ReviewBiological procedures online2019
An Overview of Methods for Reconstructing 3-D Chromosome and Genome Structures from Hi-C Data.
Review in Biological procedures online, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 85 papers.
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Who cites it
85 citing papers in PubMed.
- Physics-Based Modeling of Sparse Single-Cell Hi-C Uncovers Structural and Epigenetic Variability.International journal of molecular sciences · 2026Article
- Simultaneous modeling of chromatin conformation changes from multiple single-cell interaction maps with ChromMovie.Genome research · 2026Article
- Uchimata: a toolkit for visualization of 3D genome structures on the web and in computational notebooks.Bioinformatics (Oxford, England) · 2026Article
- From 2D to 4D: a containerized workflow and browser to explore dynamic chromatin architecture.BMC bioinformatics · 2026Article
- EmbedTAD Using Graph Embedding and Unsupervised Learning to Identify TADs from High-Resolution Hi-C Data.Communications biology · 2025Article
- DiCARN-DNase: enhancing cell-to-cell Hi-C resolution using dilated cascading ResNet with self-attention and DNase-seq chromatin accessibility data.Bioinformatics (Oxford, England) · 2025Article
- The challenge of chromatin model comparison and validation: A project from the first international 4D Nucleome Hackathon.PLoS computational biology · 2025Article
- From 2D to 4D: a Containerized Workflow and Browser to Explore Dynamic Chromatin Architecture.bioRxiv : the preprint server for biology · 2025Article
- Genome Mountaineering: Expanding Horizons of the 3D Genome for the Intrepid Evolutionary Adventurer.Genome biology and evolution · 2025Review
- 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
- Chromatin structures from integrated AI and polymer physics model.PLoS computational biology · 2025Article
- From Data to Cure: A Comprehensive Exploration of Multi-omics Data Analysis for Targeted Therapies.Molecular biotechnology · 2025Review
- Single-cell 3D genome reconstruction in the haploid setting using rigidity theory.Journal of mathematical biology · 2025Article
- Article
- Reconstructing 3D chromosome structures from single-cell Hi-C data with SO(3)-equivariant graph neural networks.NAR genomics and bioinformatics · 2025Article
- Deciphering single-cell genomic architecture: insights into cellular heterogeneity and regulatory dynamics.Genomics & informatics · 2025Review
- Physical models of bacterial chromosomes.Molecular microbiology · 2025Review
- Mapping the 3D genome architecture.Computational and structural biotechnology journal · 2025Review
- Article
- ScHiCAtt: Enhancing single-cell Hi-C data resolution using attention-based models.Computational and structural biotechnology journal · 2025Article
25 more citing papers are in PubMed but not listed here.
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3 authors.
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No grant is acknowledged in the PubMed record.
Abstract
Over the past decade, methods for predicting three-dimensional (3-D) chromosome and genome structures have proliferated. This has been primarily due to the development of high-throughput, next-generation chromosome conformation capture (3C) technologies, which have provided next-generation sequencing data about chromosome conformations in order to map the 3-D genome structure. The introduction of the Hi-C technique-a variant of the 3C method-has allowed researchers to extract the interaction frequency (IF) for all loci of a genome at high-throughput and at a genome-wide scale. In this review we describe, categorize, and compare the various methods developed to map chromosome and genome structures from 3C data-particularly Hi-C data. We summarize the improvements introduced by these methods, describe the approach used for method evaluation, and discuss how these advancements shape the future of genome structure construction.
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