This project is concerned with fundamental computational research in molecular evolution. It has two main focus areas:1. Molecular evolution of infectious diseaseThe majority of infectious diseases with public health relevance are caused by RNA viruses. Examples are HIV/AIDS, influenza, dengue fever, or measles. RNA viruses mutate rapidly and frequently evolve on a time scale of weeks to months. In this project, we aim to develop theoretical and computer models of how RNA viruses evolve as they spread through a host population, and we also aim to develop analytic methods to infer past (and possibly future) evolutionary dynamics from samples of viral sequences.2. Biophysical mechanisms of genetic diseaseAll genetic diseases have at their origin specific biophysical mechanisms; some part of the molecular machinery is not correctly specified in the genetic material and as a consequence mis-functions in some way. By analyzing genome-wide patterns of molecular evolution in many species, we aim to identify the most common mechanisms that lead to genetic disease. Preliminary evidence suggests that protein misfolding and aggregation are among the most common causes of genetic disease, and that all cellular organisms experience strong selection pressures to avoid misfolding and aggregation.
