Hi-C

Determining mesoscale chromatin structure parameters from spatially correlated cleavage data using a coarse-grained oligonucleosome model

This paper develops a modeling framework to interpret RICC-seq data by simulating oligonucleosome structures and extracting nucleosome repeat lengths using a convolutional neural network.

SnapHiC-G: identifying long-range enhancer-promoter interactions from single-cell Hi-C data via a global background model

SnapHiC-G identifies long-range enhancer-promoter interactions from scHi-C data using a global background model, showing high sensitivity and cell-type-specific enrichment of neuropsychiatric disease SNPs.

Long-Range Enhancer Networks Gradually Emerge as Key Regulators During Human Cortical Neurogenesis

The paper maps long-range enhancer networks in human, macaque, and mouse fetal cortex, showing human-specific enhancers and neuropsychiatric disorder-linked SNPs regulate gene expression during neurogenesis.

Spatial organization of the 3D genome encodes gene co-expression programs in single cells

The paper investigates how 3D genome organization, specifically through Cohesin, influences gene co-expression in single cells and reveals its role in maintaining long-range chromatin interactions.

Integration of CTCF Loops, Methylome, and Transcriptome in Differentiating LUHMES as a Model for Imprinting Dynamics of the 15q11-q13 Locus in Human Neurons

The paper integrates CTCF loops, methylome, and transcriptome data from LUHMES neurons to study imprinting dynamics at the 15q11-q13 locus during differentiation.

Shared and unique chromatin accessibility and 3D functional interactions of substance use disorder loci implicate cell types beyond the brain

This paper identifies shared and unique chromatin accessibility and 3D interactions of SUD loci, implicating non-neural cell types like pancreatic β-cells and showing a causal link between T2D and AUD.

Puzzle Hi-C: an accurate scaffolding software

Puzzle Hi-C improves chromosome-scale genome assembly by reducing scaffolding interference through a triangle region strategy and dynamic window expansion.

Deletion of an evolutionarily conserved TAD boundary compromises spermatogenesis in mice

This study shows that deleting a conserved TAD boundary near Dmrtb1 and Lrp8 in mice impairs spermatogenesis but not fertility.

SMCHD1 maintains heterochromatin and genome compartments in human myoblasts

This study shows SMCHD1 maintains heterochromatin and genome compartments in human myoblasts by anchoring heterochromatin domains and preventing epigenome modification.

Three-dimensional genome architecture persists in a 52,000-year-old woolly mammoth skin sample

This paper reports the 3D genome architecture of a 52,000-year-old woolly mammoth using a novel method, revealing conserved epigenetic features across elephantids.

Enhancing Hi-C contact matrices for loop detection with Capricorn, a multi-view diffusion model

Capricorn enhances low-coverage Hi-C contact matrices using a multi-view diffusion model to improve loop detection accuracy across cell lines and chromosomes.

scGrapHiC: Deep learning-based graph deconvolution for Hi-C using single cell gene expression

scGrapHiC uses deep learning to predict cell-type-specific scHi-C contact maps from scRNA-seq data, improving recovery of Topologically Associating Domains by 23.2% over baselines.

ENT3C: an entropy-based similarity measure for Hi-C and micro-C derived contact matrices

ENT3C measures similarity between Hi-C and micro-C contact matrices using entropy-based complexity changes in diagonal regions.

High efficient chromatin conformation capture without pre-enrichment (HiChew) in single cells

HiChew improves chromatin conformation capture in single cells with higher efficiency, fewer false positives, and more contacts per cell compared to Dip-C.

hictk: blazing fast toolkit to work with .hic and .cool files

hictk is a toolkit for efficiently processing .hic and .cool files, outperforming existing tools and supporting both formats natively.

Spatial chromosome organization and adaptation of Escherichia coli under heat stress

This study investigates how Escherichia coli's chromosome structure and transcriptomic responses change under heat stress, revealing shifts in chromosome interactions and compactness.

Estrogen-induced chromatin looping changes identify a subset of functional regulatory elements

The paper identifies estrogen-induced chromatin looping changes in endometrial cancer cells and shows their correlation with transcriptional responses, though not all loops are essential for estrogen regulation.

Three-dimensional chromatin mapping of sensory neurons reveals that cohesin-dependent genomic domains are required for axonal regeneration

This study maps the 3D chromatin architecture of adult sensory neurons and shows cohesin is required for axonal regeneration by organizing genomic domains.

Figeno: multi-region genomic figures with long-read support

Figeno generates publication-quality genomic figures with support for multi-region views, long reads, and epigenomic data.

Direct CCUT: A Versatile and Standardized Framework to Train 3C Deep Restoration Models

Direct CCUT trains deep models to reconstruct high-resolution chromatin interaction matrices from low-resolution Pore-C and 3C data using consumer GPUs.

Pairtools: from sequencing data to chromosome contacts

Pairtools processes sequencing data into contact pairs for 3C+ analysis, offering high-performance and flexible tools for various protocols.

Multi-omics analysis of longitudinal patient samples reveals the molecular mechanism of AML progression

This study uses multi-omics analysis to identify genetic and epigenetic changes in AML progression and relapse.

Transcription decouples estrogen-dependent changes in enhancer-promoter contact frequencies and spatial proximity

The paper investigates how estrogen receptor activation affects enhancer-promoter contact frequencies and spatial proximity, finding they change independently during gene activation.

HiCDiff: single-cell Hi-C data denoising with diffusion models

HiCDiff denoises single-cell Hi-C data using diffusion models, outperforming existing methods and working well on bulk Hi-C data.

DNA Methylation-Based High-Resolution Mapping of Long-Distance Chromosomal Interactions in Nucleosome-Depleted Regions

This paper introduces MTAC, a method to map long-distance chromosomal interactions in yeast, revealing new insights into 3D genome organization.

Improving Cell-type-specific 3D Genome Architectures Prediction Leveraging Graph Neural Networks

This paper introduces GRACHIP, a graph neural network model that improves prediction of cell-type-specific 3D genome architectures by incorporating genomic interaction information, showing better accuracy and generalizability than existing methods.

Improved cohesin HiChIP protocol and bioinformatic analysis for robust detection of chromatin loops and stripes

The paper introduces an improved cohesin HiChIP protocol and analysis pipeline to enhance detection of chromatin loops and stripes.

Embryo spatial 3D genomics

A spatial 3D genomics approach was developed to analyze hierarchical chromatin conformation in situ in tissue sections, revealing organ-specific and conserved chromatin interactions.

Cooltools: enabling high-resolution Hi-C analysis in Python

Cooltools provides scalable and flexible analysis tools for high-resolution Hi-C data, addressing challenges in storage, memory, and customization.

Polycomb protein binding and looping mediated by Polycomb Response Elements in the ON transcriptional state

The paper investigates how Polycomb Response Elements (PREs) function in the ON transcriptional state, showing that PREs can still loop and interact with enhancers while some PcG proteins remain bound.