ArticleBMC molecular and cell biology2020
GSDB: a database of 3D chromosome and genome structures reconstructed from Hi-C data.
Article in BMC molecular and cell biology, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. An erratum has been issued. Cited by 20 papers.
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Who cites it
20 citing papers in PubMed.
- Uchimata: a toolkit for visualization of 3D genome structures on the web and in computational notebooks.Bioinformatics (Oxford, England) · 2026Article
- ChromPolymerDB: a high-resolution database of single-cell 3D chromatin structures for functional genomics.Nucleic acids research · 2026Article
- Design Space and Declarative Grammar for 3D Genomic Data Visualization.IEEE transactions on visualization and computer graphics · 2026Article
- ChromPolymerDB: A High-Resolution Database of Single-Cell 3D Chromatin Structures for Functional Genomics.bioRxiv : the preprint server for biology · 2025Article
- Uchimata: a toolkit for visualization of 3D genome structures on the web and in computational notebooks.ArXiv · 2025Article
- Integrating Artificial Intelligence in Next-Generation Sequencing: Advances, Challenges, and Future Directions.Current issues in molecular biology · 2025Review
- Genome structural dynamics: insights from Gaussian network analysis of Hi-C data.Briefings in functional genomics · 2024Article
- ARGV: 3D genome structure exploration using augmented reality.BMC bioinformatics · 2024Article
- EVRC: reconstruction of chromosome 3D structure models using error-vector resultant algorithm with clustering coefficient.Bioinformatics (Oxford, England) · 2023Article
- ParticleChromo3D+: A Web Server for ParticleChromo3D Algorithm for 3D Chromosome Structure Reconstruction.Current issues in molecular biology · 2023Article
- HiChIPdb: a comprehensive database of HiChIP regulatory interactions.Nucleic acids research · 2023Article
- Telomere-to-telomere and haplotype-resolved genome assembly of the Chinese cork oak (Frontiers in plant science · 2023Article
- HiC-GNN: A generalizable model for 3D chromosome reconstruction using graph convolutional neural networks.Computational and structural biotechnology journal · 2023Article
- ParticleChromo3D: a Particle Swarm Optimization algorithm for chromosome 3D structure prediction from Hi-C data.BioData mining · 2022Article
- Article
- Hi-C scaffolded short- and long-read genome assemblies of the California sea lion are broadly consistent for syntenic inference across 45 million years of evolution.Molecular ecology resources · 2021Article
- CBCR: A Curriculum Based Strategy For Chromosome Reconstruction.International journal of molecular sciences · 2021Article
- Application of Hi-C and other omics data analysis in human cancer and cell differentiation research.Computational and structural biotechnology journal · 2021Review
- Correction to: GSDB: a database of 3D chromosome and genome structures reconstructed from Hi-C data.BMC molecular and cell biology · 2020Article
- Abasy Atlas v2.2: The most comprehensive and up-to-date inventory of meta-curated, historical, bacterial regulatory networks, their completeness and system-level characterization.Computational and structural biotechnology journal · 2020Article
Corrections and comments
- Erratum issued
Authors and funding
5 authors.
Funding
Abstract
Advances in the study of chromosome conformation capture technologies, such as Hi-C technique - capable of capturing chromosomal interactions in a genome-wide scale - have led to the development of three-dimensional chromosome and genome structure reconstruction methods from Hi-C data. The three dimensional genome structure is important because it plays a role in a variety of important biological activities such as DNA replication, gene regulation, genome interaction, and gene expression. In recent years, numerous Hi-C datasets have been generated, and likewise, a number of genome structure construction algorithms have been developed.In this work, we outline the construction of a novel Genome Structure Database (GSDB) to create a comprehensive repository that contains 3D structures for Hi-C datasets constructed by a variety of 3D structure reconstruction tools. The GSDB contains over 50,000 structures from 12 state-of-the-art Hi-C data structure prediction algorithms for 32 Hi-C datasets.GSDB functions as a centralized collection of genome structures which will enable the exploration of the dynamic architectures of chromosomes and genomes for biomedical research. GSDB is accessible at http://sysbio.rnet.missouri.edu/3dgenome/GSDB.
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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.