Education

Ph.D., Pennsylvania State University, USA

Research Interests

Comparative Genomics, Cancer Genomics, Molecular Evolution and Algorithm design & analysis.

Research Description

Research in my laboratory is focused on study of genome variation and genetic diversity, and its consequences on species health and survival. We are 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. Our 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.

Publications

Representative publications:

• Ratan, A., Miller, W., Guillory, J., Stinson, J., Seshagiri, S., & Schuster, S. C. (2013). Comparison of Sequencing Platforms for Single Nucleotide Variant Calls in a Human Sample. PLoS ONE, 8(2), e55089.
• Giardine, B. M., Riemer, C., Burhans, R., Ratan, A., & Miller, W. (2012). Some phenotype association tools in Galaxy: looking for disease SNPs in a full genome. Current Protocols in Bioinformatics / Editorial Board, Andreas D. Baxevanis … [et Al.], Chapter 15, Unit15.2.
• Ratan, A., Zhang, Y., Hayes, V. M., Schuster, S. C., & Miller, W. (2010). Calling SNPs without a reference sequence. BMC Bioinformatics, 11(1), 130.

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.

Representative publications:

• Perry, G. H., Louis, E. E., Ratan, A., Bedoya-Reina, O. C., Burhans, R. C., Lei, R., … Miller, W. (2013). Aye-aye population genomic analyses highlight an important center of endemism in northern Madagascar. Proceedings of the National Academy of Sciences of the United States of America, 110(15), 5823–8.
• Bedoya-Reina, O. C., Ratan, A., Burhans, R., Kim, H. L., Giardine, B., Riemer, C., … Miller, W. (2013). Galaxy tools to study genome diversity. GigaScience, 2(1), 17.
• Miller, W., Hayes, V. M., Ratan, A., Petersen, D. C., Wittekindt, N. E., Miller, J., … others. (2011). Genetic diversity and population structure of the endangered marsupial Sarcophilus harrisii (Tasmanian devil). Proceedings of the National Academy of Sciences, 108(30), 12348–12353.

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.