ArticleNucleic acids research2019
Nucleosome Dynamics: a new tool for the dynamic analysis of nucleosome positioning.
Article in Nucleic acids research, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 19 papers.
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Who cites it
19 citing papers in PubMed.
- An interpretable deep learning framework uncovers features governing CRISPR-Cas9 genome-editing efficiency.Bioinformatics (Oxford, England) · 2026Article
- Deciphering chromatin architecture and dynamics in Plasmodium falciparum using the nucDetective pipeline.PLoS computational biology · 2026Article
- Comparative modes of chromatin engagement by PAX::FOXO1 fusions in rhabdomyosarcoma.bioRxiv : the preprint server for biology · 2026Article
- Article
- DiabetesOmic: A comprehensive multi-omics diabetes database.Computational and structural biotechnology journal · 2025Article
- Inferring differential protein binding from time-series chromatin accessibility data.Bioinformatics advances · 2025Article
- Prohibitin 2 orchestrates long noncoding RNA and gene transcription to accelerate tumorigenesis.Nature communications · 2024Article
- An integrated machine-learning model to predict nucleosome architecture.Nucleic acids research · 2024Article
- The PCNA-Pol δ complex couples lagging strand DNA synthesis to parental histone transfer for epigenetic inheritance.Science advances · 2024Article
- Nucleosome-bound NR5A2 structure reveals pioneer factor mechanism by DNA minor groove anchor competition.Nature structural & molecular biology · 2024Article
- Skeletal muscle differentiation induces wide-ranging nucleosome repositioning in muscle gene promoters.Scientific reports · 2024Article
- Genome-wide chromatin interaction map for Trypanosoma cruzi.Nature microbiology · 2023Article
- Novel biological insights revealed from the investigation of multiscale genome architecture.Computational and structural biotechnology journal · 2023Review
- MiOS, an integrated imaging and computational strategy to model gene folding with nucleosome resolution.Nature structural & molecular biology · 2022Article
- Reconstituted TAD-size chromatin fibers feature heterogeneous nucleosome clusters.Scientific reports · 2022Article
- Mapping nucleosome and chromatin architectures: A survey of computational methods.Computational and structural biotechnology journal · 2022Review
- NucHMM: a method for quantitative modeling of nucleosome organization identifying functional nucleosome states distinctly associated with splicing potentiality.Genome biology · 2021Article
- Impact of DNA methylation on 3D genome structure.Nature communications · 2021Article
- Chromatin-modifying drugs and metabolites in cell fate control.Cell proliferation · 2020Review
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Authors and funding
14 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
We present Nucleosome Dynamics, a suite of programs integrated into a virtual research environment and created to define nucleosome architecture and dynamics from noisy experimental data. The package allows both the definition of nucleosome architectures and the detection of changes in nucleosomal organization due to changes in cellular conditions. Results are displayed in the context of genomic information thanks to different visualizers and browsers, allowing the user a holistic, multidimensional view of the genome/transcriptome. The package shows good performance for both locating equilibrium nucleosome architecture and nucleosome dynamics and provides abundant useful information in several test cases, where experimental data on nucleosome position (and for some cases expression level) have been collected for cells under different external conditions (cell cycle phase, yeast metabolic cycle progression, changes in nutrients or difference in MNase digestion level). Nucleosome Dynamics is a free software and is provided under several distribution models.
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