Primary AppointmentPublic Health Sciences
MSB-6131F; West Complex, 1300 JPA
Charlottesville, VA 22908
Genomics, Molecular Evolution, Algorithm Design and Analysis
My research is focused on study of genome variation and genetic diversity, and its consequences on species health and survival. I am interested in local changes consisting of substitutions and small indels that alter a few base pairs, as well as large-scale changes that consist of larger indels, rearrangements and copy number variations. My efforts are concentrated in the following areas: 1. Identification of variants: We are developing methods to identify and map variants (SNPs, indels, and large-scale rearrangements) from large-scale sequencing datasets. This includes identification of variants in species with a haploid representation (reference genome), species with multiple representations, as well as species where we lack a reference genome. 2. Study of genetic diversity: Genome-wide assessments of genetic diversity provide a powerful analytical tool that informs of the similarities, differences, origins and the evolutionary history of a species. We apply methods developed in (1) to identify variants among and between members of several species. The observed allele frequencies are then used to calculate metrics of population differentiation such as the fixation index, and can be correlated with phenotypes to identify adaptations, or used to detect the causative mutations for a genetic trait. 3. Cancer Genomics: Tumor sequencing experiments can provide insight into the changes driving tumorigenesis. The current sequencing platforms provide (given adequate coverage of the genomes) the high level of sensitivity and accuracy required to properly characterize the differences between a tumor/normal pair. We use the methods developed in (1) to view the unique somatic mutations accrued by a tumor, and germline mutations in the matched normal tissue. We are currently applying our methods to understand how genomic changes contribute to the pathogenesis of the T-cell form of Large Granular Lymphocyte (LGL) leukemia in collaboration with the Loughran lab at University of Virginia.