ArticleBiophysical journal2018
A Polymer Model for the Quantitative Reconstruction of Chromosome Architecture from HiC and GAM Data.
Article in Biophysical journal, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 25 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
25 citing papers in PubMed.
- Single-molecule chromatin tracing reveals a diversity of megabase heterochromatin domains.Nature structural & molecular biology · 2026Article
- RepliSage: a stochastic graph-based framework for 3D chromatin modeling across the cell cycle.Nucleic acids research · 2026Article
- A universal polymer signature in Hi-C resolves cohesin loop density and supports monomeric extrusion.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
- Revealing the biophysics of lamina-associated domain formation by integrating theoretical modeling and high-resolution imaging.Nature communications · 2025Article
- The challenge of chromatin model comparison and validation: A project from the first international 4D Nucleome Hackathon.PLoS computational biology · 2025Article
- Chromatin structures from integrated AI and polymer physics model.PLoS computational biology · 2025Article
- Article
- Multiscale molecular modeling of chromatin with MultiMM: From nucleosomes to the whole genome.Computational and structural biotechnology journal · 2024Article
- Hi-C-guided many-polymer model to decipher 3D genome organization.Biophysical journal · 2024Article
- Replicating Chromosomes in Whole-Cell Models of Bacteria.Methods in molecular biology (Clifton, N.J.) · 2024Article
- Polymer folding through active processes recreates features of genome organization.Proceedings of the National Academy of Sciences of the United States of America · 2023Article
- A maximum-entropy model to predict 3D structural ensembles of chromatin from pairwise distances with applications to interphase chromosomes and structural variants.Nature communications · 2023Article
- Dissecting the cosegregation probability from genome architecture mapping.Biophysical journal · 2022Article
- Uncovering the Quantitative Relationships Among Chromosome Fluctuations, Epigenetics, and Gene Expressions of Transdifferentiation on Waddington Landscape.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2022Article
- Extracting multi-way chromatin contacts from Hi-C data.PLoS computational biology · 2021Article
- The 3D Genome: From Structure to Function.International journal of molecular sciences · 2021Review
- A Hi-C data-integrated model elucidates E. coli chromosome's multiscale organization at various replication stages.Nucleic acids research · 2021Article
- A unified framework for inferring the multi-scale organization of chromatin domains from Hi-C.PLoS computational biology · 2021Article
- Self assembly of model polymers into biological random networks.Computational and structural biotechnology journal · 2021Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
3 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
It is widely believed that the folding of the chromosome in the nucleus has a major effect on genetic expression. For example, coregulated genes in several species have been shown to colocalize in space despite being far away on the DNA sequence. In this manuscript, we present a new, to our knowledge, method to model the three-dimensional structure of the chromosome in live cells based on DNA-DNA interactions measured in high-throughput chromosome conformation capture experiments and genome architecture mapping. Our approach incorporates a polymer model and directly uses the contact probabilities measured in high-throughput chromosome conformation capture experiments and genome architecture mapping experiments rather than estimates of average distances between genomic loci. Specifically, we model the chromosome as a Gaussian polymer with harmonic interactions and extract the coupling coefficients best reproducing the experimental contact probabilities. In contrast to existing methods, we give an exact expression of the contact probabilities at thermodynamic equilibrium. The Gaussian effective model reconstructed with our method reproduces experimental contacts with high accuracy. We also show how Brownian dynamics simulations of our reconstructed Gaussian effective model can be used to study chromatin organization and possibly give some clue about its dynamics.
Indexed as
Identifiers
What OpenQuestion holds
Registered trials
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.