Hi-C

This study uses Hi-C to compare genome organization between virulent and avirulent Mycobacterium tuberculosis strains, finding differences in Chromosome Interacting Domain (CID) size and gene distribution.

The paper creates a high-density chromatin interaction network across species by integrating 3C experiments, showing improved prediction of coexpression and eQTL for long-range and trans chromatin contacts.

The paper combines promoter-capture Hi-C and Hi-C data to analyze 3D chromatin architecture in colorectal cancer, identifying dysregulated genes and histone modifications associated with tumor-suppressive programs.

The paper introduces liCHi-C, a low-input Hi-C method, to map promoter-enhancer interactions in clinical samples and identify disease-relevant regulatory elements and structural variants.

Falign improves alignment of fragmented long noisy 3C data by addressing fragment boundary issues and increasing data utilization.

This paper introduces a rapid method to classify heterochromatin and euchromatin using Hi-C data, providing intuitive visual interpretation of contact frequencies.

This study shows that topoisomerases I and II regulate condensin DC translocation on the X chromosome in C. elegans, with TOP-2 affecting long-range movement and TOP-1 affecting short-range movement, both essential for gene repression.

This paper introduces scDEC-Hi-C, a deep generative framework for analyzing single cell Hi-C data, showing improved clustering and imputation over existing methods.

The paper shows that some Topologically Associating Domains (TADs) persist without cohesin, supported by Hi-C data, polymer simulations, and 3D structural analysis in mouse and human cells.

This study shows mitotic chromosomes scale with cell size and nucleo-cytoplasmic ratio in Xenopus, distinct from other subcellular structures, through mechanisms involving condensin I and importin pathways.

PENGUIN reconstructs protein interactions at enhancer-promoter regions and identifies cancer-associated SNPs in prostate cancer cell lines.

This study shows that Xist regulates Xi compaction and TAD boundaries in B cells, impacting XCI maintenance and X-linked gene expression.

The paper maps promoter interactions in human ILC3s using PCHi-C and links GWAS risk variants to target genes, identifying new autoimmune disease risk genes.

The paper shows that ROW cooperates with BEAF-32 to regulate long-range transcription through chromatin loops at TAD boundaries.

This paper introduces a computational model called WEChroM to simulate DNA and nucleosome mechanics, showing it can reproduce DNA structure, supercoiling behavior, and nucleosome unwrapping.

The paper generates genome assemblies and linkage maps for Leptidea species to study structural rearrangements, finding extensive fissions, fusions, and polymorphisms, with LINEs and LTR elements enriched at fusion breakpoints.

The paper investigates epigenomic and 3D chromatin conformation changes in human frontal cortex and hippocampus development using sn-m3C-seq, finding distinct chromatin conformations in neurons and glial cells and linking risk variants to regulatory regions.

The paper identifies human-specific 3D genome re-wiring in conserved loci, linking accelerated evolution to regulatory rewiring in neural progenitor cells.

This study compares two single-cell Hi-C protocols, showing that whole-genome amplification introduces more artifacts and noise than PCR-based amplification.

Fast-Higashi improves scHi-C analysis by jointly identifying cell identities and chromatin meta-interactions with tensor decomposition and a novel algorithm, enhancing rare cell type detection and developmental trajectory reconstruction.

This study examines how 3D chromatin organization changes in muscle stem cells during aging, revealing static global structures and rewired local contacts linked to transcription factor binding and gene expression changes.

ParticleChromo3D uses particle swarm optimization to reconstruct 3D chromosome and genome structures from Hi-C data, showing higher accuracy than existing methods.

The paper maps multi-way chromatin contacts using long reads and identifies cell type-specific transcription clusters by integrating contacts with chromatin accessibility and gene expression.

The paper introduces pTADbit, a machine learning method that improves 3D genome modeling using Hi-C data and microscopy distances, achieving higher accuracy and faster computation.

The paper uses targeted chromatin interaction profiling to identify causal genes at type 2 diabetes GWAS loci with higher sensitivity and resolution than genome-wide methods.

The paper shows that transcriptional units form discrete 3D domains that constrain bacterial chromosome organization at a fine scale.

This study demonstrates that microorganisms in activated sludge can acquire synthetic plasmids via transformation under kanamycin pressure, using Hi-C sequencing to identify transformants.

PHi-C2 converts Hi-C data into dynamic 3D genome models using polymer modeling and provides an optimized algorithm and Colab workflow for analysis.

This study uses a coarse-grained polymer model to simulate mitotic chromosome mechanics, finding they are ten times stiffer than interphase chromosomes and exhibit viscoelastic behavior.

The paper investigates the role of CTCF and cohesin in LAD positioning, finding they reinforce borders but do not position LADs, and mediate fine-tuning of nuclear lamina interactions.