ArticleGenomics, proteomics & bioinformatics2014
nuMap: a web platform for accurate prediction of nucleosome positioning.
Article in Genomics, proteomics & bioinformatics, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 6 papers.
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Who cites it
6 citing papers in PubMed.
- Linker histone H1 drives heterochromatin condensation via phase separation in Arabidopsis.The Plant cell · 2024Article
- Comprehensive computational analysis of epigenetic descriptors affecting CRISPR-Cas9 off-target activity.BMC genomics · 2022Article
- Temporal gene regulation by p53 is associated with the rotational setting of its binding sites in nucleosomes.Cell cycle (Georgetown, Tex.) · 2021Article
- A deformation energy model reveals sequence-dependent property of nucleosome positioning.Chromosoma · 2021Article
- Nucleosome allostery in pioneer transcription factor binding.Proceedings of the National Academy of Sciences of the United States of America · 2020Article
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Authors and funding
5 authors.
Funding
Abstract
Nucleosome positioning is critical for gene expression and of major biological interest. The high cost of experimentally mapping nucleosomal arrangement signifies the need for computational approaches to predict nucleosome positions at high resolution. Here, we present a web-based application to fulfill this need by implementing two models, YR and W/S schemes, for the translational and rotational positioning of nucleosomes, respectively. Our methods are based on sequence-dependent anisotropic bending that dictates how DNA is wrapped around a histone octamer. This application allows users to specify a number of options such as schemes and parameters for threading calculation and provides multiple layout formats. The nuMap is implemented in Java/Perl/MySQL and is freely available for public use at http://numap.rit.edu. The user manual, implementation notes, description of the methodology and examples are available at the site.
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Registered trials
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