My research program is focused on understanding the genome level determinants of the diversification between evolutionary lineages. The approach that I use towards this end is computationally based and consists of the comparative analysis of large-scale genomic sequence, expression and functional data sets. This approach is facilitated by the accumulation of genome-scale data sets and the continuing development of the computational applications and infrastructure needed to exploit such data. Ultimately, I hope to integrate our understanding of how evolutionary forces play out at distinct levels of biological organization. More specifically, I am interested in understanding the nature of evolutionary innovations that have led to the emergence of complexity in eukaryotic lineages. I currently explore three distinct research areas relating to the evolution of eukaryotic genome complexity: i-the contributions of transposable elements to host gene regulatory and protein coding sequences, ii-the tempo and mode of gene regulatory and expression divergence and iii-convergent evolution of gene function.