Hi-C

The paper introduces a method to impute TAD architectures across cell/tissue types using existing epigenetic data and scRNA-seq, revealing gene clustering patterns in TADs during differentiation and in tumors.

LungCancer3D integrates HiC with multi-omics data to visualize lung cancer chromatin architecture and gene regulation mechanisms.

The paper develops a molecular dynamics model to study how epigenetic-structural changes in X chromosomes drive Xic pairing during early differentiation of mouse embryonic stem cells.

This paper develops deep-learning methods to enhance Hi-C data resolution using genome sequence information and provides open-source code.

The paper shows RNA polymerase II is necessary for spatial chromatin reorganization after mitosis, as demonstrated by Hi-C and in silico modeling.

The paper assembles and resolves two haplotypes of a cassava line using multiple sequencing technologies, revealing over 5,000 large structural variants.

The paper confirms that SSIM depends on Hi-C matrix properties and provides improved methods for identifying differential 3D genome conformation.

The paper introduces a reference-free quality control method for Hi-C sequencing data, demonstrating its accuracy on simulated and real datasets.

Higashi improves scHi-C data analysis by enhancing quality and extracting 3D genome features, revealing cell-to-cell variability and new gene regulation connections in human prefrontal cortex cells.

SMILE integrates single-cell omics data by learning discriminative representations through mutual information maximization, effectively removing batch effects and aligning diverse data types.

This study shows enhancers recruit cohesin to form chromatin domains, engage CTCF sites, and activate distant genes, with transcription factors and mediator required for all distances but cohesin specifically for long-range activation.

This study identifies DIDO3 binding at active chromatin and topological boundaries in mouse stem cells, linking it to chromatin organization and transcriptional regulation.

The paper integrates single-cell RNA-seq, ATAC-seq, and Hi-C data to study nuclear configuration and gene expression changes during stem cell differentiation and X inactivation, revealing discrete structural changes and delayed chromatin compaction.

The paper shows that low membrane fluidity in bacteria triggers lipid phase separation and protein segregation without disrupting membrane function.

HPRep quantifies reproducibility in HiChIP and PLAC-seq data by using a stratified and weighted correlation metric, outperforming existing Hi-C-based measures.

This paper introduces 4DMax, a method that predicts dynamic chromosome structures from time-series Hi-C data, effectively interpolating chromatin positions and recovering structural features at unobserved time points.

The paper uses Hi-C data to show that E. coli chromosome loci exhibit coordinate-dependent sub-diffusive motion, driven by Hi-C-guided long-range interactions.

The paper presents a high-quality Arabidopsis thaliana genome assembly using long-read sequencing and Hi-C data, resolving previously missing regions and centromeres.

This study shows that β-actin levels influence chromatin remodeling activities and 3D genome architecture in mouse embryonic fibroblasts.

This study shows DNA hypomethylation disrupts replication timing precision and 3D genome organisation in colorectal cancer DNMT1 and DNMT3B knockout cells.

This study evaluates 3C-based assays to understand how experimental parameters affect chromatin interaction detection and quantification, leading to the development of Hi-C 3.0.

This paper reviews methods for identifying functional interactions from Hi-C data by classifying approaches into three categories: domain discovery, statistical significance detection, and epigenomic integration.

The paper shows cohesin maintains chromatid organisation during anaphase in yeast, despite being thought to be removed by separase cleavage.

The paper develops a multi-modal data integration approach to improve genome structure modeling and shows that rare contact events are essential for predicting nuclear architecture.

The paper investigates how genome structure responds to nuclear swelling, finding that global topology remains elastic and robust despite dramatic volume changes.

The paper compares PCC and PCHiC methods using different restriction enzymes to assess their sensitivity in detecting promoter interactions and their association with regulatory features and genetic variation.

This paper introduces a minimalistic 3D chromatin polymer model that uses sparse interactions to generate single-cell chromatin conformations consistent with experimental data and reveals insights into chromatin structure and function.

The paper compares Hoxd gene regulation in mammalian vibrissae and avian feather primordia with trunk elongation in mice and chickens, showing lineage-specific enhancer usage and functional divergence in conserved CREs.