Rolf (dot) Ypma (at) rivm (dot) nl
Rolf is interested in the way in which genetic and epidemiological data can be used to quantify infectious disease dynamics. This requires knowledge on the mutational processes of pathogens, the within-host dynamics of these pathogens, and the transmission dynamics between cases.
The core of his research is formed by the reconstruction of transmission trees, estimating who infected whom. Although this is traditionally done using only epidemiological data, genetic information can be extremely valuable in reconstructing the tree, especially when both the sampling fraction of cases and the substitution rate of the pathogen are high. He used these techniques to find evidence that highly pathogenic avian influenza is spread by wind, by comparing the direction of transmission to hourly wind directions [1-2].
When genotypes are defined through means other than genetic sequences, full transmission trees can no longer be reconstructed, but meaningful inference is still possible. For example, by analyzing the distribution of genotypic cluster sizes, he showed that spread of tuberculosis in the Netherlands is characterized by superspreading . Such 'coarser resolution' genetic data can also be useful in automatically identifying local outbreaks of a contagious disease, by mining molecular epidemiological databases.
 Ypma RJF et al. J Infect Dis. 2013. 207(5):730-5.
 Ypma RJF et al. Proc Biol Sci. 2012. 279(1728):444-50.
 Ypma RJF et al. Epidemiology. In press.