Study systems include
Usually RNA viruses, most notably dengue virus, influenza virus, and rabies virus, although l also publish on DNA viruses and occasionally bacteria.
Lam TT-Y, Ip HS, Ghedin E, et al. (2012). Migratory flyway and geographical distance are barriers to the gene flow of influenza virus among North American birds. Ecol.Lett. 15, 24-33.
Holmes EC. (2011). What does virus evolution tell us about virus origins? J.Virol. 85, 5247-5251.
Holmes EC, Ghedin E, Halpin RA, et al. (2011). Extensive geographical mixing of human H1N1/09 influenza A virus in a single university community. J.Virol. 85, 6923-6929.
Kitchen A, Shackelton L & Holmes EC. (2011). Family level phylogenies reveal modes of macroevolution in RNA viruses. Proc.Natl.Acad.Sci.USA 108, 238-243.
Simon-Loriere E & Holmes EC. (2011). Why do RNA viruses recombine? Nat.Rev.Micro. 9, 617-626.
Holmes EC. (2010). The comparative genomics of viral emergence. Proc.Natl.Acad.Sci.USA. 107, 1742-1746.
Holmes EC. (2009). The Evolution and Emergence of RNA Viruses. Oxford Series in Ecology and Evolution (OSEE). Oxford University Press, Oxford.
(From a total of 324 peer reviewed papers, >18,000 total citations, h-index = 69)
My research integrates ideas from a number of different fields, most notably evolutionary genetics, virology, infectious disease epidemiology, and bioinformatics. I am currently concentrating on three main areas, mainly using RNA virus study systems.
Virus Evolutionary genetics
I am investigating questions such as:
- The evolutionary factors that underpin the process of cross-species virus transmission (i.e. viral emergence).
- The roles played by mutation, natural selection, recombination, and gene flow in shaping patterns of genetic diversity on RNA viruses.
- Collaborative experimental studies on the intra- and inter-host evolution of influenza and dengue viruses.
Virus Comparative genomics
My work in this area includes:
- Understanding the factors that have generated the diversity of genome organizations observed in RNA viruses.
- Revealing the origins of viruses and particularly how they relate to the evolution of mutation rates.
Virus Molecular epidemiology
Much of my research in this area fits within the emerging disciplines of phylodynamics and phylogeography.
- Understanding the patterns and processes of evolutionary change in specific viruses including influenza, dengue and rabies.
- Determining the major phylodynamic patterns exhibited by human viruses.