Hi-C

The paper develops a stochastic model of histone dynamics at the replication fork, showing that differential diffusivity explains histone inheritance patterns and predicts epigenomic patterns observed in experiments.

MCIBox is a toolkit for analyzing single-molecule chromatin interactions and identifying micro-domains through visualization and clustering algorithms.

The paper systematically coarse-grains chromatin using Micro-C data to predict polymer properties, showing beads are soft and overlapping with distinct behavior at TAD boundaries.

This study uses a multi-omic approach to analyze complex genomic rearrangements in head and neck cancers, identifying HPV-mediated instability and enhancer hijacking as drivers of oncogene overexpression.

This study creates a human fetal cerebellar cell atlas to identify transitional progenitors linked to aggressive medulloblastoma subgroups and their oncogenic mechanisms.

This study shows that constricted migration in cancer cells leads to stable 3D genome structure changes associated with increased migration efficiency and altered gene expression.

This study shows that WAPL regulates T cell 3D genome structure, affecting activation, proliferation, and GVHD severity.

SnapHiC-D identifies differential chromatin contacts between two scHi-C datasets with high sensitivity and accuracy, showing correlation with cell-type-specific gene expression and epigenomic features.

This paper introduces InfoHiC, a method to predict 3D cancer genome folding from genomic rearrangements, identifying functional impacts of non-coding rearrangements in breast and medulloblastoma cancers.

The paper shows GATA6 and NANOG bind shared regulatory elements to drive divergent cell fates in mouse blastocysts by modulating chromatin accessibility and transcriptional activation.

Nucleome Browser integrates heterogeneous 4D Nucleome data into an interactive platform for visualization and exploration across biological contexts.

The paper introduces a 3D visualization module to the WashU Epigenome Browser, enabling integration of 1D and 2D genomic data with 3D chromatin structures for better interpretation of genomic information.

The paper develops LIMe-Hi-C to study how Polycomb repressive complex 2 and lamina association regulate heterochromatin sub-compartments.

This study investigates how DNA sequence and internucleosomal interactions influence nucleosome array compaction using Atomic Force Microscopy and develops a theoretical model to explain the results.

The paper identifies genetic and regulatory mechanisms underlying heterosis in the rice hybrid Y900 by analyzing genome and transcriptome data from its parental lines.

NucleoMap identifies nucleosome positions from ultra-high resolution contact maps, outperforming existing methods and revealing associations between nucleosome organization and chromatin functions.

Hi-TrAC identifies active sub-TADs with median size 100 kb, revealing fractal nesting of super-enhancers and their disruption by Cohesin and H3K4me1 perturbations.

The paper compares loop-extrusion and polymer phase-separation models against chromatin data, finding they can co-exist in shaping single-cell chromatin architecture.

The paper develops CTG, a diffusion-based method to improve Hi-C data reliability and reveal structural genomic regulation.

This paper introduces an algorithm to reconstruct 3D chromosome structures in single human diploid cells using allele-specific SNVs without imputation, achieving resolutions of 40-kb to 1-Mb.

The paper develops a Hi-C data analysis pipeline to study repeat family interactions in plant genome 3D organization, finding preferential homotypic interactions among ribosomal DNA, transposons, and some LTR retrotransposons.

The paper investigates TAD remodeling during mouse thymocyte differentiation using Capture Hi-C, finding transcription can directly alter chromatin structure.

The paper links SNPs to genes using functionally informed strategies, revealing enhancer-related and master-regulator genes contribute to autoimmune disease heritability.

The paper shows that long-term heat shock causes chromatin conformation changes in K562 cells due to cell cycle arrest, not chromatin accessibility changes.

The paper develops a computational framework to model loop extrusion by condensin I and II during mitosis, showing changes in loop size and structure across cell types.

Hi-C-LSTM uses a recurrent neural network to learn low-dimensional representations of Hi-C data, enabling the identification of genomic elements that define chromatin conformation.

The paper introduces CscoreTool-M, a model-based method for inferring 3D genome sub-compartments from Hi-C data, showing higher accuracy in identifying heterochromatin regions and quantifying sub-compartment heterogeneity in cell populations.

The paper investigates how chromatin organization influences replication origin activation and fork directionality using multi-omics data from primary and tumor cells.

This study investigates the 3D genome organization of pepper, showing how chromatin structure relates to gene expression and evolution.

HiCImpute identifies structural zeros in scHi-C data and improves imputation, leading to more accurate clustering and subtype discovery in neuronal cells.