Bioinformatics

Engineered a custom cfDNA analysis pipeline for somatic variant calling, navigating challenges such as low coverage. Analyzed tumor-bearing mouse samples to evaluate drug-induced increases in ctDNA abundance, providing support for evaluating the efficacy of a candidate liquid-biopsy enhancement drug.

Executed comprehensive single-cell RNA-seq analysis using Seurat and Harmony. Characterized novel epithelial and immune cell subtypes, assessed differential expression in response to COVID-19 infection and vaccination, and validated cell-type distributions using external datasets from CELLxGENE. Investigated chemokine-driven recruitment mechanisms, supporting research on immune cell infiltration into breast milk.

Identified genes linked to the inception of bioluminescence via dN/dS analysis, time series analysis, and set theory. Reconstructed DNA MSAs from protein alignments and transcriptomes to supply the nucleotide context a published pipeline lacked. Automated a transcription assembly pipeline.

Generated AlphaFold structures for a set of assay-associated protein mutations, performed structural analysis using KNN clustering and local RMSD visualization, discovered mutation-driven structural patterns correlated with assay scores, and identified variant combinations for further validation.