CURRENT RESEARCH
I am a computational evolutionary biologist with expertise in comparative genomics and other genetic analysis pipelines. My research approach involves designing custom mathematical models consistent with alternative hypotheses and applying them to genomic data sets. The application of these models will ultimately allow biologists to ask broader conceptual questions about evolution and the mechanisms involved on various levels of biological organization. These complex models are designed to contain parameters that are informative about the underlying biological processes, can be differentiated using the techniques of model selection, and are better at answering more fundamental questions than standard statistical methods.
My current postdoctoral work is on modeling the unusual process of DNA rearrangement in a model ciliate species, Oxytricha trifallax. Oxytricha trifallax is a stichotrich ciliate, that has a germline micronucleous and a somatic macronucleous made up of hundreds of thousands of nanochromsomes, most of which only contain a single gene. Oxytricha trifallax is particularly unique because it has a large number of genes that are "scrambled" and require rearranged during development following sexual reproduction. I am working on building and testing models to systematically describe the process of rearrangement. To do this, I am utilizing long-read PacBio data that reveal intermediate genetic molecules over various time points during development.
During my PhD, I explored the mechanisms that lead to pathway diversification between species. The mechanisms of interest are ones that lead to retention of duplicated genes. While dosage balance constraints are acting on duplicated genes after whole genome duplication events, mutation and selection may drive these duplicated genes to undergo subfuctionalization and neofunctionalization. One of my PhD projects explored the myostatin pathway in salmonids and how specificity of the interactions between functional partners may have changed as the pathway duplicated twice. I also sought to address if the pathway has diversified, and how diversification could potentially have occurred due to various processes as selection has acted on these whole genome duplication events.
​Duplicated genes are an important source of opportunities for evolution to occur. Another one of my PhD projects got at more specific models of the mechanisms and driving forces that cause these genes to be retained. Retention of genes following consecutive whole genome duplication events in Salmonids show an unexpected trend; gene duplication from one event seems to be independent of the retention state from the previous event. During my PhD, I built nested models for various hypotheses to test against fish and plants who have had recent whole genome duplications to solidify our understanding of the underlying process that leads to these results.
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In general, modeling in the biological sciences is a powerful tool. I am interested in how modeling can be applied to other areas of biology as well. For instance, modeling can aid in disease prevention and treatment, as well as conservation and diversity ecology research. For example, building and applying such models with appropriate parameters can allow us to have a stronger understanding of how urbanization and geographic mosaics influence population fragmentation and species extinction. Some models could be borrowed from existing computational biology models by adjusting the parameters to make them more applicable and good representations of the underlying process.
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Additionally, I am especially interested in using game theory models to understand the trade offs between different evolutionary strategies.
