Hi-C

The paper shows SATB2 influences 3D genome structure in cortical neurons, affecting gene expression and cognitive-related functions.

DiffModeler uses diffusion models to accurately model protein complex structures from low-resolution cryo-EM maps, achieving high TM-Scores across various resolutions.

This study introduces SCA-seq to resolve spatial chromatin interactions at single-molecular resolution and demonstrates its application in analyzing epigenomic markers.

The paper investigates cross-TAD enhancer-promoter communication during limb development using ORCA and simulations, finding that boundary stacking enables such interactions and explains architectural stripes.

DiffDomain identifies structurally reorganized TADs using Hi-C and single-cell Hi-C data, outperforming existing methods in accuracy and detecting new TAD subtypes.

Chromosome-scale inshore hagfish genome places 1R before the cyclostome-gnathostome split and 2R in the gnathostome stem, and reveals two cyclostome-specific duplications (CR1, CR2).

The paper investigates how Alu and L1-rich chromosome bands influence the structural reorganization of the inactive X chromosome and SAHFs, showing resistance of Alu-rich regions to condensation.

The paper identifies a critical noncoding superenhancer region essential for regulating anterior HOXA genes in craniofacial development, showing its deletion causes severe developmental defects in mice and a human patient.

mosGraphGen generates multi-omics signaling graphs to enable integrative and interpretable graph AI model development by converting multi-omics data into biologically meaningful graphs.

The paper identifies PU.1 cis-regulatory elements in human blood cell lineages and shows how chromatin structure and 3D architecture influence their function as enhancers or silencers.

The paper investigates network properties of chromosome structure networks derived from Hi-C data and their connections to genome annotations, finding that semi-local properties better characterize biological features than local or diffusive features.

This paper evaluates deep-learning methods for improving Hi-C resolution using experimentally generated datasets and finds they perform poorly on sparse data, with retraining offering limited improvement.

The paper identifies active transposable element candidates in Nishikigoi using ROH islands and long-read sequencing, revealing unique genetic features and a novel approach for TE detection.

This paper uses machine learning to analyze Hi-C data from E. Coli, revealing structural patterns and predicting DNA dynamics, showing that a subset of contact pairs suffices for accurate predictions.

This study shows that ASF1 histone binding is essential for fertility in Sordaria macrospora, but not for genome stability, and identifies a chromosomal duplication linked to the mutant phenotype.

The paper investigates how chromatin compaction affects protein search kinetics using models and experimental data, finding optimal compaction minimizes protein residence time.

The paper investigates mitotic chromosome architecture across species and cell types, finding species-specific loop sizes but no cell type differences, and links loop size to chromosome arm compaction.

The paper shows that genes coding for adhesome receptor proteins are spatially co-localized and co-regulated in the nucleus, with transcription factors also co-localizing to reinforce extracellular matrix sensing.

TRFill improves genome assembly of tandem repeats using HiFi and Hi-C data, enhancing completeness and enabling population-level analysis of subtelomeric repeats.

The paper introduces a computational framework linking chromatin structure to gene regulation using polymer models and Hi-C data, showing how CTCF deletion affects gene expression in limb development.

The paper investigates 3D-genome organization and transcription regulation in distinct cell types of the mouse brain, finding cell-type-specific nuclear architecture and chromatin compartmentalization correlated with transcriptional activity and MeCP2 regulation.

The paper examines how XIST regulatory networks evolve in primates, showing extensive diversification and the role of transposons and enhancers in different species.

The paper shows that the structural similarity index from CHESS is unreliable due to noise in Hi-C data, warning against its biological interpretation.

This paper introduces Hi-C metainference, a Bayesian method to model chromatin organization, revealing that gene loci in mouse embryonic stem cells are dynamically condensed and organized as crumpled globules.

This study shows that CTCF-mediated 3D chromatin structure pre-establishes gene expression programs required for spermatogenesis by forming meiosis-specific super-enhancers and regulating chromatin loops.

This study examines how HPV integration affects host chromatin structure and gene regulation in cervical cancer, finding that integrations are enriched in active chromatin regions and induce local and long-range transcriptional upregulation within TADs.

This study investigates how positive and negative supercoiling influence 3D genome organization in E. coli using Hi-C and ChIP-seq data, finding positive supercoiling enhances spatial contacts more than negative supercoiling.

The paper introduces an optimized Hi-C protocol, Hi-C2B, for studying chromosomal contacts in synchronized meiotic S. cerevisiae cells, improving reproducibility and reducing noise.

This study shows that 3D culture of breast cancer cells alters chromatin structure and gene expression, with LATS1 kinase playing a key role in CTCF displacement and hormonal response.