ArticleProceedings of the National Academy of Sciences of the United States of America2015
Topology, structures, and energy landscapes of human chromosomes.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 114 papers.
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Who cites it
114 citing papers in PubMed.
- Euchromatin forms condensed domains with short active regions on the surface.Nature genetics · 2026Article
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- Investigating Phase Separation in Genome Folding via Multiscale Computational Modeling.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Review
- Architecture and regulation of nanoscale chromatin domains.Nature communications · 2026Review
- Exploring the energy landscape of bacterial chromosome segregation.Proceedings of the National Academy of Sciences of the United States of America · 2026Article
- An experimentally-informed polymer model reveals high resolution organization of genomic loci.Nature communications · 2026Article
- A data-driven chromatin model reveals spatial and dynamic features of genome organization.Proceedings of the National Academy of Sciences of the United States of America · 2026Article
- Motorized chromosome models of mitotic chromosome folding.Nature communications · 2025Article
- Transcriptional condensates encode a "golden mean" to optimize enhancer-promoter communication across genomic distances.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- GNNs surpass transformers in tumor medical image segmentation.Scientific reports · 2025Article
- Polymer model integrates imaging and sequencing to reveal how nanoscale heterochromatin domains influence gene expression.Nature communications · 2025Article
- Chromatin structures from integrated AI and polymer physics model.PLoS computational biology · 2025Article
- Energy landscape analysis of the development of the chromosome structure across the cell cycle.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- Polymer models of chromatin organization in virally infected cells.Biochemical Society transactions · 2025Review
- ChromoGen: Diffusion model predicts single-cell chromatin conformations.Science advances · 2025Article
- Integrative Modeling of 3D Genome Organization by Bayesian Molecular Dynamics Simulations with Hi-C Metainference.Methods in molecular biology (Clifton, N.J.) · 2025Article
- Node features of chromosome structure networks and their connections to genome annotation.Computational and structural biotechnology journal · 2024Article
- Polymer Physics Models Reveal Structural Folding Features of Single-Molecule Gene Chromatin Conformations.International journal of molecular sciences · 2024Article
- Article
- Polymer physics models reveal structural folding features of single-molecule gene chromatin conformations.bioRxiv : the preprint server for biology · 2024Article
54 more citing papers are in PubMed but not listed here.
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2 authors.
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No grant is acknowledged in the PubMed record.
Abstract
Chromosome conformation capture experiments provide a rich set of data concerning the spatial organization of the genome. We use these data along with a maximum entropy approach to derive a least-biased effective energy landscape for the chromosome. Simulations of the ensemble of chromosome conformations based on the resulting information theoretic landscape not only accurately reproduce experimental contact probabilities, but also provide a picture of chromosome dynamics and topology. The topology of the simulated chromosomes is probed by computing the distribution of their knot invariants. The simulated chromosome structures are largely free of knots. Topologically associating domains are shown to be crucial for establishing these knotless structures. The simulated chromosome conformations exhibit a tendency to form fibril-like structures like those observed via light microscopy. The topologically associating domains of the interphase chromosome exhibit multistability with varying liquid crystalline ordering that may allow discrete unfolding events and the landscape is locally funneled toward "ideal" chromosome structures that represent hierarchical fibrils of fibrils.
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