Jie Liang

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.

G-SPRI predicts cancer driver events from missense mutations by integrating structural and mutation-specific features using a graph model.

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.

CASTpFold extends the CASTp tool to provide accurate and comprehensive protein surface topography analysis using AlphaFold2 structures and functional annotations.

SPRI predicts the pathogenicity of missense variants and identifies spatially organized mutational clusters linked to cancer and Mendelian diseases.

The paper shows that stochastic signaling is converted into sustained olfactory neurogenesis through spatially restricted self-assembly of progenitor cell neighborhoods in zebrafish.

This paper introduces a minimalistic 3D chromatin polymer model that uses sparse interactions to generate single-cell chromatin conformations consistent with experimental data and reveals insights into chromatin structure and function.

The paper introduces a computational method to reconstruct high-resolution 3D chromatin conformations from population Hi-C data, revealing chromatin structure dynamics during Drosophila embryogenesis.

CHROMATIX reconstructs many-body chromatin interactions from Hi-C data and identifies functional features in transcriptionally active loci.