Hi-C

GEM-Finder: dissecting GWAS variants via long-range interacting cis-regulatory elements with differentiation-specific genes

GEM-Finder identifies disease-associated CREs by integrating transcriptomic, epigenomic, and chromatin interaction data during endothelial differentiation, revealing 7.6 times more associations than conventional methods.

ScHiCAtt: Enhancing Single-Cell Hi-C Resolution Using Attention-Based Models

ScHiCAtt improves single-cell Hi-C resolution using attention mechanisms, outperforming existing methods across different organisms and downsampling conditions.

Response eQTLs, chromatin accessibility, and 3D chromatin structure in chondrocytes provide mechanistic insight into osteoarthritis risk

The paper identifies OA risk genes by integrating eQTLs, chromatin accessibility, and 3D chromatin structure in human chondrocytes, revealing 13 putative risk genes, 10 of which are novel.

Widespread 3D genome reorganization precedes programmed DNA rearrangement in Oxytricha trifallax

The paper maps 3D genome organization in Oxytricha trifallax to understand its role in programmed DNA rearrangement during development.

Uncovering topologically associating domains from three-dimensional genome maps with TADGATE

TADGATE identifies TADs from sparse Hi-C maps, enhances their structure, and reveals functional elements and cell-type-specific regulatory mechanisms.

Global and genetic regulation of gene expression in human endothelial and vascular smooth muscle cells

The paper maps epigenetic and genetic regulation in human endothelial and vascular smooth muscle cells, showing strong correlations between gene expression and chromatin features, and demonstrates SNP effects on gene expression through chromatin loops.

A universal tool for chromatin loop annotation in bulk and single-cell Hi-C data

Polaris is a tool for chromatin loop annotation in bulk and single-cell Hi-C data that outperforms existing methods across different datasets and conditions.

3D genome organization during TGFB-induced transcription requires nuclear microRNA and G-quadruplexes

The paper shows that nuclear miR-9 is required for chromatin features and promoter-super-enhancer looping during TGFB1-induced transcriptional activation.

A Constitutive Heterochromatic Region Shapes Genome Organization and Impacts Gene Expression in Neurospora crassa

The paper investigates how a constitutive heterochromatic region in Neurospora crassa affects genome organization and gene expression by altering chromatin structure and nuclear positioning.

The Hitchhiker's Guide to Sequencing Data Types and Volumes for Population-Scale Pangenome Construction

This study evaluates optimal long-read data types and volumes for chromosome-level haplotype-resolved pangenome assembly, providing guidelines for sequencing platform selection and coverage.

Androgen stimulation rapidly reorganizes temporal 3D genome and epigenome states to trigger AR-mediated transcription in prostate cancer.

This study investigates how androgen stimulation reorganizes 3D genome and epigenome states in prostate cancer cells to activate AR-mediated transcription.

Integrative analysis of the 3D genome and epigenome in mouse embryonic tissues

The paper maps chromatin interactions in mouse fetal tissues and links them to gene expression and disease risk variants in humans.

Pervasive RNA Binding Protein Enrichment on TAD Boundaries Regulates TAD Organization

This study identifies RNA binding proteins (RBPs) as key regulators of TAD organization through their enrichment at TAD boundaries and synergistic interaction with nascent transcripts.

COCOA: A Framework for Fine-scale Mapping Cell-type-specific Chromatin Compartmentalization Using Epigenomic Information

COCOA infers fine-scale chromatin compartment patterns from histone modifications, showing accurate results and cell-type-specific predictions.

A comprehensive catalog of 3D genome organization in diverse human genomes facilitates understanding of the impact of structural variation on chromatin structure

The paper develops a Hi-C analysis pipeline to catalog TADs and loops in human genomes and quantifies the impact of SVs on chromatin structure and gene expression.

VSS-Hi-C: Variance-stabilized signals for chromatin contacts

VSS-Hi-C stabilizes variance in Hi-C data to improve visualization and analysis by transforming read counts into unit variance signals.

CHARMER: detecting and harmonizing high-confidence chromatin interactions across tissues and Hi-C protocols

CHARMER detects and harmonizes high-confidence chromatin interactions across tissues and Hi-C protocols, providing statistically significant, queryable data for downstream analysis.

Telomere interactions and structural variants in ALT cells revealed with TelSPRITE

The paper introduces TelSPRITE to analyze telomere spatial organization in ALT cells, revealing telomere contact patterns and their association with structural variants.

Transient histone deacetylase inhibition induces cellular memory of gene expression and three-dimensional genome folding

The paper shows that transient histone deacetylase inhibition in mESCs induces cellular memory of gene expression and 3D genome folding, with genome architecture maintaining perturbed conformations.

Integrating Chromosome Conformation and DNA Repair in a Computational Framework to Assess Cell Radiosensitivity

The paper develops a computational framework integrating Hi-C data and DNA repair models to simulate radiation effects and assess cell radiosensitivity.

CTCF depletion decouples enhancer-mediated gene activation from chromatin hub formation during cellular differentiation

The paper shows that CTCF depletion disrupts chromatin hub formation but not enhancer-promoter interactions, which still drive gene expression during differentiation.

PRC1 and CTCF-Mediated Transition from Poised to Active Chromatin Loops Drives Bivalent Gene Activation

The paper identifies PRC1 and CTCF's role in forming chromatin loops that maintain bivalent genes in a poised state for activation during differentiation.

Single cell variant to enhancer to gene map for coronary artery disease

This paper links CAD GWAS variants to causal genes in SMCs using single-cell chromatin accessibility and Hi-C data, creating a scV2E2G map for disease mechanism discovery.

Fluctuating chromatin facilitates enhancer-promoter communication by regulating transcriptional clustering dynamics

The paper develops chromatin models to study enhancer-promoter communication, finding that dynamic chromatin structures enhance transcriptional clustering and promote E-P interactions.

3D chromatin maps of a brown alga reveal U/V sex chromosome spatial organisation

The paper maps the 3D chromatin structure of sex chromosomes in the brown alga Ectocarpus, revealing their spatial organization and links to gene expression and sex determination.

JOnTADS: a unified caller for TADs and stripes in Hi-C data

JOnTADS identifies TADs and stripes in Hi-C data across different experimental contexts, improving robustness and computational efficiency.

Chromosome-scale genome assembly of Apocynum pictum, a drought-tolerant medicinal plant from the Tarim Basin

This study presents a chromosome-level genome assembly of Apocynum pictum and identifies drought-responsive genes.

Decoding the Epigenetics and Chromatin Loop Dynamics of Androgen Receptor-Mediated Transcription

The paper investigates how AR-bound CREs influence gene expression through epigenetic changes and chromatin looping, finding that contact frequency with promoters drives expression.

ChromaFold predicts the 3D contact map from single-cell chromatin accessibility

ChromaFold predicts 3D chromatin contact maps from scATAC-seq data, outperforming bulk-based methods and enabling cell-type-specific interaction analysis.

Statistical curve models for inferring 3D chromatin architecture

The paper improves a method for inferring 3D chromatin structure from Hi-C data by introducing a new framework that addresses initialization issues and extends distribution models for contact counts.