ArticleBriefings in functional genomics2020
Computational methods for predicting 3D genomic organization from high-resolution chromosome conformation capture data.
Article in Briefings in functional genomics, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 24 papers.
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Who cites it
24 citing papers in PubMed.
- Simultaneous modeling of chromatin conformation changes from multiple single-cell interaction maps with ChromMovie.Genome research · 2026Article
- esBAF and INO80C fine-tune subcompartments and differentially regulate enhancer-promoter interactions.Genetics · 2026Article
- Review
- esBAF and INO80C fine-tune subcompartments and differentially regulate enhancer-promoter interactions.bioRxiv : the preprint server for biology · 2025Article
- The challenge of chromatin model comparison and validation: A project from the first international 4D Nucleome Hackathon.PLoS computational biology · 2025Article
- ChromMovie: A Molecular Dynamics Approach for Simultaneous Modeling of Chromatin Conformation Changes from Multiple Single-Cell Hi-C Maps.bioRxiv : the preprint server for biology · 2025Article
- Advancements and future directions in single-cell Hi-C based 3D chromatin modeling.Computational and structural biotechnology journal · 2024Review
- ARGV: 3D genome structure exploration using augmented reality.BMC bioinformatics · 2024Article
- Comparative study on chromatin loop callers using Hi-C data reveals their effectiveness.BMC bioinformatics · 2024Article
- Mapping robust multiscale communities in chromosome contact networks.Scientific reports · 2023Article
- Techniques for and challenges in reconstructing 3D genome structures from 2D chromosome conformation capture data.Current opinion in cell biology · 2023Review
- 3D genomic organization in cancers.Quantitative biology (Beijing, China) · 2023Review
- Strong interactions between highly dynamic lamina-associated domains and the nuclear envelope stabilize the 3D architecture of Drosophila interphase chromatin.Epigenetics & chromatin · 2023Article
- ParticleChromo3D+: A Web Server for ParticleChromo3D Algorithm for 3D Chromosome Structure Reconstruction.Current issues in molecular biology · 2023Article
- ParticleChromo3D: a Particle Swarm Optimization algorithm for chromosome 3D structure prediction from Hi-C data.BioData mining · 2022Article
- Imputation-free reconstructions of three-dimensional chromosome architectures in human diploid single-cells using allele-specified contacts.Scientific reports · 2022Article
- Uncovering the Principles of Genome Folding by 3D Chromatin Modeling.Cold Spring Harbor perspectives in biology · 2022Review
- Integrative approaches in genome structure analysis.Structure (London, England : 1993) · 2022Review
- Minimalistic 3D chromatin models: Sparse interactions in single cells drive the chromatin fold and form many-body units.Current opinion in structural biology · 2021Review
- Modeling the 3D genome of plants.Nucleus (Austin, Tex.) · 2021Article
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Authors and funding
2 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The advent of high-resolution chromosome conformation capture assays (such as 5C, Hi-C and Pore-C) has allowed for unprecedented sequence-level investigations into the structure-function relationship of the genome. In order to comprehensively understand this relationship, computational tools are required that utilize data generated from these assays to predict 3D genome organization (the 3D genome reconstruction problem). Many computational tools have been developed that answer this need, but a comprehensive comparison of their underlying algorithmic approaches has not been conducted. This manuscript provides a comprehensive review of the existing computational tools (from November 2006 to September 2019, inclusive) that can be used to predict 3D genome organizations from high-resolution chromosome conformation capture data. Overall, existing tools were found to use a relatively small set of algorithms from one or more of the following categories: dimensionality reduction, graph/network theory, maximum likelihood estimation (MLE) and statistical modeling. Solutions in each category are far from maturity, and the breadth and depth of various algorithmic categories have not been fully explored. While the tools for predicting 3D structure for a genomic region or single chromosome are diverse, there is a general lack of algorithmic diversity among computational tools for predicting the complete 3D genome organization from high-resolution chromosome conformation capture data.
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