Lin Du

CHROME improves regulatory genomics predictions by integrating physically validated chromatin interactions into graph models, enhancing accuracy and interpretability for ChIP-seq, eQTL, and variant pathogenicity.

The paper develops a polymer simulation framework to distinguish specific-folding interactions from polymer compaction in E. coli, revealing SFIs shape chromosome organization and gene expression.

This study uses 3D polymer models to show that LAD-lamin interactions influence chromatin organization and induce super long-range chromatin contacts in mouse cells.

ChromPolymerDB reconstructs single-cell 3D chromatin structures from bulk Hi-C data and provides a database for analyzing chromatin conformation across 50 human cell types.

The paper develops a method to analyze Hi-C and eQTL data to understand how 3D chromatin structures influence gene regulation through non-random interactions and ensemble modeling.

This study uses a minimal model and ACME method to show that Cro2 binding at OR3 and CI2 at OR1 affect lysogeny stability during prophage induction.

The paper introduces an algorithm that uses 3D chromatin interactions to identify functional non-coding regulatory variants and their target genes, reducing false positives in eQTL analysis.