Recently, impressive sequencing endeavors have made available whole-genome sequences for a number of species. One of the stated goals of these projects is to better our understanding of modern organisms through comparative analyses. The rationale is that insights into the dynamics of the evolution of genomes can help ascertain the underlying mechanisms influencing these organisms. In fact, studying the similarities between distant genomes can highlight some of their crucial components. The main focus of my group is to explore functional genomics questions that can benefit from a comparative perspective. The topics covered include: the evolution of regulatory sequences, the role of transposable elements in host gene regulation and the impact of genome rearrangements in evolution and in cancer.