Hi-C

DeepChIA-PET predicts ChIA-PET interactions from Hi-C and ChIP-seq data using deep dilated networks, outperforming existing methods and generalizing to non-CTCF interactions.

This study shows that retrocopies and their parental genes colocalize in 3D genome organization, leading to increased transcription, translation, and evolutionary conservation.

This paper analyzes Hi-C data to reveal that chromosome folding is not strictly hierarchical but includes nested and non-nested community structures, with active chromatin associated with nesting.

The paper maps chromosomal interaction domains in E. coli under triclosan stress and links them to genetic, epigenetic, and transcriptome changes.

This study investigates enhancer-promoter contact architecture and communication, finding that RNA polymerase II and PARP1 activity stabilize these contacts.

The paper develops L-HiC-Reg to predict long-range regulatory interactions in new cell lines and applies it to interpret GWAS SNPs in complex diseases.

The paper identifies cis-regulatory elements controlling ORF68 expression in KSHV and shows how their 3D genomic positioning changes during the viral lifecycle.

HiCognition enables visual exploration and hypothesis testing of 3D genomic structure by integrating 1D genomics profiles and machine learning.

HiC4D forecasts spatiotemporal Hi-C data using a novel ResConvLSTM model, outperforming existing methods on four Hi-C datasets.

The paper identifies chromatin loop rewiring in adipogenesis and discovers novel regulators and gene-trait associations relevant to obesity and diabetes.

This study shows that depleting lamins B1 and B2 changes chromatin mobility and gene expression through mesoscale-motion dependent mechanisms.

FusNet predicts protein-mediated chromatin loops using genome sequence, open chromatin, and ChIP-seq data, showing high consistency with Hi-C and associations with regulatory functions and disease risk variants.

The paper compares 3D genome structures between neural retina and RPE to identify tissue-specific cis-regulatory interactions at retinal disease loci.

The paper introduces multiplex-GAM, a ligation-free method for genome-wide chromatin contact mapping, showing it detects different strong contacts compared to Hi-C, particularly involving active genomic regions.

This paper introduces an S1 nuclease-based Hi-C method for chromatin conformation capture, offering improved chromatin fragmentation and library preparation compared to DNase I Hi-C.

This study investigates the effects of retinoic acid signaling on the epigenome and chromatin architecture during zebrafish embryonic development using multi-omics approaches.

This study shows Prmt5 regulates gene expression and chromatin organization during adipogenesis by modulating TAD boundaries and chromatin loop anchors.

AraENCODE provides a comprehensive epigenomic database for Arabidopsis thaliana with 4,511 datasets and integrated resources for studying epigenetic regulation.

This study maps the 3D chromatin structure of rhabdomyosarcoma subtypes using Hi-C, revealing structural variations and gene regulatory patterns.

The paper investigates how allelic chromatin structure at the Peg13-Kcnk9 locus influences imprinted gene expression during neurogenesis in mice.

scHiMe predicts single-cell DNA methylation levels using single-cell Hi-C data and DNA sequences, achieving high accuracy and enabling cell-type classification.

The paper uses ultra-deep Hi-C and a new computational method to fine-map nuclear compartments, revealing that active promoters and enhancers localize in the A compartment even when adjacent sequences are inactive.

Epiphany predicts cell-type-specific Hi-C contact maps from epigenomic signals, showing robust performance across cell types and species.

HiCLift converts chromatin interaction data between genome assemblies efficiently, outperforming re-mapping approaches in speed while maintaining accuracy.

This study presents a chromosome-level genome assembly of Eleginops maclovinus and compares its circadian gene repertoire with Antarctic cryonotothenioids, finding greater conservation with the Antarctic clade.

EPCOT is a deep learning framework that predicts epigenome, chromatin organization, transcriptome, and enhancer activity, showing generalizability across cell types and modalities.

This study identifies PfAP2-MRP as a master regulator controlling parasite growth, chromatin structure, and var gene expression during malaria parasite blood stages.

The paper investigates how enhancer interactomes reconfigure during senescence and aging, identifying hyper-connected enhancer communities linked to gene expression and potential therapeutic targets.

This study investigates how morphine affects the 3D chromatin architecture of primate cortical neurons using DLO Hi-C, finding significant changes in chromosome territories, TADs, and differential loops.