Eddie Holmes, PhD

Member, Center for Infection and Immunity
Professor in Biology, Pennsylvania State University
Eberly College of Science Distinguished Senior Scholar
Phone: 814.863.4689
Email: ech15@psu.edu


  • University of London, UK (University College), B.Sc. in Anthropology, First Class Honours, 1986.
  • University of Cambridge, Department of Zoology, UK, Ph.D., Thesis entitled ‘Pattern and Process in the Molecular Evolution of the Order Primates.’ Supervisor: Dr. AE Friday, 1990.
  • University of California, Davis, Department of Genetics, Postdoctoral research with Dr. CH Langley, 1990-1991.
  • University of Edinburgh, UK, Postdoctoral research (MRC funded) with Dr. AJ Leigh Brown, Institute of Cell, Animal and Population Biology, 1991-1993.
  • University of Oxford, UK, Postdoctoral research (SERC funded) with Prof. PH Harvey, FRS, Department of Zoology,1993-1994.
  • University of Oxford, UK, Wellcome Trust Fellow in Biodiversity Research, 1994-1997.
  • Fellow by Special Election of St. Catherine's College, Oxford, UK, 1994-1998.
  • Royal Society University Research Fellow, University of Oxford, UK, 1994-2002.
  • Tutorial Fellow in Biological Sciences, New College, Oxford, UK, 1999-2004.
  • University of Oxford, UK, University Lecturer in Evolutionary Biology, 1999-2004.
  • The Pennsylvania State University, University Park, PA, (Full) Professor of Biology, 2005-Present.
  • Fogarty International Center, National Institutes of Health, Bethesda, MD, Affiliate member,  2006-Present.
  • The Pennsylvania State University, University Park, PA, Eberly College of Science Distinguised Senior Scholar, 2007-Present.


My research integrates ideas from a number of different fields, most notably evolutionary genetics, virology and the epidemiology of infectious disease. I am currently concentrating on three main areas, using RNA virus study systems.

Evolutionary Genetics

I am investigating questions such as:

  • The roles played by mutation, natural selection, recombination, and gene flow in shaping patterns of genetic diversity on RNA viruses.
  • The evolutionary factors that underpin the process of cross-species virus transmission (i.e. of viral emergence).

Comparative Genetics

My work in this area includes:

  • Understanding the factors that have generated the diversity of genome structures and organizations observed in RNA viruses.
  • Revealing the origins of RNA viruses and particularly how they relate to the early 'RNA-protein' world.

Molecular Epidemiology

Much of my research in this area fits within the emerging discipline of phylodynamics.

  • Understanding the patterns and processes of evolutionary change in such key human viruses as influenza and dengue.
  • Collaborative experimental studies on the intra- and inter-host evolution of influenza viruses and parvoviruses.


  • Holmes EC. (2009). The Evolution and Emergence of RNA Viruses. Oxford Series in Ecology and Evolution (OSEE). Series edited by PH Harvey & RM May. Oxford University Press, Oxford. (http://ukcatalogue.oup.com/product/9780199211135.do).
  • Holmes EC. (2009). The evolutionary genetics of emerging viruses. Annu.Rev.Ecol.Evol.Syst. 40, 353-372.
  • Holmes EC. (2008). The evolutionary history and phylogeography of human viruses. Annu.Rev.Microbiol. 62, 307-328.
  • Rambaut A, Pybus OG, Nelson MI, Viboud C, Taubenberger JK & Holmes EC. (2008). The genomic and epidemiological dynamics of human influenza A virus. Nature 453, 615-619.
  • Duffy S, Shackelton LA & Holmes EC. (2008). Rates of evolutionary change in viruses: Patterns and determinants. Nat.Rev.Genet. 9, 267-276.
  • Aaskov J, Buzacott K, Thu HM, Lowry K & Holmes EC. (2006). Long-term transmission of defective RNA viruses in humans and Aedes mosquitoes. Science 311, 236-238.

Click here to see more publications.