Hi-C

TAPIOCA predicts chromatin topology using epigenetic features without Hi-C data, outperforming existing methods across cell lines.

The paper investigates how chromosome organization and topologically-associating domains (TADs) influence chromatin motion, showing that TAD compaction drives transitions between liquid-like and gel-like dynamical states.

This paper presents a computational method to determine complete chromosomal haplotypes using bulk long-range sequencing and Hi-C data, achieving high precision and completeness in diploid human genomes.

This study shows environmental enrichment alters chromatin structure, transcription factor binding, and 3D genome organization in mice, affecting cognitive function and gene regulation.

This study investigates how H2A.Z.1 modulates RNA Polymerase II dynamics during transcription initiation and elongation in embryonic stem cells, revealing its role in pausing and re-initiation.

This paper introduces ScHiC-Rep, a framework for single-cell Hi-C clustering that improves imputation and feature extraction, outperforming existing methods on human and mouse datasets.

This study examines the 3D genome organization of dinoflagellates, finding that transcription-induced supercoiling drives domain-scale structure without chromatin loops.

The paper identifies and corrects phase switches in Hi-C data for dikaryotic fungus assemblies using Nanopore and HiFi sequencing, showing HiFi's superiority in phasing low heterozygosity genomes.

FALCON-Phase uses long-read sequencing and Hi-C data to create phased diploid genome assemblies, achieving high accuracy in non-human species but lower accuracy in humans.

VEHiCLE enhances Hi-C contact map resolution using a variational autoencoder and adversarial training, improving downstream analysis capabilities.

This study shows that replication timing (RT) is essential for maintaining the global epigenetic state and genome compartmentalization in human cells, with RIF1 playing a central role in this process.

The paper uses magnetic forces to manipulate a genomic locus in live human cells, revealing chromatin's viscoelastic properties and challenging the gel-like model.

This study identifies subtype-specific epigenomic and 3D genome structures in bladder cancer, linking NPAS2 to luminal subtype regulation and clinical outcomes.

The paper uses Hi-C data to show that changes in chromatin compartmentalization classify prostate cancer progression, with specific gene clusters switching compartments and contributing to disease progression.

GENOVA is an R-package for analysing Hi-C data, demonstrating that cohesin subunits SA1 and SA2 differentially affect loop formation and genome compartmentalisation.

The paper introduces TSA-seq to identify decondensed large-scale chromatin regions (DLCDs) and shows their association with chromatin domain boundaries.

The paper presents LT1, a high-quality human reference genome assembled using long-read and Hi-C data, and reports its genomic features and availability as a public resource.

This study evaluates the impact of mouse read removal and library preparation on Hi-C data quality in patient-derived xenografts, finding that library strategy has the largest effect.

The paper uses Hi-M to study cis-regulatory loops in Drosophila development, showing they form before TADs and gene activation, and are independent of cell fate.

The paper investigates how 1,6-hexanediol modulates liquid-liquid phase separation and its impact on 3D chromatin organization in living cells.

The paper uses Hi-C data to link genetic risk variants for smoking and alcohol use to specific genes and pathways in brain regions involved in addiction.

This study shows that H3K27 acetylation retention during mitosis accelerates transcriptional and topological resetting of stem cell genes in mouse pluripotent stem cells upon G1 entry.

This study investigates how MLL3/MLL4 histone methyltransferase activity influences enhancer-promoter contacts and gene activation during mouse embryonic stem cell differentiation.

The paper identifies cell type-specific super-interactive promoters in blood lineage cells using Hi-C data and shows their association with ATAC-seq peaks and GWAS variants.

The paper uses polymer simulations to study chromatin structure changes at genomic rearrangements in B-cells and shows how these changes affect proto-oncogene expression.

BART3D identifies transcriptional regulators linked to differential chromatin interactions using Hi-C data and ChIP-seq, showing effectiveness in detecting TRs during cellular differentiation or perturbation.

This paper introduces BandNorm and 3DVI to normalize and de-noise scHi-C data, improving performance in cell type separation and 3D genomic structure recovery.

This study shows that type I and type II interferons induce similar epigenomic and transcriptional changes in macrophages, including 3D chromatin rearrangements and increased DNA accessibility at ISG loci.

The paper uses simulations to study how chromatin networks affect droplet formation and coalescence in nuclei, finding that protein-chromatin interactions stabilize multi-droplet states.

The paper develops an integrated resource to analyze small RNA profiles in mosquitoes, revealing evolutionary dynamics and host responses to viruses and transposons.