Development of novel computational tools to decipher genome evolution

As Theodosius Dobzhansky famously stated, ¿nothing in biology makes sense except in the light of evolution¿. This is an often under appreciated truth in the emerging field of bioinformatics. With the availability of many completely sequenced genomes, we now can attempt to understand genome evolution and relate it to the evolution of organisms. In the past several years it became clear that different genes in the same genome have different histories, and therefore one has to be careful in inferring organismal evolutionary history from the analyses of just one or several genes. I am proposing to develop and improve tools for comparative genome analyses. In particular, I will work on the development of better models and visual diagrams for representation of evolutionary history of genes in the genomes. I will also explore if there are genome characteristics (other than genes) that might be useful for understanding genome evolution. Many diseases are caused by microorganisms and understanding the evolutionary dynamics of their genomes is important for medical practice. In particular, unraveling molecular characteristics of the genomes that were essential for a pathogenic organism to conquer its ecological niche will ultimately help to select appropriate drug targets and aid in monitoring of emerging pathogens.