ArticleGenome biology2014
CapR: revealing structural specificities of RNA-binding protein target recognition using CLIP-seq data.
Article in Genome biology, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 47 papers.
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Who cites it
47 citing papers in PubMed, 89 citations in OpenAlex.
- LinearCapR: linear-time computation of per-nucleotide structural-context probabilities of RNA without base-pair span limits.Bioinformatics (Oxford, England) · 2026Article
- Bridging sequence-structure motifs and genetic variants for genome-wide dynamic RNA-protein interaction profiling.Nature communications · 2026Article
- RNA Structure and Its Function.Methods in molecular biology (Clifton, N.J.) · 2026Article
- Diagnostic and Therapeutic Aptamers: A Promising Pathway to Improved Cardiovascular Disease Management.JACC. Basic to translational science · 2024Review
- ConsAlign: simultaneous RNA structural aligner based on rich transfer learning and thermodynamic ensemble model of alignment scoring.Bioinformatics (Oxford, England) · 2023Article
- Rtools: A Web Server for Various Secondary Structural Analyses on Single RNA Sequences.Methods in molecular biology (Clifton, N.J.) · 2023Article
- Genome-Wide RNA Secondary Structure Prediction.Methods in molecular biology (Clifton, N.J.) · 2023Article
- DeepRaccess: high-speed RNA accessibility prediction using deep learning.Frontiers in bioinformatics · 2023Article
- QRNAstruct: a method for extracting secondary structural features of RNA via regression with biological activity.Nucleic acids research · 2022Article
- DeepPN: a deep parallel neural network based on convolutional neural network and graph convolutional network for predicting RNA-protein binding sites.BMC bioinformatics · 2022Article
- PhyloPGM: boosting regulatory function prediction accuracy using evolutionary information.Bioinformatics (Oxford, England) · 2022Article
- Integrative genome-wide analysis reveals EIF3A as a key downstream regulator of translational repressor protein Musashi 2 (MSI2).NAR cancer · 2022Article
- Introduction to Bioinformatics Resources for Post-transcriptional Regulation of Gene Expression.Methods in molecular biology (Clifton, N.J.) · 2022Article
- LinAliFold and CentroidLinAliFold: fast RNA consensus secondary structure prediction for aligned sequences using beam search methods.Bioinformatics advances · 2022Article
- Protein-Specific Prediction of RNA-Binding Sites Based on Information Entropy.Computational intelligence and neuroscience · 2022Article
- Bioinformatics Approaches for Determining the Functional Impact of Repetitive Elements on Non-coding RNAs.Methods in molecular biology (Clifton, N.J.) · 2022Article
- Secondary structures in RNA synthesis, splicing and translation.Computational and structural biotechnology journal · 2022Review
- Multi-resBind: a residual network-based multi-label classifier for in vivo RNA binding prediction and preference visualization.BMC bioinformatics · 2021Article
- Spatial correlation statistics enable transcriptome-wide characterization of RNA structure binding.Cell reports methods · 2021Article
- A Max-Margin Model for Predicting Residue-Base Contacts in Protein-RNA Interactions.Life (Basel, Switzerland) · 2021Article
Corrections and comments
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Authors and funding
6 authors at 3 institutions in 3 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
RNA-binding proteins (RBPs) bind to their target RNA molecules by recognizing specific RNA sequences and structural contexts. The development of CLIP-seq and related protocols has made it possible to exhaustively identify RNA fragments that bind to RBPs. However, no efficient bioinformatics method exists to reveal the structural specificities of RBP-RNA interactions using these data. We present CapR, an efficient algorithm that calculates the probability that each RNA base position is located within each secondary structural context. Using CapR, we demonstrate that several RBPs bind to their target RNA molecules under specific structural contexts. CapR is available at https://sites.google.com/site/fukunagatsu/software/capr.
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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.