Garyoung Gary Lee

Histone modifications define distinct nucleosome positions in cell-free DNA

This paper identifies histone modification-associated nucleosome positions in cfDNA that correlate with tumor fraction and cancer state across multiple cancers.

Transcription Factor Subtype Governs Response and Resistance to DLL3-Directed T-Cell Engagement in Small Cell Lung Cancer

This study investigates how transcription factor subtypes in small cell lung cancer influence response and resistance to DLL3-targeted therapy, revealing subtype-specific mechanisms of resistance.

SNAP: Streamlined Nextflow Analysis Pipeline for Immunoprecipitation-Based Epigenomic Profiling of Circulating Chromatin

SNAP improves classification performance for cell-free chromatin data while maintaining data retention through optimized quality filters and modular design.

A chromatin fiber model explains cell-free DNA fragmentation signatures of active regulatory elements

The paper infers enhancer activity from cfDNA fragmentation patterns and proposes a chromatin fiber model to explain these signatures.

FROG Analysis Ensures the Reproducibility of Genome Scale Metabolic Models

The paper introduces FROG analysis to standardize reproducibility assessments of genome-scale metabolic models, resulting in full reproducibility of all tested models.

Prediction of metabolites associated with somatic mutations in cancers by using genome-scale metabolic models and mutation data

The paper develops a computational workflow to predict metabolite-gene-pathway associations in cancers using genome-scale metabolic models and mutation data, showing significant associations with specific somatic mutations.

De novo production of an antitumor precursor actinocin and other medicinal molecules from kynurenine pathway in Escherichia coli