We pursue three main lines of research:
- Evolutionary innovation in gene coding sequences. The repertoire of human genes is a mosaic of genes of very ancient origin, present in all eukaryotes, and other genes that have a more recent origin. We have dated the appearance of the genes in the human genome across the eukaryotic phylogeny, and shown that the more recent genes show accelerated evolutionary rates. We have performed several studies to undersand the mechanisms of formation of new genes.We are also interested in understanding the contribution of short DNA motif and single amino acid tandem repeats to taxon-specific innovations.
- Gene transcription networks. Gene upstream regions are rich in motifs involved in the regulation of transcription. We have developed different methods to predict regulatory motifs (PROMO, PEAKS), using pathway information and the conservation of motif arrangements across many different human and mouse genes. We have identified a large number of novel regulatory motifs that are likely to be important for tissue-specific gene expression regulation.
- Prediction of virus-host interactions. We have used sequence profile-based searches to capture distant gene homology between virus and human and mouse genomes, indicating events of horizontal gene transfer between host and pathogen. The identification of conserved residues in multiple alignments has led to the prediction of virus-host protein interactions in the context of immune response pathways.