Hi-C

STRIDE: A Sequencing Depth-Insensitive Metric for Robust Comparison between Sparse Chromosome Conformation Capture Data

This paper introduces STRIDE, a sequencing depth-insensitive metric for comparing sparse single-cell Hi-C data, enabling robust analysis of 3D genome organization.

A molecular framework of chromatin extrusion in plants

This study identifies PDS5A as a key regulator of chromatin loop extrusion and TAD-like domains in Arabidopsis, revealing a promoter- and motif-based mechanism for loop anchoring and transcriptional control.

Exploring DNA movement through the application of droplet based high efficient chromatin conformation capture (DropHiChew) and loop velocity

This paper introduces DropHiChew and loop velocity to study DNA movement dynamics, enabling accurate trajectory estimation with shallow sequencing.

Cell-cycle-resolved Hi-C reveals unexpected plasticity of A/B compartments across interphase

This study uses Hi-C in mouse embryonic stem cells to show A/B compartment strength increases during S-phase, challenging previous views on cell-cycle dynamics.

EWS::WT1 Isoform-Dependent Regulation of Neogenes in Desmoplastic Small Round Cell Tumors

This study identifies DSRCT-specific neogenes regulated by the EWS::WT1 fusion protein and shows their potential as biomarkers and therapeutic targets in desmoplastic small round cell tumors.

Fetal signatures in the 3D genome of iPSC-derived neurons and their implications for disease modeling

This study compares chromatin architecture in iPSC-derived neurons to fetal and mature neurons, finding iPSC-derived neurons resemble fetal neurons and have distinct chromatin features.

3D Reconstruction of Dinoflagellate Chromosomes from Hi-C Data Challenges the Cholesteric Liquid Crystal Hypothesis

This study uses Hi-C data to challenge the Cholesteric Liquid Crystal model of dinoflagellate chromosomes by showing no evidence of cholesteric discs and demonstrating transcription occurs throughout chromosomes.

Euchromatin forms condensed domains with short active regions on the surface

The paper develops a simulation framework to infer nucleosome-resolution chromatin structures from RCMC data, revealing euchromatin as condensed domains with accessible promoter/enhancer regions.

Cell Cycle-Dependent Chromatin Motion: A Role for DNA Content Doubling Over Cohesion

The paper uses Hi-D to track chromatin motion in live human cells and finds that DNA content doubling, not cohesin, reduces chromatin mobility during the cell cycle.

A Scaffolding Element Rewires Local 3D Chromatin Architecture During Differentiation

This study identifies a scaffolding element that drives chromatin rewiring during differentiation by modulating 3D structure and transcription.

Regulation of immune signal integration and memory by inflammation-induced chromosome conformation

This study shows that inflammation-induced changes in 3D genome conformation regulate immune signal integration and transcriptional memory in macrophages.

Reversibility of Nuclear and 3D Genomic Changes in Non-Cancerous Fibroblasts After Constricted Migration

This study shows that non-cancerous fibroblasts experience reversible nuclear and 3D genomic changes after constricted migration, unlike stable changes in cancer cells.

Overcoming artificial structures in resolution-enhanced Hi-C data by signal decomposition and multi-scale attention

This paper introduces SHARP, a method to enhance Hi-C data resolution while avoiding artificial structures by decomposing signals and using multi-scale attention.

DUCK-Net: Automated deep learning segmentation of Ductular Reaction in murine liver injury captures multicellular niche dynamics from H&E morphology

This paper introduces DUCK-Net, a deep learning model for automated segmentation of Ductular Reactions in murine liver injury, showing high accuracy and correlation with spatial transcriptomic data.

Conformational asymmetry of replicated human chromosomes

The paper reveals a genome-wide asymmetry in sister chromatid alignment due to replication fork asymmetry, maintained by cohesive cohesins.

Differential analysis of image-based chromatin tracing data with Dory

Dory identifies differential spatial patterns in chromatin tracing data by analyzing structural differences between groups, linking changes to gene regulation.

HiCPotts: An R/Bioconductor package to identify significant interactions in chromosome conformation capture data and model sources of biases.

HiCPotts is an R/Bioconductor package that identifies significant chromatin interactions in Hi-C data while modeling biases using a zero-inflated Negative Binomial distribution.

Hi-Cformer enables multi-scale chromatin contact map modeling for single-cell Hi-C data analysis

Hi-Cformer models multi-scale chromatin contact maps from single-cell Hi-C data, improving cell type separation and imputation of 3D genome features.

Integrative spatial profiling of 3D genome organization and gene expression in tissue

This paper introduces Spatial Hi-C-RNA, a spatial multi-omics technology that co-maps chromatin conformation and transcriptome in tissue, revealing spatially coherent domains and new insights into gene regulation.

Loss of SUMOylation drives aberrant PRC1 clustering and 3D genome rewiring independent of H3K27me3

This study shows that SUMOylation loss in Drosophila disrupts PRC1 condensates, causing 3D genome rewiring and gene misregulation without affecting H3K27me3 levels.

Genomic indicators of gene function: A systematic assessment of the human genome

The paper assesses genomic indicators of gene function in the human genome, finding that transcriptional activity and evolutionary conservation are strongest predictors of functional regions.

WAVE2 and REST/NRSF Regulate Clustered Gene Expression by Maintaining Heterochromatin Organization

This study shows WAVE2 and REST/NRSF regulate clustered gene expression by maintaining heterochromatin organization through chromatin dynamics and spatial reorganization.

BioMaster: Multi-agent System for Automated Bioinformatics Analysis Workflow

BioMaster automates complex bioinformatics workflows using a multi-agent system, improving accuracy, efficiency, and scalability across tasks like RNA-seq and Hi-C processing.

The piRNA pathway mediates transcriptional silencing of LTR retrotransposons in ovaries and somatic tissues of Aedes mosquitoes

This study shows that Piwi6 in Aedes mosquitoes suppresses LTR retrotransposons in both gonadal and somatic tissues by guiding H3K9me3 histone deposition.

map3C: a computational tool for processing multiomic single-cell Hi-C data

map3C improves the quality of multiomic single-cell Hi-C data and aids in identifying structural variant locations.

Single-cell analysis of the epigenome and 3D chromatin architecture in the human retina

The paper performs single-cell multiomics analysis of the human retina to identify regulatory elements and develop predictors for non-coding risk variants.

Human Body Single-Cell Atlas of 3D Genome Organization and DNA Methylation

The paper maps 3D genome organization and DNA methylation across 86,689 single nuclei from 16 human tissues, revealing cell-type-specific variations and discrepancies between methylation and chromatin structure.

Epigenetic and 3D genome reprogramming during the aging of human hippocampus

This study examines age-related changes in the human hippocampus using multi-omics data, revealing cell-type loss and epigenetic reprogramming linked to cognitive decline.

HiC2Self: self-supervised denoising for bulk and single-cell Hi-C contact maps

HiC2Self denoises Hi-C contact maps using self-supervised learning, reconstructing 3D chromatin structures from low-coverage data across bulk and single-cell samples.

Foundation model reveals the shared organization of transcription and topologically associating domains

The paper develops a foundation model to analyze TADs and their impact on transcription, finding that TADs enhance co-regulation and this effect declines with aging and changes in cancer cells.