Hi-C

GOntact: using chromatin contacts to infer target genes and Gene Ontology enrichments for cis-regulatory elements

GOntact uses chromatin contact data to predict CRE target genes and their Gene Ontology enrichments, showing more specific functional annotations than genomic proximity.

Regulatory architecture of the RCA gene cluster captures an intragenic TAD boundary, CTCF-mediated chromatin looping and a long-range intergenic enhancer

The paper identifies regulatory elements and chromatin structures in the RCA gene cluster, revealing long-range interactions and a TAD boundary within CR1 that influence gene expression and autoimmune disease susceptibility.

Gene structure heterogeneity drives transcription noise within human chromosomes

The paper uses simulations to link 3D gene structure with transcription noise in human chromosomes, showing structural heterogeneity drives gene expression variability.

ZipHiC: a novel Bayesian framework to identify enriched interactions and experimental biases in Hi-C data

ZipHiC identifies enriched interactions and experimental biases in Hi-C data using a Bayesian framework with hidden Markov random field and approximate Bayesian computation.

Large-scale multi-omics analysis suggests specific roles for intragenic cohesin in transcriptional regulation

The paper identifies a new subset of cohesin binding sites, DICs, with distinct functions in transcriptional regulation across human cell types.

Characterizing collaborative transcription regulation with a graph-based deep learning approach

The paper introduces ECHO, a graph-based deep learning model that predicts chromatin features using 3D chromatin organization, showing improved performance over sequence-based models.

Chromosome-level genome assembly of Rorippa aquatica revealed its allotetraploid origin and mechanisms of heterophylly upon submergence

This study assembled the chromosome-level genome of Rorippa aquatica to investigate its allotetraploid origin and the molecular mechanisms of heterophylly under submergence.

scGAD: single-cell gene associating domain scores for exploratory analysis of scHi-C data

scGAD provides a dimension reduction tool for scHi-C data to explore gene-level chromatin interactions and integrate with other single-cell modalities.

Hi-TrAC reveals fine-scale chromatin structures organized by transcription factors

Hi-TrAC identifies high-resolution chromatin loops and reveals TFs' roles in organizing long- and short-range chromatin structures.

Nuclear position modulates long-range chromatin interactions

The paper investigates how nuclear position affects long-range chromatin interactions by analyzing single-cell data, finding position-dependent interactions that vary by cell type and chromatin type.

Polycomb-mediated Genome Architecture Enables Long-range Spreading of H3K27 methylation

The paper investigates how Polycomb-mediated genome architecture facilitates long-range H3K27 methylation spreading in ESCs and iPSCs, revealing RNA-dependent DNA looping and developmental gene roles in chromatin organization.

Context-dependent 3D genome regulation by cohesin and related factors

This study investigates how cohesin and related factors regulate 3D genome structure and gene expression by analyzing depletion effects on chromatin, transcriptome, and epigenome data.

HiCUP-Plus: a fast open-source pipeline for accurately processing large scale Hi-C sequence data

HiCUP-Plus improves Hi-C data processing by integrating HiSAT2 and Dragen aligners, enhancing speed and accuracy while maintaining compatibility with Bowtie2.

Chromosome folding and prophage activation reveal gut-specific genome dynamics of bacteria in the OMM12 consortium

The paper uses Hi-C to study chromosome folding and prophage activation in gut bacteria, identifying functional prophages and their environmental dynamics.

Physical models for chromosome organization to predict multi-contact statistics

The paper develops three predictors of multi-contact frequencies using physical models and applies them to experimental data, finding that loop-extrusion explains observed three-point contacts.

Glucocorticoid Receptor-Regulated Enhancers Play a Central Role in the Gene Regulatory Networks Underlying Drug Addiction

The paper investigates how drug exposure alters gene regulatory networks in the brain using multi-omics approaches, identifying enhancer repression and transcription factor involvement in addiction-related behaviors.

Antimicrobial resistance genes predict plasmid generalism and network structure in wastewater

The paper uses Hi-C data to show AMR-carrying plasmids form more connected networks than non-AMR plasmids, enhancing AMR gene spread.

Phase separation and correlated motions in motorized genome

This study simulates the human genome using active forces to show their impact on heterochromatin localization and long-range spatial correlations.

The 4D Nucleome Data Portal: a resource for searching and visualizing curated nucleomics data

The paper introduces the 4DN Data Portal, a resource for searching and visualizing curated nucleomics data, including Hi-C and other chromosome architecture datasets.

Role of the EGR2 promoter antisense RNA in modulating chromatin accessibility and spatial genome organization

This study shows that the EGR2 promoter antisense RNA modulates chromatin accessibility and spatial genome organization by interacting with histone modification complexes.

Dynamic Features of Chromosomal Instability during Culture of Induced Pluripotent Stem Cells

The paper tracks chromosomal instability in iPSCs during culture, finding trisomy 12 dominance and novel structural variations acquired over time.

A benchmark of Hi-C scaffolders using reference genomes and de novo assemblies

The paper benchmarks five Hi-C scaffolders on four reference genomes, finding HiRise and Lachesis perform best across various conditions.

Analysis of sub-kilobase chromatin topology reveals nano-scale regulatory interactions with variable dependence on cohesin and CTCF

The paper analyzes sub-kilobase chromatin topology to show that nano-scale regulatory interactions depend on CTCF but not cohesin, and that cohesin affects longer-range enhancer-promoter interactions.

Connecting high-resolution 3D chromatin organization with epigenomics

The paper develops a deep learning model, CAESAR, to predict high-resolution 3D chromatin structures from epigenomic data and validates its accuracy across 91 human tissues and cell lines.

HiCHub: A Network-Based Approach to Identify Domains of Differential Interactions from 3D Genome Data

HiCHub identifies domains of differential chromatin interactions from 3D genome data by detecting clusters of genomic elements with concurrent interaction changes and state concordance.

3DPolyS-LE: an accessible simulation framework to model the interplay between chromatin and loop extrusion

3DPolyS-LE simulates chromatin loop extrusion and its impact on 3D chromosome structure, enabling comparison with Hi-C data.

Markov chains improve the significance computation of overlapping genome annotations

The paper introduces MCDP, a tool that computes p-values for genome annotation overlaps using Markov chains, improving efficiency and accuracy over existing methods.

Individual transcription factors modulate both the micromovement of chromatin and its long-range structure

This study shows that individual transcription factors modulate both local chromatin mobility and long-range chromatin structure in living cells.

A multi-omic dissection of super-enhancer driven oncogenic gene expression programs in ovarian cancer

This study identifies clinically relevant super-enhancers in ovarian cancer using multi-omic approaches and shows their role in driving oncogenic gene expression programs.

Chromatin interaction aware gene regulatory modeling with graph attention networks

This paper introduces GraphReg, a deep learning model that uses graph attention networks to predict gene expression from epigenomic data and genomic sequences, outperforming existing methods in modeling gene regulation and identifying functional enhancers.