ArticleNature communications2019
Integrating Hi-C and FISH data for modeling of the 3D organization of chromosomes.
Article in Nature communications, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 44 papers.
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Who cites it
44 citing papers in PubMed.
- Simultaneous modeling of chromatin conformation changes from multiple single-cell interaction maps with ChromMovie.Genome research · 2026Article
- ChromInSight: Revealing DNA Double-Strand Breaks Through Chromatin Structural Insights With an Interpretable Graph Neural Network Framework.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2025Article
- The challenge of chromatin model comparison and validation: A project from the first international 4D Nucleome Hackathon.PLoS computational biology · 2025Article
- ChromMovie: A Molecular Dynamics Approach for Simultaneous Modeling of Chromatin Conformation Changes from Multiple Single-Cell Hi-C Maps.bioRxiv : the preprint server for biology · 2025Article
- Tensor-FLAMINGO unravels the complexity of single-cell spatial architectures of genomes at high-resolution.Nature communications · 2025Article
- Single-cell 3D genome reconstruction in the haploid setting using rigidity theory.Journal of mathematical biology · 2025Article
- geomeTriD: a Bioconductor package for interactive and integrative visualization of 3D structural model with multi-omics data.Bioinformatics advances · 2025Article
- Advancements and future directions in single-cell Hi-C based 3D chromatin modeling.Computational and structural biotechnology journal · 2024Review
- scHiClassifier: a deep learning framework for cell type prediction by fusing multiple feature sets from single-cell Hi-C data.Briefings in bioinformatics · 2024Article
- Hi-C-guided many-polymer model to decipher 3D genome organization.Biophysical journal · 2024Article
- Enhancer-driven 3D chromatin domain folding modulates transcription in human mammary tumor cells.Life science alliance · 2024Article
- Computational methods for analysing multiscale 3D genome organization.Nature reviews. Genetics · 2024Review
- Hi-BDiSCO: folding 3D mesoscale genome structures from Hi-C data using brownian dynamics.Nucleic acids research · 2024Article
- Chromosome structure modeling tools and their evaluation in bacteria.Briefings in bioinformatics · 2024Review
- Large-scale data-driven and physics-based models offer insights into the relationships among the structures, dynamics, and functions of chromosomes.Journal of molecular cell biology · 2023Review
- EVRC: reconstruction of chromosome 3D structure models using error-vector resultant algorithm with clustering coefficient.Bioinformatics (Oxford, England) · 2023Article
- Techniques for and challenges in reconstructing 3D genome structures from 2D chromosome conformation capture data.Current opinion in cell biology · 2023Review
- (Tn5-)FISH-based imaging in the era of 3D/spatial genomics.Biophysics reports · 2023Article
- Complementing Hi-C information for 3D chromatin reconstruction by ChromStruct.Frontiers in bioinformatics · 2023Article
- Constricted migration is associated with stable 3D genome structure differences in cancer cells.EMBO reports · 2022Article
Corrections and comments
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Authors and funding
10 authors.
Funding
Abstract
The new advances in various experimental techniques that provide complementary information about the spatial conformations of chromosomes have inspired researchers to develop computational methods to fully exploit the merits of individual data sources and combine them to improve the modeling of chromosome structure. Here we propose GEM-FISH, a method for reconstructing the 3D models of chromosomes through systematically integrating both Hi-C and FISH data with the prior biophysical knowledge of a polymer model. Comprehensive tests on a set of chromosomes, for which both Hi-C and FISH data are available, demonstrate that GEM-FISH can outperform previous chromosome structure modeling methods and accurately capture the higher order spatial features of chromosome conformations. Moreover, our reconstructed 3D models of chromosomes revealed interesting patterns of spatial distributions of super-enhancers which can provide useful insights into understanding the functional roles of these super-enhancers in gene regulation.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.