ArticleNucleic acids research2021
The Nucleome Data Bank: web-based resources to simulate and analyze the three-dimensional genome.
Article in Nucleic acids research, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 16 papers.
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Who cites it
16 citing papers in PubMed.
- Epigenetics is all you need: A transformer to decode chromatin structural compartments from the epigenome.PLoS computational biology · 2025Article
- Energy landscape analysis of the development of the chromosome structure across the cell cycle.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- Hi-C-guided many-polymer model to decipher 3D genome organization.Biophysical journal · 2024Article
- Chromatin alternates between A and B compartments at kilobase scale for subgenic organization.Nature communications · 2023Article
- Structural reorganization and relaxation dynamics of axially stressed chromosomes.Biophysical journal · 2023Article
- Interphase chromosomes of the Aedes aegypti mosquito are liquid crystalline and can sense mechanical cues.Nature communications · 2023Article
- Uncovering the Quantitative Relationships Among Chromosome Fluctuations, Epigenetics, and Gene Expressions of Transdifferentiation on Waddington Landscape.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2022Article
- Extracting physical characteristics of higher-order chromatin structures from 3D image data.Computational and structural biotechnology journal · 2022Article
- HISNAPI: a bioinformatic tool for dynamic hot spot analysis in nucleic acid-protein interface with a case study.Briefings in bioinformatics · 2021Article
- Understanding 3D genome organization by multidisciplinary methods.Nature reviews. Molecular cell biology · 2021Review
- The 2021 Nucleic Acids Research database issue and the online molecular biology database collection.Nucleic acids research · 2021Article
- A new precision medicine initiative at the dawn of exascale computing.Signal transduction and targeted therapy · 2021Review
- A Liquid State Perspective on Dynamics of Chromatin Compartments.Frontiers in molecular biosciences · 2021Review
- Application of Hi-C and other omics data analysis in human cancer and cell differentiation research.Computational and structural biotechnology journal · 2021Review
- Interactions Between Nucleosomes: From Atomistic Simulation to Polymer Model.Frontiers in molecular biosciences · 2021Article
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9 authors.
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Abstract
We introduce the Nucleome Data Bank (NDB), a web-based platform to simulate and analyze the three-dimensional (3D) organization of genomes. The NDB enables physics-based simulation of chromosomal structural dynamics through the MEGABASE + MiChroM computational pipeline. The input of the pipeline consists of epigenetic information sourced from the Encode database; the output consists of the trajectories of chromosomal motions that accurately predict Hi-C and fluorescence insitu hybridization data, as well as multiple observations of chromosomal dynamics in vivo. As an intermediate step, users can also generate chromosomal sub-compartment annotations directly from the same epigenetic input, without the use of any DNA-DNA proximity ligation data. Additionally, the NDB freely hosts both experimental and computational structural genomics data. Besides being able to perform their own genome simulations and download the hosted data, users can also analyze and visualize the same data through custom-designed web-based tools. In particular, the one-dimensional genetic and epigenetic data can be overlaid onto accurate 3D structures of chromosomes, to study the spatial distribution of genetic and epigenetic features. The NDB aims to be a shared resource to biologists, biophysicists and all genome scientists. The NDB is available at https://ndb.rice.edu.
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Registered trials
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