ArticleNucleic acids research2013
Recovering ensembles of chromatin conformations from contact probabilities.
Article in Nucleic acids research, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 41 papers.
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Who cites it
41 citing papers in PubMed.
- One chromatin, many structures: From ensemble contact maps to single-cell 3D organization.Biophysical journal · 2026Article
- One Chromatin, Many Structures: From Ensemble Contact Maps to Single-Cell 3D Organization.bioRxiv : the preprint server for biology · 2026Article
- The challenge of chromatin model comparison and validation: A project from the first international 4D Nucleome Hackathon.PLoS computational biology · 2025Article
- Advancements and future directions in single-cell Hi-C based 3D chromatin modeling.Computational and structural biotechnology journal · 2024Review
- Replicating Chromosomes in Whole-Cell Models of Bacteria.Methods in molecular biology (Clifton, N.J.) · 2024Article
- Efficient Hi-C inversion facilitates chromatin folding mechanism discovery and structure prediction.Biophysical journal · 2023Article
- Efficient Hi-C inversion facilitates chromatin folding mechanism discovery and structure prediction.bioRxiv : the preprint server for biology · 2023Article
- Theory of chromatin organization maintained by active loop extrusion.Proceedings of the National Academy of Sciences of the United States of America · 2023Article
- Heterogeneous interactions and polymer entropy decide organization and dynamics of chromatin domains.Biophysical journal · 2022Article
- Analysis of three-dimensional chromatin packing domains by chromatin scanning transmission electron microscopy (ChromSTEM).Scientific reports · 2022Article
- Uncovering the Principles of Genome Folding by 3D Chromatin Modeling.Cold Spring Harbor perspectives in biology · 2022Review
- Biology and Model Predictions of the Dynamics and Heterogeneity of Chromatin-Nuclear Lamina Interactions.Frontiers in cell and developmental biology · 2022Review
- Multiscale modeling of genome organization with maximum entropy optimization.The Journal of chemical physics · 2021Article
- Application of Hi-C and other omics data analysis in human cancer and cell differentiation research.Computational and structural biotechnology journal · 2021Review
- Computational approaches for inferring 3D conformations of chromatin from chromosome conformation capture data.Methods (San Diego, Calif.) · 2020Review
- Computational methods for predicting 3D genomic organization from high-resolution chromosome conformation capture data.Briefings in functional genomics · 2020Article
- Computing 3D Chromatin Configurations from Contact Probability Maps by Inverse Brownian Dynamics.Biophysical journal · 2020Article
- Integrating Hi-C and FISH data for modeling of the 3D organization of chromosomes.Nature communications · 2019Article
- An Overview of Methods for Reconstructing 3-D Chromosome and Genome Structures from Hi-C Data.Biological procedures online · 2019Review
- A Polymer Model for the Quantitative Reconstruction of Chromosome Architecture from HiC and GAM Data.Biophysical journal · 2018Article
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2 authors.
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Abstract
The 3D higher order organization of chromatin within the nucleus of eukaryotic cells has so far remained elusive. A wealth of relevant information, however, is increasingly becoming available from chromosome conformation capture (3C) and related experimental techniques, which measure the probabilities of contact between large numbers of genomic sites in fixed cells. Such contact probabilities (CPs) can in principle be used to deduce the 3D spatial organization of chromatin. Here, we propose a computational method to recover an ensemble of chromatin conformations consistent with a set of given CPs. Compared with existing alternatives, this method does not require conversion of CPs to mean spatial distances. Instead, we estimate CPs by simulating a physically realistic, bead-chain polymer model of the 30-nm chromatin fiber. We then use an approach from adaptive filter theory to iteratively adjust the parameters of this polymer model until the estimated CPs match the given CPs. We have validated this method against reference data sets obtained from simulations of test systems with up to 45 beads and 4 loops. With additional testing against experiments and with further algorithmic refinements, our approach could become a valuable tool for researchers examining the higher order organization of chromatin.
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