Research Interests
My research interests include phylogenetics, modeling biological data, statistical analysis of molecular data, and parallel computing. I am particularly interested in reconstructing species phylogenies from multilocus sequences. My colleagues and I have developed several phylogenetic methods for estimating the evolutionary history of species.
Research Interest
My lab is using experimental and computational approaches to study genomic changes occurring during mammalian evolution and disease development. The goal is to understand the roles of genomic changes playing in these normal and abnormal processes, as well as the mechanism through which these changes have taken place. The lab has two ongoing projects currently. The first one is to identify bona fide colorectal cancer genes via a novel comparative genomics and oncology strategy – by searching for genes that are commonly altered in human, dog and mouse colorectal tumors. The second project focuses on “the junk DNA” of the human genome, which has allowed us to discover two giant composite retrotransposon-like elements DA and Xiao. We are now conducting experiments to understand the nature of DA/Xiao and to explore their potential application in medicine and research.
Research Interest
The long-term goal of our research is to understand the information encoded in the DNA to the extent that we can accurately predict properties of an organism, including its responses to external stimuli, from its genomic sequence. A common approach currently used is to find all genes and open reading frames in a genome, to predict their function from protein sequence comparisons, and, with the predicted complement of all proteins of the organism at hand, to speculate about its metabolic, environmental, cellular, and morphological characteristics.
Our research centers on discovery and analysis of sequence features not directly associated with genes and proteins, and their possible roles in the organism’s physiology and evolution. We are particularly interested in those sequence features that affect DNA structure and/or promote conformational transitions in the DNA molecule.
Research Interest
Research in our lab is focused on understanding the evolutionary design principles of cellular signaling proteins, such as protein kinases, which are implicated in many human cancers. We are using a combination of computational and experimental approaches to understand how mutations, and other genomic alterations, in these proteins contribute to human diseases.
How do eukaryotic genomes evolve? Our lab is interested in parasite genomics and the biology of genome evolution. The genomes of parasitic eukaryotes are often highly reduced, devoid of recognizable mobile elements and riddled with intracellular and lateral gene transfers. Our approach is to apply molecular, computational and phylogenetic tools to the analysis of dozens of complete parasite genomes. Projects include the development of tools for data mining and data integration including ontology development; comparative genomics and assessment of the phylogenetic distribution of genes. We welcome students interested in working on the bench, at the computer, or both.
