Dissertation research on the evolution of natural antibiotics and their targets.

• Developed a scalable Nextflow pipeline on HPC to estimate origination dates of bacterial gene families.
• Created an R package and novel algorithm for extracting dated branches from phylogenetic reconciliations.
• Built GAM, GLM and GAMLSS models to evaluate the effect of gene and branch type on rates of evolution, transfer and duplication of gene families.
• Applied t-SNE to reduce dimensionality of drug interactions and evaluate network topology in the evolution of metabolic and protein interaction networks.

• Prepared LC-MS/MS proteomic samples of Aurantiochytrium limacinum across life-cycle stages.
• Implemented differential expression analysis for proteomics (SVA, limma) and publication-quality figures.
• Ran nf-core pipelines (RNA-seq, differential abundance, taxprofiler) on RNA-seq data.

• Instructed an upper-level undergraduate class of 120 students.
• Developed labs on GitHub Classroom and AWS covering genomics, phylogenetics, RNA-seq and algorithmic thinking.

• Developed an Opentrons OT-2 robotic pipetting protocol in Python for high-throughput drug interaction testing.
• Developed colorimetric assays and flow cytometry protocols to determine cell viability.

• Measured and analyzed yield and height of quinoa cultivars in a field site in Teruel, Spain.
• Quantified seed area, size and roundness with ImageJ and analyzed amino acid, saponin, fiber and iron data.