ArticleBMC genomics2019
EVR: reconstruction of bacterial chromosome 3D structure models using error-vector resultant algorithm.
Article in BMC genomics, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 14 papers.
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Who cites it
14 citing papers in PubMed.
- ChromInSight: Revealing DNA Double-Strand Breaks Through Chromatin Structural Insights With an Interpretable Graph Neural Network Framework.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2025Article
- Physical models of bacterial chromosomes.Molecular microbiology · 2025Review
- Advancements and future directions in single-cell Hi-C based 3D chromatin modeling.Computational and structural biotechnology journal · 2024Review
- Spatial Chromosome Organization and Adaptation ofMicroorganisms · 2024Article
- Hi-BDiSCO: folding 3D mesoscale genome structures from Hi-C data using brownian dynamics.Nucleic acids research · 2024Article
- Chromosome structure modeling tools and their evaluation in bacteria.Briefings in bioinformatics · 2024Review
- EVRC: reconstruction of chromosome 3D structure models using error-vector resultant algorithm with clustering coefficient.Bioinformatics (Oxford, England) · 2023Article
- Techniques for and challenges in reconstructing 3D genome structures from 2D chromosome conformation capture data.Current opinion in cell biology · 2023Review
- The Spatial Organization of Bacterial Transcriptional Regulatory Networks.Microorganisms · 2022Article
- Intelligent Three-Dimensional Reconstruction Algorithm-Based Ultrasound-Guided Nerve Block in Intraoperative Anesthesia and Postoperative Analgesia of Orthopedic Surgery.Computational and mathematical methods in medicine · 2022Article
- Application of Hi-C and other omics data analysis in human cancer and cell differentiation research.Computational and structural biotechnology journal · 2021Review
- Generating Chromosome Geometries in a Minimal Cell From Cryo-Electron Tomograms and Chromosome Conformation Capture Maps.Frontiers in molecular biosciences · 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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2 authors.
Funding
Abstract
backgroundMore and more 3C/Hi-C experiments on prokaryotes have been published. However, most of the published modeling tools for chromosome 3D structures are targeting at eukaryotes. How to transform prokaryotic experimental chromosome interaction data into spatial structure models is an important task and in great need.
resultsWe have developed a new reconstruction program for bacterial chromosome 3D structure models called EVR that exploits a simple Error-Vector Resultant (EVR) algorithm. This software tool is particularly optimized for the closed-loop structural features of prokaryotic chromosomes. The parallel implementation of the program can utilize the computing power of both multi-core CPUs and GPUs.
conclusionsEVR can be used to reconstruct the bacterial 3D chromosome structure based on the contact frequency matrix derived from 3C/Hi-C experimental data quickly and precisely.
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