ArticleGenome biology2017
Chrom3D: three-dimensional genome modeling from Hi-C and nuclear lamin-genome contacts.
Article in Genome biology, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 136 papers.
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Who cites it
136 citing papers in PubMed, 212 citations in OpenAlex.
- Effects of chromatin-lamina attachment on extra-long-range chromatin interactions.Biophysical journal · 2026Article
- Deep learning enabled prediction of nuclear lamina-associated chromatin.Patterns (New York, N.Y.) · 2026Article
- Genome assembly of Astatotilapia latifasciata uncovers B chromosome-linked chromatin reorganization.Heredity · 2026Article
- Highly efficient chromatin conformation capture with post-enrichment in single cells by HiChew.Genome biology · 2026Article
- The pangenome ofiScience · 2026Article
- Dynamic changes in Lamin B1 and heterochromatin coincide with chromatin condensation during human erythropoiesis.Genome biology · 2026Article
- SCW: building the whole-genome 3D structures based on extremely sparse single-cell Hi-C data.BMC bioinformatics · 2026Article
- Loss of multilevel 3D genome organization during breast cancer progression.Genome research · 2026Article
- Design Space and Declarative Grammar for 3D Genomic Data Visualization.IEEE transactions on visualization and computer graphics · 2026Article
- Reconstructing the three-dimensional architecture of extrachromosomal DNA with ec3D.Nature communications · 2025Article
- SLUR(M)-py: a SLURM powered Pythonic pipeline for parallel processing of 3D (Epi)genomic profiles.Epigenomics · 2025Article
- The 3D nuclear position and compartmentalization of genes prime their response to mechano-confinement.bioRxiv : the preprint server for biology · 2025Article
- p53 Regulates Nuclear Architecture to Reduce Carcinogen Sensitivity and Mutagenic Potential.bioRxiv : the preprint server for biology · 2025Article
- Translocations can drive expression changes of multiple genes in regulons covering entire chromosome arms.Nucleic acids research · 2025Article
- The challenge of chromatin model comparison and validation: A project from the first international 4D Nucleome Hackathon.PLoS computational biology · 2025Article
- SMCHD1 maintains heterochromatin, genome compartments and epigenome landscape in human myoblasts.Nature communications · 2025Article
- Polymer model integrates imaging and sequencing to reveal how nanoscale heterochromatin domains influence gene expression.Nature communications · 2025Article
- Single-cell 3D genome reconstruction in the haploid setting using rigidity theory.Journal of mathematical biology · 2025Article
- Cryo-EM structures of the BAF-Lamin A/C complex bound to nucleosomes.Nature communications · 2025Article
- Structural basis of differential gene expression at eQTLs loci from high-resolution ensemble models of 3D single-cell chromatin conformations.Bioinformatics (Oxford, England) · 2025Article
76 more citing papers are in PubMed but not listed here.
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Authors and funding
11 authors at 5 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Current three-dimensional (3D) genome modeling platforms are limited by their inability to account for radial placement of loci in the nucleus. We present Chrom3D, a user-friendly whole-genome 3D computational modeling framework that simulates positions of topologically-associated domains (TADs) relative to each other and to the nuclear periphery. Chrom3D integrates chromosome conformation capture (Hi-C) and lamin-associated domain (LAD) datasets to generate structure ensembles that recapitulate radial distributions of TADs detected in single cells. Chrom3D reveals unexpected spatial features of LAD regulation in cells from patients with a laminopathy-causing lamin mutation. Chrom3D is freely available on github.
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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.