Bioinformatics
Evaluating the Efficacy of a Liquid Biopsy Enhancement Drug
2025Engineered 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.
scRNA-seq Characterization of A Novel Epithelial Cell Type in Breast Milk
2024Executed 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.
Investigating Genes Related to Endogenous Biosynthesis of Luciferin in Cypridinid Ostracods
2023Identified 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.
Discovering Structure–Function Links in PCSK9 Variants
2023Generated 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.