ArticleBioinformatics (Oxford, England)2021
CSynth: an interactive modelling and visualization tool for 3D chromatin structure.
Article in Bioinformatics (Oxford, England), 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 15 papers.
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Who cites it
15 citing papers in PubMed.
- H3K27me3 spreading organizes canonical PRC1 chromatin architecture to regulate developmental programs.Nature genetics · 2026Article
- Uchimata: a toolkit for visualization of 3D genome structures on the web and in computational notebooks.Bioinformatics (Oxford, England) · 2026Article
- Design Space and Declarative Grammar for 3D Genomic Data Visualization.IEEE transactions on visualization and computer graphics · 2026Article
- Uchimata: a toolkit for visualization of 3D genome structures on the web and in computational notebooks.ArXiv · 2025Article
- ARGV: 3D genome structure exploration using augmented reality.BMC bioinformatics · 2024Article
- An architecture for collaboration in systems biology at the age of the Metaverse.NPJ systems biology and applications · 2024Article
- 3D models of fungal chromosomes to enhance visual integration of omics data.NAR genomics and bioinformatics · 2023Article
- YASARA Model-Interactive Molecular Modeling from Two Dimensions to Virtual Realities.Journal of chemical information and modeling · 2023Article
- Connectome and regulatory hubs of CAGE highly active enhancers.Scientific reports · 2023Article
- PROFASA-a web-based protein fragment and structure analysis workstation.Frontiers in bioengineering and biotechnology · 2023Article
- Nucleome programming is required for the foundation of totipotency in mammalian germline development.The EMBO journal · 2022Article
- Bioinformatics and the Metaverse: Are We Ready?Frontiers in bioinformatics · 2022Article
- Hi-C detects genomic structural variants in peripheral blood of pediatric leukemia patients.Cold Spring Harbor molecular case studies · 2022Article
- Application of Hi-C and other omics data analysis in human cancer and cell differentiation research.Computational and structural biotechnology journal · 2021Review
- Super-Resolution Microscopy of Chromatin.Genes · 2019Review
Corrections and comments
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Authors and funding
8 authors.
Funding
Abstract
motivationThe 3D structure of chromatin in the nucleus is important for gene expression and regulation. Chromosome conformation capture techniques, such as Hi-C, generate large amounts of data showing interaction points on the genome but these are hard to interpret using standard tools.
resultsWe have developed CSynth, an interactive 3D genome browser and real-time chromatin restraint-based modeller to visualize models of any chromosome conformation capture (3C) data. Unlike other modelling systems, CSynth allows dynamic interaction with the modelling parameters to allow experimentation and effects on the model. It also allows comparison of models generated from data in different tissues/cell states and the results of third-party 3D modelling outputs. In addition, we include an option to view and manipulate these complicated structures using Virtual Reality (VR) so scientists can immerse themselves in the models for further understanding. This VR component has also proven to be a valuable teaching and a public engagement tool. AVAILABILITYAND IMPLEMENTATION: CSynth is web based and available to use at csynth.org. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
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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.