Mining fungal genomes for novel drugs- Predictive Machine Learning models & metatranscriptomics to QC & expedite RNAseq- Codon transition probability gene scoring for gene expression prediction- Primer design tool for cloning whole biosynthetic gene clusters

Bioinformatics and data science to make microbes that replace synthetic Nitrogen fertilizer- Predictive modeling of lab to field product performance.- Compositional analysis of competitive bacterial colonization and microbiomes. Plant-microbe interactions.- Revamped bacterial and plant RNA-seq pipeline and analyses. RNA-seq analyses of plant and microbial data.- Performed various analyses of field data such as crop yield, N content, bacterial colonization, as well as power analyses and experimental design thereof before Pivot built up a field data science team (2019 - early 2020).- Introduced compositionally-robust methods for microbiome and competitive bacterial abundance assays.- Provide statistical advice and analyses for enzymatic assays, metabolic characterization assays, and other in vitro data.

- Statistical Genetics: QTL mapping in mice of a modifier locus of the major cardiac development transcription factor Tbx5; WGS family-based rare variant search for Huntington’s Disease (HTT) modifier loci; GWAS and candidate gene association of cognitive delays post-treatment for pediatric brain cancer.- Tool building: cardiomyocyte maturation drug screen; power simulations of neuron survival; human gut metagenomic pipeline built using Nextflow; (Human Papilloma Virus) HPV typing by phylogenetic placement of short sequence reads.- Other projects or data types: bulk and single-cell RNA-seq; targeted gene expression assays; alternative gene splicing; CLIP-seq; ATAC-seq; ChIP-seq.

Genomics of dog ancestry and health.- Developed algorithms for reference panel based geographic placement of village dogs.- Rewrote code for generating village dog world maps to improve it and make it more robust.- Improved dog weight predictions by incorporating weight adjustments for breed and for inbreeding.

- Taught R portion of the Bioinformatics course for upper level undergraduates and masters students.- Added Git to the course materials.- Transferred all assignment handling to GitHub repositories.

- Developed a heterogenous HMM (Hidden Markov Model) for genotyping QTL populations and applied it to a population of 545 inbred lines, each with 12 chromosomes and 296,093 DNA variants.- Used sparse/regularized regression to infer single locus and epistatic QTL for 25 traits with up to 307,340 potential QTL, in a population of 545 BC2 and BC3 inbred lines.- Modified an existing codon model to lower the number of free parameters to better suit our data.- Used 5 different phylogenetic codon models to test a number of hypotheses for ~14,000 genes in 6 species.- Modeled gene expression evolution for ~20,000 genes in four species using Brownian Motion (with one and two rates) and Ornstein-Uhlenbeck models to assess whether a gene is evolving under stabilizing selection versus other modes of evolution such as an accelerated change in expression.- Conducted a phylogenetic-GWAS study of salt stress and regional adaptation in tomato and its 16 closest relatives to find crop improvement genes. This work comprises 51-80 genotypes (3-5 per species) and thousands of plants.- Investigated the evolution of a tomato starch branching enzyme and its potential role in fruit sweetness through a combination of phylogenetic modeling, breeding genetics, and metabolite and enzymatic activity assays.- Conducted a cold stress growth dynamics study in 10 tomato species, including transcriptomes of 3 of the species.

Researched the biomechanics of Catasetum pollinarium expulsion and redirection, and the molecular phylogenetics of subtribe Catasetinae.

While in graduate school I taught eight semesters as a Teaching Fellow. I taught the following courses: Plant Biology, Genetics and Genomics, Plant Developmental Genetics, and Feeding Yourself -- Feeding the World.

Tested microarray data capture and management software.Wrote the software manual.Kept the company abreast of developments in biological research.

I worked on the development of a nanomotor. The aim of this nanotechnology project was to engineer the use of an F0F1-ATPase as a motor. I was in charge of protein expression, from fermentor grown E. coli and extremophile bacteria (halophiles and thermophiles), and for protein purification.

Teaching Assistant for Principles of Physical Chemistry.