Katie Atkins (BSc MSc PhD)

Chancellor's Fellow & Reader


I work on Evolutionary Epidemiology. My work focuses on understanding the dynamics of infectious disease through modelling and phylogenetics. 

My ERC Starting Grant uses quantitative tools to understand HIV infection immediately after exposure. Our recent work published in Science found that more genetic variants are transmitted during the early stages of infection. Ongoing work is trying to understand why some routes of transmission are incredibly permissive to HIV infection despite showing similar genetic bottlenecks as those less permissive, and whether this can be explained by events happening in the first week after exposure. We integrate mathematical modelling with phylogenetics to understand processes that cannot be monitored directly.

My work funded by the Wellcome Trust is understanding how drug resistant bacteria are transmitted between people, and how this is affected by vaccines. Specifically, we are modelling a cluster randomised trial for pneumococcal conjugate vaccine in Vietnam. For this, we are using mathematical modelling tools in addition to phylogenetic analysis


BSc (Mathematics), MSc (Mathematical Biology), PhD (Biological Sciences)

Postgraduate teaching

Course Director of Infectious Disease Epidemiology, a core module on the MSc Epidemiology 

Open to PhD supervision enquiries?


Areas of interest for supervision

PhD Supervisor on

  • Precision Medicine Programme (MRC)
  • Hosts, Pathogens, and Global Health (Wellcome)
  • Edinburgh Clinical Academical Track (Wellcome)

PhD students

  • Dr Germander Soothill (ECAT Wellcome)
  • James Baxter (MRC Precision Medicine)
  • Emma Pujol-Hodge (HPGH, Wellcome) 


  • Julián Villabona-Arenas (ERC, LSHTM)
  • Hannah Lepper (Wellcome)