecosystems. Using genome sequencing and other technologies we can now investigate these processes in unprecedented detail, and use the insights gained to tackle global challenges such as biodiversity loss, food production, and emerging epidemics. I feel fortunate to be a biologist at such an exciting time in the subject's history.

Most of my research concerns the evolutionary and ecological dynamics of infectious disease. Many pathogens evolve so rapidly that their ecology and evolution are coupled, requiring new inter-disciplinary methods of inquiry. Understanding this joint behaviour, sometimes called phylodynamics, is fundamental to applied problems including outbreak surveillance, vaccine design, and the evolution of drug resistance. I contribute to the theoretical development of phylodynamics and its application to public health and other fields. I develop new computational methods for the evolutionary analysis of genetic sequence data. More generally I am interested in topics at the interface of ecology and evolution, including molecular ecology, ancient DNA, portable genomics, spatial ecology, and statistical genetics.

Additional Information: I am a Professorial Fellow of New College and a Co-Director of the Oxford Martin School Programme on Pandemic Genomics. I am a Chief Editor of the open access journal Virus Evolution. I also hold a Professorship at the Royal Veterinary College.

For details of our current and past research please visit my research group website.

  • Epidemiological hypothesis testing using a phylogeographic and phylodynamic framework

  • Parallel Evolution in the Emergence of Highly Pathogenic Avian Influenza A Viruses

  • A dynamic nomenclature proposal for SARS-CoV-2 lineages to assist genomic epidemiology.

  • A computationally tractable birth-death model that combines phylogenetic and epidemiological data

  • Crowding and the shape of COVID-19 epidemics.

  • Clinical, immunological and virological characterization of COVID-19 patients that test re-positive for SARS-CoV-2 by RT-PCR.

  • Evolution and epidemic spread of SARS-CoV-2 in Brazil.

  • Identification of Common Deletions in the Spike Protein of Severe Acute Respiratory Syndrome Coronavirus 2.

  • More
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