ReviewPLoS computational biology2011
Bridging the resolution gap in structural modeling of 3D genome organization.
Review in PLoS computational biology, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 52 papers.
What it found
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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.
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Who cites it
52 citing papers in PubMed, 88 citations in OpenAlex.
- Investigating Phase Separation in Genome Folding via Multiscale Computational Modeling.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Review
- An experimentally-informed polymer model reveals high resolution organization of genomic loci.Nature communications · 2026Article
- Understanding and Simulating the Dynamics of a Polymer-Like Chromatin.Methods in molecular biology (Clifton, N.J.) · 2025Review
- ARGV: 3D genome structure exploration using augmented reality.BMC bioinformatics · 2024Article
- Machine learning meets physics: A two-way street.Proceedings of the National Academy of Sciences of the United States of America · 2024Article
- Interplay between epigenome and 3D chromatin structure.BMB reports · 2023Review
- EVRC: reconstruction of chromosome 3D structure models using error-vector resultant algorithm with clustering coefficient.Bioinformatics (Oxford, England) · 2023Article
- Benchmark study for evaluating the quality of reference genomes and gene annotations in 114 species.Frontiers in veterinary science · 2023Article
- emDNA - A Tool for Modeling Protein-decorated DNA Loops and Minicircles at the Base-pair Step Level.Journal of molecular biology · 2022Article
- Multiscale modeling of genome organization with maximum entropy optimization.The Journal of chemical physics · 2021Article
- Article
- PHi-C: deciphering Hi-C data into polymer dynamics.NAR genomics and bioinformatics · 2020Article
- Chromatin and Cytoskeletal Tethering Determine Nuclear Morphology in Progerin-Expressing Cells.Biophysical journal · 2020Article
- Nonequilibrium Biophysical Processes Influence the Large-Scale Architecture of the Cell Nucleus.Biophysical journal · 2020Article
- Visualizing the genome in high resolution challenges our textbook understanding.Nature methods · 2020Review
- Toward understanding the dynamic state of 3D genome.Computational and structural biotechnology journal · 2020Review
- Hi-C analysis: from data generation to integration.Biophysical reviews · 2019Review
- Topological Constraints in Eukaryotic Genomes and How They Can Be Exploited to Improve Spatial Models of Chromosomes.Frontiers in molecular biosciences · 2019Article
- Challenges and guidelines toward 4D nucleome data and model standards.Nature genetics · 2018Review
- From dynamic chromatin architecture to DNA damage repair and back.Nucleus (Austin, Tex.) · 2018Review
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
2 authors at 2 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Over the last decade, and especially after the advent of fluorescent in situ hybridization imaging and chromosome conformation capture methods, the availability of experimental data on genome three-dimensional organization has dramatically increased. We now have access to unprecedented details of how genomes organize within the interphase nucleus. Development of new computational approaches to leverage this data has already resulted in the first three-dimensional structures of genomic domains and genomes. Such approaches expand our knowledge of the chromatin folding principles, which has been classically studied using polymer physics and molecular simulations. Our outlook describes computational approaches for integrating experimental data with polymer physics, thereby bridging the resolution gap for structural determination of genomes and genomic domains.
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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.