• Evolution, structural diversity, and interactions of transmembrane proteins. We develop methods to predict inter- and intramolecular contacts and to delineate membrane protein folds from amino acid sequences based on patterns of helix-helix interactions. 
  • Computational analysis of dynamic, tissue- and isoform-specific networks of protein interactions. We investigate how genetic aberrations caused by cancer re-wire molecular networks. In particular, we are interested in the impact of disease mutations on the interactions of membrane proteins.
  • Development and optimization of in-silico methods for the prediction of tumor antigen-specific T-cell receptors
  • Bioinformatics of viruses. We investigate longitudinal evolution of RNA viruses and develop methods to predict the course and outcome of infections. We also study the expression of Human Endogenous Viruses (HERV) in health and disease.
  • Evolution and structure of mRNAs. We investigate structural constraints imposed on mRNA evolution by secondary structural elements and develop databases and prediction methods to describe the variety of mRNA structures in RNA viruses.
  • Chaperonin-assisted protein folding. What are the common features of chaperone substrates and why?
  • Cancer bioinformatics, including the analysis of copy number alterations