I designed and implemented a Python- and R-based pipeline to identify differentially expressed genes (DEGs) for a successfully funded USDA DOE Bioenergy grant. The genes identified by this pipeline will be the basis of further large-scale projects for SNP discovery to understand genetic control of complex traits in loblolly pine. I cleaned, re-analyzed and collated SNP and DEG data to identify a preliminary set of candidate genes, and wrote a manuscript describing those results that is in preparation for submission. I mentored a graduate student with a background in forest ecology in bioinformatics analysis.

I funded this position by writing a successfully funded grant for a USDA NIFA postdoctoral fellowship ($150k). I designed and implemented a Python-based pipeline to analyzed genomic data from more than 300 samples to identify candidate SNPs for a disease-resistance gene in loblolly pine. The SNPs I identified will be followed-up with large-scale experiments to develop assays to screen loblolly pine families for disease-resistance traits. I wrote and submitted a manuscript describing those results, and contributed a chapter on the genomics of disease-resistance to a book on the loblolly pine genome. As part of my fellowship experience, I also taught guest lectures on genomics and bioinformatics in undergrad and graduate courses, and presented my results to scientists from the forestry industry, government agencies, and academia. I mentored two international graduate students in bioinformatics analysis, and, as side projects, I assembled and annotated the genomes of Populus nigra (black poplar) and Argopecten irradians (bay scallop).

For my Ph.D. research at the University of Utah, I worked on a variety of genome annotation projects, which gave me experience in collaborating with teams from a variety of fields. I co-wrote a popular guide (536 citations) to genome annotation that was published in Nature Reviews Genetics. I annotated the genomes of Megachile rotundata (alfalfa-leafcutting bee), Cephus cinctus (wheat stem sawfly), Cardiocondyla obscurior (myrmicine ant), Cronartium quercuum f.sp. fusiforme (fusiform rust fungus), Apis dorsata (giant honey bee), and Trichomonas vaginalis (human STI pathogen). I mentored visiting students and new graduate students and co-taught workshops on genome annotation.

During my one year working with Bryan Carstens at LSU, I implemented and validated a phylogenetics software pipeline in Java based on a design by Professor Carstens. As part of this project, I adapted open-source libraries. I wrote scripts to validate the pipeline, and wrote a manuscript with Professor Carstens to publish the software in Molecular Ecology Resources.