ArticleBioinformatics (Oxford, England)2019
GenomeFlow: a comprehensive graphical tool for modeling and analyzing 3D genome structure.
Article in Bioinformatics (Oxford, England), 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 17 papers.
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Who cites it
17 citing papers in PubMed.
- Cell-cycle-resolved Hi-C reveals unexpected plasticity of A/B compartments across interphase.eLife · 2026Article
- Design Space and Declarative Grammar for 3D Genomic Data Visualization.IEEE transactions on visualization and computer graphics · 2026Article
- A heat stress-responsive epigenome defines the dynamic 3D chromatin structure in Chinese cabbage.Plant physiology · 2025Article
- An integrative 3D-genome database for plants.Plant communications · 2025Article
- Reconstructing 3D chromosome structures from single-cell Hi-C data with SO(3)-equivariant graph neural networks.NAR genomics and bioinformatics · 2025Article
- Hierarchical architecture of neo-sex chromosomes and accelerated adaptive evolution in tortricid moths.Genome research · 2025Article
- ScHiCAtt: Enhancing single-cell Hi-C data resolution using attention-based models.Computational and structural biotechnology journal · 2025Article
- Remodeling of Il4-Il13-Il5 locus underlies selective gene expression.Nature immunology · 2024Article
- 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
- 3D models of fungal chromosomes to enhance visual integration of omics data.NAR genomics and bioinformatics · 2023Article
- Single-cell Hi-C data enhancement with deep residual and generative adversarial networks.Bioinformatics (Oxford, England) · 2023Article
- ParticleChromo3D: a Particle Swarm Optimization algorithm for chromosome 3D structure prediction from Hi-C data.BioData mining · 2022Article
- CSynth: an interactive modelling and visualization tool for 3D chromatin structure.Bioinformatics (Oxford, England) · 2021Article
- A compendium and comparative epigenomics analysis of cis-regulatory elements in the pig genome.Nature communications · 2021Article
- GSDB: a database of 3D chromosome and genome structures reconstructed from Hi-C data.BMC molecular and cell biology · 2020Article
- An Overview of Methods for Reconstructing 3-D Chromosome and Genome Structures from Hi-C Data.Biological procedures online · 2019Review
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4 authors.
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Abstract
motivationThree-dimensional (3D) genome organization plays important functional roles in cells. User-friendly tools for reconstructing 3D genome models from chromosomal conformation capturing data and analyzing them are needed for the study of 3D genome organization.
resultsWe built a comprehensive graphical tool (GenomeFlow) to facilitate the entire process of modeling and analysis of 3D genome organization. This process includes the mapping of Hi-C data to one-dimensional (1D) reference genomes, the generation, normalization and visualization of two-dimensional (2D) chromosomal contact maps, the reconstruction and the visualization of the 3D models of chromosome and genome, the analysis of 3D models and the integration of these models with functional genomics data. This graphical tool is the first of its kind in reconstructing, storing, analyzing and annotating 3D genome models. It can reconstruct 3D genome models from Hi-C data and visualize them in real-time. This tool also allows users to overlay gene annotation, gene expression data and genome methylation data on top of 3D genome models. AVAILABILITY AND IMPLEMENTATION: The source code and user manual: https://github.com/jianlin-cheng/GenomeFlow. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
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