ArticleNature methods2022
Integrative genome modeling platform reveals essentiality of rare contact events in 3D genome organizations.
Article in Nature methods, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 40 papers.
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Who cites it
40 citing papers in PubMed.
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- Effects of chromatin-lamina attachment on extra-long-range chromatin interactions.Biophysical journal · 2026Article
- Mega-enhancers compartmentalize transcriptionally active long genes in the brain.Nature cell biology · 2026Article
- map3C: a computational tool for processing multiomic single-cell Hi-C data.Bioinformatics (Oxford, England) · 2026Article
- Loss of multilevel 3D genome organization during breast cancer progression.Genome research · 2026Article
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- Generating three-dimensional genome structures with a variational quantum algorithm.Briefings in bioinformatics · 2025Article
- map3C: a computational tool for processing multiomic single-cell Hi-C data.bioRxiv : the preprint server for biology · 2025Article
- FAIR sharing of Chromatin Tracing datasets using the newly developed 4DN FISH Omics Format.ArXiv · 2025Article
- 3D genome organization shapes DNA damage susceptibility to platinum-based drugs.Nucleic acids research · 2025Article
- MaxComp: Predicting single-cell chromatin compartments from 3D chromosome structures.PLoS computational biology · 2025Article
- Article
- Tensor-FLAMINGO unravels the complexity of single-cell spatial architectures of genomes at high-resolution.Nature communications · 2025Article
- Comparing chromatin contact maps at scale: methods and insights.Nature methods · 2025Article
- Unveiling the role of chromosome structure morphology on gene function through chromosome conformation analysis.Genome biology · 2025Article
- Visualization of chromosomal reorganization induced by heterologous fusions in the mammalian nucleus.Nature communications · 2025Article
- ChromoGen: Diffusion model predicts single-cell chromatin conformations.Science advances · 2025Article
- Motif distribution in genomes gives insights into gene clustering and co-regulation.Nucleic acids research · 2025Article
- ImputeHiFI: An Imputation Method for Multiplexed DNA FISH Data by Utilizing Single-Cell Hi-C and RNA FISH Data.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2024Article
- Polymer Physics Models Reveal Structural Folding Features of Single-Molecule Gene Chromatin Conformations.International journal of molecular sciences · 2024Article
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9 authors.
Funding
Abstract
A multitude of sequencing-based and microscopy technologies provide the means to unravel the relationship between the three-dimensional organization of genomes and key regulatory processes of genome function. Here, we develop a multimodal data integration approach to produce populations of single-cell genome structures that are highly predictive for nuclear locations of genes and nuclear bodies, local chromatin compaction and spatial segregation of functionally related chromatin. We demonstrate that multimodal data integration can compensate for systematic errors in some of the data and can greatly increase accuracy and coverage of genome structure models. We also show that alternative combinations of different orthogonal data sources can converge to models with similar predictive power. Moreover, our study reveals the key contributions of low-frequency ('rare') interchromosomal contacts to accurately predicting the global nuclear architecture, including the positioning of genes and chromosomes. Overall, our results highlight the benefits of multimodal data integration for genome structure analysis, available through the Integrative Genome Modeling software package.
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