Hi-C

Unraveling three-dimensional chromatin structural dynamics during spermatogonial differentiation

The paper investigates 3D chromatin structural changes during spermatogonial differentiation in pigs using Hi-C, RNA-seq, and ChIP-seq, revealing altered chromatin architecture and gene regulation.

Loop detection using Hi-C data with HiCExplorer

The paper introduces a chromatin loop detection algorithm using Hi-C data with strict candidate selection and statistical testing.

Hi-C detects genomic structural variants in peripheral blood of pediatric leukemia patients

The paper demonstrates that Hi-C can detect structural variants, including translocations, in peripheral blood samples of pediatric B-ALL patients, offering a non-invasive alternative to bone marrow biopsies.

Multi-scale phase separation by explosive percolation with single chromatin loop resolution

The paper models chromatin folding using explosive percolation theory and shows that 80% of loops are needed for 3D condensation across cell lines.

Pairs and Pairix: a file format and a tool for efficient storage and retrieval for Hi-C read pairs

The paper introduces Pairs, a compressed file format for Hi-C read pairs, and Pairix, a tool for indexing and querying these files, along with a quality control tool.

Multiscale 3D Genome Reorganization during Skeletal Muscle Stem Cell Lineage Progression and Muscle Aging

This study maps 3D genome reorganization during skeletal muscle stem cell activation, proliferation, and aging using Hi-C, revealing how chromatin architecture influences gene expression and lineage progression.

GRaNIE and GRaNPA: Inference and evaluation of enhancer-mediated gene regulatory networks applied to study macrophages

The paper introduces GRaNIE and GRaNPA, tools for inferring and evaluating enhancer-mediated gene regulatory networks in macrophages, identifying PURA as a regulator of pro-inflammatory polarization.

Capturing large genomic contexts for accurately predicting enhancer-promoter interactions

TransEPI improves enhancer-promoter interaction prediction by using a Transformer model to capture long-range genomic dependencies across different cell types and chromosomes.

Modeling the Three-Dimensional Chromatin Structure from Hi-C Data with Transfer Learning

This paper introduces TECH-3D, a transfer learning method for 3D chromatin structure prediction from Hi-C data, outperforming previous methods without assuming contact frequency equals Euclidean distance.

Dynamic interplay between structural variations and 3D chromosome organization in pancreatic cancer

The paper investigates structural variations and 3D chromatin organization in pancreatic cancer using SMRT and Hi-C sequencing, revealing their interplay and impact on gene expression and genome stability.

Black chromatin is indispensable for accurate simulations of Drosophila melanogaster chromatin structure.

This paper shows that black chromatin is essential for accurate Drosophila melanogaster chromatin structure simulations, while other methods like loop extrusion or Hi-C data are not required for basic structure reconstruction.

Rec8 cohesin-mediated axis-loop chromatin architecture is required for meiotic recombination

This study shows that Rec8 cohesin forms axis-loop structures in fission yeast meiosis, which are necessary for LinE assembly and meiotic recombination, independent of sister chromatid cohesion.

HolistiC: Leveraging Hi-C and Whole Genome Shotgun Sequencing for Double Minute Chromosome Discovery

HolistIC integrates Hi-C and WGS data to accurately predict double minutes in cancer genomes, resolving ambiguities from overlapping amplicon coordinates.

Flexibility and rigidity index for chromosome packing, flexibility and dynamics analysis

The paper introduces a flexibility-rigidity index (FRI) model to quantify chromosome flexibility using Hi-C data, showing improved accuracy and efficiency compared to Gaussian network model (GNM).

cLoops2: a full-stack comprehensive analytical tool for chromatin interactions

cLoops2 provides a comprehensive tool for analyzing 3D chromatin interactions, including loop detection and annotation, with open-source code available on GitHub.

Epstein-Barr virus nuclear antigen 2 (EBNA2) extensively rewires the human chromatin landscape at autoimmune risk loci

This study shows EBNA2 alters chromatin structure and gene expression at autoimmune risk loci, linking viral infection to genetic risk mechanisms in autoimmune diseases.

The three-dimensional chromatin structure of the major human pancreatic cell types reveals lineage-specific regulatory architecture of T2D risk

The paper uses 3D chromatin maps to identify cell-type-specific regulatory architecture of type 2 diabetes risk by analyzing pancreatic cell types.

HiCArch: A Deep Learning-based Hi-C Data Predictor

HiCArch predicts high-resolution Hi-C contact matrices from 1D epigenomic features, achieving high correlation scores and identifying TADs with 10kb resolution.

The haplotype-resolved chromosome pairs and transcriptome of a heterozygous diploid African cassava cultivar

This study presents haplotype-resolved chromosome pairs and transcriptome of a diploid African cassava cultivar using HiFi sequencing and Hi-C, revealing structural variations and allele-specific expression patterns.

Functional Organization of the Maternal and Paternal Human 4D Nucleome

The paper investigates allele-specific relationships between gene expression and genome structure in human cells using integrated haplotype-resolved data.

Fast alignment and preprocessing of chromatin profiles with Chromap

Chromap provides a fast and accurate method for aligning and preprocessing chromatin profiles, outperforming existing tools in speed while maintaining alignment accuracy.

Genome Compartmentalization with Nuclear Landmarks: Random yet Precise

This study uses polymer simulations to model how the diploid human genome organizes relative to nuclear bodies, showing that co-phase separation explains genome compartmentalization and spatial arrangement.

A Multigraph model of the 3D genome

This paper introduces a multigraph model for 3D genome organization using Hi-C data, revealing known chromatin structures in barley and rice.

ATM-dependent formation of a novel chromatin compartment regulates the Response to DNA Double Strand Breaks and the biogenesis of translocations

The paper identifies a novel chromatin compartment formed by ATM-dependent clustering of damaged TADs, which enhances DNA damage response but increases translocations.

Long reads and Hi-C sequencing illuminate the two-compartment genome of the model arbuscular mycorrhizal symbiont Rhizophagus irregularis

The paper uses long reads and Hi-C sequencing to analyze genome structure and compartmentalization in Rhizophagus irregularis, revealing two distinct chromatin compartments with different gene and repeat content.

Extracting multi-way chromatin contacts from Hi-C data

This paper derives analytic expressions to predict multi-way chromatin contacts from Hi-C data, showing good correlation with experimental measurements.

ChromeBat: A Bio-Inspired Approach to 3D Genome Reconstruction

ChromeBat uses a bio-inspired algorithm to reconstruct 3D genome structures from Hi-C data, achieving state-of-the-art performance.

Non-coding loci without epigenomic signals can be essential for maintaining global chromatin organization and cell viability

The paper identifies non-coding genomic regions critical for chromatin organization and cell viability, showing their structural importance despite lacking epigenomic signals or annotated elements.

preciseTAD: A transfer learning framework for 3D domain boundary prediction at base-pair resolution

preciseTAD predicts 3D domain boundaries at base-pair resolution using transfer learning, supported by experimental evidence and applicable without Hi-C data.

Deciphering the species-level structure of topologically associating domains

The paper introduces a method to impute TAD architectures across cell/tissue types using existing epigenetic data and scRNA-seq, revealing gene clustering patterns in TADs during differentiation and in tumors.