Short tandem repeats (STRs) are ubiquitous throughout the human genome and routinely vary within human populations but have largely been excluded from genome-wide analyses of variant contributions to human phenotypes. In my thesis work, I and my collaborators demonstrate that current bioinformatic advances now allow for the inclusion of STRs in suc...
The three-dimensional (3D) organization of the human genome plays a crucial role in gene regulation, influencing interactions between genes and regulatory elements. Despite significant progress in genomics, the diversity of 3D chromatin contact patterns across human populations remains underexplored. This dissertation uses machine learning to predi...
Published in Molecular and biochemical parasitology
We developed microsatellite markers to use in studying the population genetics of the trematode Alloglossidium renale, a fluke with a precocious life cycle where sexual maturation occurs in a grass shrimp. Among 21 tested loci in a Mississippi population sample, 14 were polymorphic, 12 of which significantly deviated from Hardy-Weinberg Equilibrium...
The northeastern regions of Siberia and the North American Arctic are some of the last regions of the world to be inhabited by humans; there, sophisticated technologies were developed for hunting marine mammals. Continued migration waves of ancient Western Eurasians and ancient East Asians into northeastern Siberia led to the early formation of the...
Understanding the evolutionary past using genetic data requires the development and application of statistical tools and coalescent models that accurately capture the underlying evolutionary processes. Migration and dispersal are important evolutionary forces which leave signatures in the genome, but the signal of these processes can be challenging...
Sheep, which were domesticated in the Fertile Crescent about 10,000-12,000 years ago, have been a key resource for human populations ever since. We, however, know little about how they were domesticated, and what happened to them after their initial expansion from their domestication area into all corners of Eurasia and later Africa and the America...
Determining the relative importance of sexual and asexual reproduction is critical for determining how genetic diversity is partitioned within and among populations. Macroalgae exhibit reproductive system variability, with many species capable of both sexual and asexual reproduction. Thus, rates of fragmentation (asexual) versus sporic recruitment ...
In this thesis, we present MOSHPIT (Multi-allelic Outbred Strain Haplotype Phasing and Inference Tool), a novel framework for analyzing genomic datasets of outbred populations. MOSHPIT integrates different variant mutation models into a single Hidden Markov Model (HMM), enabling the simultaneous utilization of single nucleotide polymorphisms (SNPs)...
Fishes are the most abundant vertebrates in the animal kingdom. They play important biological and ecological roles. Various anthropogenic and climatic factors have led to the decline of natural population and increased the risk of extinction. CBD emphasized the conservation of biodiversity at all levels from genes to ecosystems. However, little at...
