I work on the fundamental problem of comparative genomics: the determination of the origins and evolutionary history of the nucleotides in all extant genomes. My work incorporates various aspects of genomics, including the reconstruction of ancestral genomes (paleogenomics), the modeling of genome dynamics (phylogenomics and systems biology) and the assignment of function to genome elements (functional genomics and epigenomics).

In addition to working on algorithms and mathematical foundations for comparative genomics, I also work on genome projects and perform large scale computational analyses. I have been a member of the mouse, rat, chicken and fly genome sequencing consortia, and the ENCODE project.

My research draws on tools from discrete mathematics, algebra and statistics. I am also interested in questions in these subjects that are motivated by biology problems.