Hi-C

This study uses epigenome-informed polymer modeling to generate chromosomal conformational ensembles from epigenomic data, revealing how genetic and epigenetic contexts shape chromosome folding landscapes.

The paper tracks viral infection in Ostreococcus tauri, showing pre-existing genome architecture dictates viral positioning and transcriptional changes during infection.

This study shows that SA1/2 are not essential for V(D)J recombination in G0/G1-arrested cells, but their absence disrupts chromatin loops and long-range Igh recombination, while Ig{kappa} recombination remains functional.

The paper develops ChromE-seq to study 3D chromatin architecture in fetal hematopoiesis, finding that T21 disrupts B-lineage development by altering chromatin connectivity and regulatory circuits.

Looplook integrates 3D chromatin topology with functional genomics to improve CRE-target gene assignment and functional inference in chromatin regulatory networks.

The paper presents an integrated analysis of somatic mosaicism across 25 individuals, revealing tissue-specific mutational processes and epigenetic states.

The paper assesses genomic indicators of gene function in the human genome, finding that transcriptional activity and evolutionary conservation are strongest predictors of functional regions.

A web atlas counts evidence from 24 types for 188,634,118 variant-gene pairs across 50 human tissues; 1,530,420 pairs pass a high-confidence cutoff, 87% of them tissue-specific.

The paper develops coarse-grained models for simulating double-stranded RNA and DNA in the CALVADOS framework to study their behavior in protein-nucleic acid condensates.

This study shows WAVE2 and REST/NRSF regulate clustered gene expression by maintaining heterochromatin organization through chromatin dynamics and spatial reorganization.

This study shows that Piwi6 in Aedes mosquitoes suppresses LTR retrotransposons in both gonadal and somatic tissues by guiding H3K9me3 histone deposition.

This study shows that BORIS, a CTCF paralog, promotes ovarian cancer by altering 3D genome organization and transcriptional programs through chromatin remodeling.

The paper links structural variation to regulatory genome function in barley by analyzing epigenomic data across multiple genotypes and developmental contexts.

Over 8,000 gapless human centromeres reveal population-stratified satellite-array, inversion and haplotype variation, multiple candidate kinetochore sites in 16.8% of centromeres, and single-base substitution rates comparable to flanking pericentromeres.

The paper performs single-cell multiomics analysis of the human retina to identify regulatory elements and develop predictors for non-coding risk variants.

The paper maps 3D genome organization and DNA methylation across 86,689 single nuclei from 16 human tissues, revealing cell-type-specific variations and discrepancies between methylation and chromatin structure.

This study examines age-related changes in the human hippocampus using multi-omics data, revealing cell-type loss and epigenetic reprogramming linked to cognitive decline.

The paper shows DNA sequence and H2A.Z histone variant jointly determine nucleosome unwrapping directionality through simulations and NMR data.

The paper constructs an integrative single-cell epigenomic atlas of the adult mouse brain, mapping chromatin states and gene regulatory programs across 100 cell subclasses.

The paper develops an integrative framework to classify and interpret promoter-centric chromatin interactions by combining Hi-C, ChIA-PET, and functional genomic data, identifying a distinct class of architectural promoter-enhancer interactions with context-dependent regulatory roles.

This study identifies reversible chromatin remodeling in Prosopis cineraria that enables survival under recurrent heat stress through epigenetic activation of heat-protective genes and metabolic buffering.

This study extends Helical Coherence Theory to model homologous DNA pairing under confinement, showing that optimal confinement accelerates pairing while avoiding tangling and metastable states.

The paper uses machine learning to identify recombination rate and chromatin environment as key factors influencing subgenome divergence in polyploid species like maize and Brassica.

The paper presents ENCODE, a comprehensive reference map of the genomic basis of gene regulation, including regulatory elements, transcripts, and their interactions in human and mouse genomes.

The paper extends a GPU-accelerated molecular dynamics simulator to support DNA models and improves efficiency for simulating chromatin interactions over long timescales.

The paper integrates multi-omics data to identify regulatory networks driving human dopaminergic neuron differentiation and highlights key transcription factors and enhancer-associated regulators.

The paper quantifies force-induced nucleosome unwrapping using a coarse-grained model, showing DNA flexibility and histone chemistry determine nucleosome stability and plasticity.

CHROME improves regulatory genomics predictions by integrating physically validated chromatin interactions into graph models, enhancing accuracy and interpretability for ChIP-seq, eQTL, and variant pathogenicity.

ORIGAMI reconstructs cis-regulatory networks using multi-omics data and deep learning, revealing synergistic transcription control and disease-associated rewiring.

HiCFoundation is a Hi-C-based model that integrates chromatin structure with epigenomic regulation across species, improving analysis of 3D genome architecture and single-cell data.