ArticleNucleic acids research2015
GBshape: a genome browser database for DNA shape annotations.
Article in Nucleic acids research, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 35 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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Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
35 citing papers in PubMed, 65 citations in OpenAlex.
- Relevance of DNA tridimensional shape in RNA:DNA:DNA triple helix formation.Computational and structural biotechnology journal · 2026Article
- MCM2-7 loading-dependent ORC release ensures genome-wide origin licensing.Nature communications · 2024Article
- Discovering DNA shape motifs with multiple DNA shape features: generalization, methods, and validation.Nucleic acids research · 2024Article
- Predicting DNA structure using a deep learning method.Nature communications · 2024Article
- Bisulfite probing reveals DNA structural intricacies.Nucleic acids research · 2023Article
- Deciphering the mechanical code of the genome and epigenome.Nature structural & molecular biology · 2022Article
- Diagnostic and therapeutic potential of RNASET2 in Crohn's disease: Disease-risk polymorphism modulates allelic-imbalance in expression and circulating protein levels and recombinant-RNASET2 attenuates pro-inflammatory cytokine secretion.Frontiers in immunology · 2022Article
- Resolving diverse protein-DNA footprints from exonuclease-based ChIP experiments.Bioinformatics (Oxford, England) · 2021Article
- Genome-wide analysis reveals a switch in the translational program upon oocyte meiotic resumption.Nucleic acids research · 2020Article
- Comprehensive analysis of indels in whole-genome microsatellite regions and microsatellite instability across 21 cancer types.Genome research · 2020Article
- A map of direct TF-DNA interactions in the human genome.Nucleic acids research · 2019Article
- Single-nucleotide-resolution mapping of DNA gyrase cleavage sites across the Escherichia coli genome.Nucleic acids research · 2019Article
- A De Novo Shape Motif Discovery Algorithm Reveals Preferences of Transcription Factors for DNA Shape Beyond Sequence Motifs.Cell systems · 2019Article
- Article
- Intrinsic DNA Shape Accounts for Affinity Differences between Hox-Cofactor Binding Sites.Cell reports · 2018Article
- Human Enhancers Harboring Specific Sequence Composition, Activity, and Genome Organization Are Linked to the Immune Response.Genetics · 2018Article
- The transcription factor Grainy head primes epithelial enhancers for spatiotemporal activation by displacing nucleosomes.Nature genetics · 2018Article
- Experimental maps of DNA structure at nucleotide resolution distinguish intrinsic from protein-induced DNA deformations.Nucleic acids research · 2018Article
- Identification of putative promoters in 48 eukaryotic genomes on the basis of DNA free energy.Scientific reports · 2018Article
- Comparison of discriminative motif optimization using matrix and DNA shape-based models.BMC bioinformatics · 2018Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
8 authors at 3 institutions in 1 country.
Funding
Abstract
Many regulatory mechanisms require a high degree of specificity in protein-DNA binding. Nucleotide sequence does not provide an answer to the question of why a protein binds only to a small subset of the many putative binding sites in the genome that share the same core motif. Whereas higher-order effects, such as chromatin accessibility, cooperativity and cofactors, have been described, DNA shape recently gained attention as another feature that fine-tunes the DNA binding specificities of some transcription factor families. Our Genome Browser for DNA shape annotations (GBshape; freely available at http://rohslab.cmb.usc.edu/GBshape/) provides minor groove width, propeller twist, roll, helix twist and hydroxyl radical cleavage predictions for the entire genomes of 94 organisms. Additional genomes can easily be added using the GBshape framework. GBshape can be used to visualize DNA shape annotations qualitatively in a genome browser track format, and to download quantitative values of DNA shape features as a function of genomic position at nucleotide resolution. As biological applications, we illustrate the periodicity of DNA shape features that are present in nucleosome-occupied sequences from human, fly and worm, and we demonstrate structural similarities between transcription start sites in the genomes of four Drosophila species.
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Registered trials
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.