Computational genomics in yeast and human: genes, regulation, evolution
The recent wealth of genome sequence information is enabling powerful new approaches for understanding principles of genome biology and evolution. In particular, our group has focused on genome-wide methods for the systematic discovery of genes, regulatory motifs, and evolutionary mechanisms. We have applied these to the analysis of the complete yeast and human genomes, based on their comparison with multiple related genomes.
Our work led to a systematic re-annotation of the yeast gene set, and more recently of the human gene set, affecting thousands of genes, and leading to the discovery of hundreds of new genes. We also carried out a systematic de novo discovery of regulatory signals in both genomes, leading to the discovery of most previously known motifs, and novel motifs involved in pre- and post-transcriptional regulation and microRNA regulation. Finally, we have shown that a whole-genome duplication has marked the ancestry of the yeast and fish genomes, allowing us to study the emergence of new functions in duplicated genes, the evolution of regulatory motifs and protein interaction networks.