ArticleBiophysical journal2020
Data-Driven Polymer Model for Mechanistic Exploration of Diploid Genome Organization.
Article in Biophysical journal, 2020. 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.
- Deep learning enabled prediction of nuclear lamina-associated chromatin.Patterns (New York, N.Y.) · 2026Article
- Investigating Phase Separation in Genome Folding via Multiscale Computational Modeling.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Review
- The Alchemist, the Scientist, and the Robot: Exploring the Potential of Human-AI Symbiosis in Self-Driving Polymer Laboratories.Macromolecular rapid communications · 2025Review
- The inner nuclear membrane protein LEMD3 organizes the 3D chromatin architecture to maintain vascular smooth muscle cell identity.Nature communications · 2025Article
- Polymer-derived distance penalties improve chromatin interaction predictions from single-cell data across crop genomes.bioRxiv : the preprint server for biology · 2025Article
- Predicting gene expression changes from chromatin structure modification.NPJ systems biology and applications · 2025Article
- Unveiling the role of chromosome structure morphology on gene function through chromosome conformation analysis.Genome biology · 2025Article
- Hi-C-guided many-polymer model to decipher 3D genome organization.Biophysical journal · 2024Article
- Article
- OpenNucleome for high resolution nuclear structural and dynamical modeling.bioRxiv : the preprint server for biology · 2024Article
- Human Coronavirus Infection Reorganizes Spatial Genomic Architecture in Permissive Lung Cells.Research square · 2024Article
- Computational methods for analysing multiscale 3D genome organization.Nature reviews. Genetics · 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
- Quantifying the large-scale chromosome structural dynamics during the mitosis-to-G1 phase transition of cell cycle.Open biology · 2023Article
- Evaluating the role of the nuclear microenvironment in gene function by population-based modeling.Nature structural & molecular biology · 2023Article
- Mesoscale, long-time mixing of chromosomes and its connection to polymer dynamics.PLoS computational biology · 2023Article
- Compartmentalization with nuclear landmarks yields random, yet precise, genome organization.Biophysical journal · 2023Article
- Interphase chromosomes of the Aedes aegypti mosquito are liquid crystalline and can sense mechanical cues.Nature communications · 2023Article
- Molecular Determinants for the Layering and Coarsening of Biological Condensates.Aggregate (Hoboken, N.J.) · 2022Article
- Insights into the cell fate decision-making processes from chromosome structural reorganizations.Biophysics reviews · 2022Article
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6 authors.
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Abstract
Chromosomes are positioned nonrandomly inside the nucleus to coordinate with their transcriptional activity. The molecular mechanisms that dictate the global genome organization and the nuclear localization of individual chromosomes are not fully understood. We introduce a polymer model to study the organization of the diploid human genome. It is data-driven because all parameters can be derived from Hi-C data; it is also a mechanistic model because the energy function is explicitly written out based on a few biologically motivated hypotheses. These two features distinguish the model from existing approaches and make it useful both for reconstructing genome structures and for exploring the principles of genome organization. We carried out extensive validations to show that simulated genome structures reproduce a wide variety of experimental measurements, including chromosome radial positions and spatial distances between homologous pairs. Detailed mechanistic investigations support the importance of both specific interchromosomal interactions and centromere clustering for chromosome positioning. We anticipate the polymer model, when combined with Hi-C experiments, to be a powerful tool for investigating large-scale rearrangements in genome structure upon cell differentiation and tumor progression.
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