Hi-C

A Chromatin-Structure-Guided Framework for Predictive and Interpretable Regulatory Genomics

CHROME improves regulatory genomics predictions by integrating physically validated chromatin interactions into graph models, enhancing accuracy and interpretability for ChIP-seq, eQTL, and variant pathogenicity.

Genome-wide absolute quantification of chromatin looping

This study calibrates Micro-C with live imaging to determine absolute chromatin looping probabilities in mouse cells, finding most loops occur at low frequencies.

Visualizing Interchromosomal Interactions at Sub-Megabase Resolution Using Network Clustering Coefficients

The paper develops network-based metrics to visualize interchromosomal interactions at sub-megabase resolution, revealing shared interaction hotspots across chromosomes.

Computational reconstruction of hierarchical cis-regulatory networks reveals synergistic transcription control and disease-associated rewiring

ORIGAMI reconstructs cis-regulatory networks using multi-omics data and deep learning, revealing synergistic transcription control and disease-associated rewiring.

A Spectrum of Free Energy Landscape Topologies Encodes Chromatin Polymorphism and Phase Separation

This paper maps the free-energy landscapes of chromatin structures and shows how linker DNA geometry and sequence modulate their topologies, influencing phase separation and structural polymorphism.

Aberrant chromatin looping by NUP98-HOXA9 is constrained by CTCF and facilitated by cohesin

This study investigates how NUP98-HOXA9 drives aberrant chromatin looping in AML by interacting with CTCF and cohesin, revealing a non-canonical mechanism involving phase separation and loop extrusion.

Hierarchical Chromatin Rewiring Orchestrates Early Transcriptional Regulation in Mouse Cerebral Cortex Following Focal Ischemia

This study shows that stroke induces hierarchical chromatin rewiring in mouse cerebral cortex, with domain context regulating transcriptional responses.

SPA-C: an hybrid tool to accurately scaffold genomes using Hi-C and Deep-Learning

SPA-C improves genome scaffolding by combining Hi-C data with a CNN and graph-solving algorithm, outperforming existing methods on benchmark genomes.

UnionLoops: a workflow for calling chromatin loops across related Hi-C datasets with improved specificity, precision, and sensitivity

UnionLoops improves chromatin loop detection across related Hi-C datasets by integrating information to enhance specificity, precision, and sensitivity.

Haplotype-resolved genome architecture mapping uncovers pervasive structural heterogeneity between human homologous chromosomes

The paper introduces CoPhasing, a method to phase chromatin contacts with haplotype specificity, revealing structural differences between homologous chromosomes.

Genome reorganization and its functional impact during breast cancer progression

The paper profiles genome organization changes during breast cancer progression using Micro-C mapping and links these changes to gene expression and enhancer activity.

A generalizable Hi-C foundation model for chromatin architecture, single-cell and multi-omics analysis across species

HiCFoundation is a Hi-C-based model that integrates chromatin structure with epigenomic regulation across species, improving analysis of 3D genome architecture and single-cell data.

Generalisable tissue-wide molecular reconstruction from histology

GHIST+ reconstructs tissue-wide molecular maps from H&E histology, enabling cohort-scale molecular reconstruction from sparse spatial transcriptomic data.

A global map for introgressed structural variation and selection in humans

Long-read phased assemblies from two Papuans plus 47 HPRC genomes map archaic introgressed structural variants, revealing 11 candidate archaic centromeres and 16 candidate adaptive SVs.

Hyper3D-lite: count-preserving representation auditing for long-read multi-contact genome data

Hyper3D-lite audits long-read multi-contact genome data by preserving counts during all-pair projections to avoid overcounting contact evidence.

Visualization of the architecture of flexible chromatin and the binding of chromatin regulators

The paper visualizes chromatin structure and chromatin regulator binding using cryo-ET and subtomogram averaging, revealing nucleosome heterogeneity as a key factor in chromatin flexibility.

Translocation-driven chr19-der(14) interaction is associated with disease-specific transcriptional programs in mantle cell lymphoma

This study identifies interchromosomal interactions between chr19 and the CCND1 locus in MCL, linking spatial genome reorganization to disease-specific transcriptional programs.

A latent interaction landscape inferred from Micro-C encodes chromatin regulatory identity and conformational diversity beyond contact frequency

This paper introduces a latent interaction landscape from Micro-C data that captures chromatin regulatory identity and structural diversity beyond contact frequency.

Single-molecule nucleosome spacing coordinates chromatin fiber interactions

The paper introduces LASSI, a method to measure nucleosome spacing in chromatin interactions, revealing fiber homotypy as a structural pattern influenced by genomic features and cohesin dynamics.

The HuBMAP Framework for Advancing Data FAIRness

The paper describes the HuBMAP framework for creating FAIR data through standardized metadata reporting across diverse assays and institutions.

CLASH (Chromatin Loop Across-sample Score Harmonizer) quantifies the relative contributions of genetic variation, methylation, and CTCF occupancy on chromatin loop strength across individuals

The paper introduces CLASH, a method to quantify how genetic variation, methylation, and CTCF occupancy affect chromatin loop strength across individuals.

CTCF regulates wild-type and recombinant AAV gene expression by shaping viral chromatin

This study identifies a CTCF-binding element in the wtAAV2 genome that enhances rAAV transgene expression by shaping chromatin structure, offering a strategy to improve gene therapy vectors.

MINTsC learns multi-way chromatin interactions from single cell high throughput chromatin conformation data

MINTsC identifies multi-way chromatin interactions from scHi-C data, revealing gene regulation by multiple enhancers and reducing multiple-testing burden in molecular QTL studies.

Characterization of Human Ectocentromeric Sites.

The paper characterizes human ectocentromeric sites as evolutionarily constrained and functionally heterogeneous elements along chromosome arms with context-dependent roles in chromatin state and transcription regulation.

From unsupervised clustering to atlas-guided annotation in cohort-scale spatial omics with HiCAT

HiCAT improves spatial omics annotation by combining unsupervised clustering with atlas guidance, revealing molecularly defined regions and enhancing downstream analysis.

Accelerated Aging Signatures in 3D Genome Organization and Transcriptome in Schizophrenia

This study identifies accelerated aging patterns in 3D genome organization and transcriptome in schizophrenia using Hi-C data and transcriptomic analysis.

A multiscale chromatin collapse underlies vascular pathology in Hutchinson -Gilford progeria syndrome

This study identifies chromatin reorganization and histone mark changes in HGPS VSMCs, linking them to vascular pathology through disrupted enhancer-promoter interactions.

Lineage-specific retrotransposon co-option reveals a conserved ASH2L isoform as an epigenetic primer of developmental gene promoters

The paper shows that a truncated ASH2L isoform, generated via a lineage-specific retrotransposon, primes developmental gene promoters during pluripotency and is required for later developmental transitions.

Analysis of multi-way chromatin interactions at sub-nucleosome resolution identifies synergistic nano-scale interactions within super-enhancers

The paper introduces mwMCC, a method to detect multi-way chromatin interactions at sub-nucleosome resolution, revealing synergistic nano-scale interactions within super-enhancers and their role in gene regulation.

Disentangling polymer confinement from specific-folding interactions reveals the drivers of E. coli chromosome organization

The paper develops a polymer simulation framework to distinguish specific-folding interactions from polymer compaction in E. coli, revealing SFIs shape chromosome organization and gene expression.