ArticleNucleic acids research2021
RNAnue: efficient data analysis for RNA-RNA interactomics.
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 13 papers.
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Who cites it
13 citing papers in PubMed, 18 citations in OpenAlex.
- Analysis of isoform complexity in pan-transcriptome graphs with atroplex.bioRxiv : the preprint server for biology · 2026Article
- A Comprehensive Review of Epigenetic Regulation of Vascular Smooth Muscle Cells During Development and Disease.Biomolecules · 2026Review
- Thorough RNA Interactome Data Analysis Based on Direct Duplex Detection Data.Methods in molecular biology (Clifton, N.J.) · 2026Article
- A comprehensive benchmark of tools for efficient genomic interval querying.Briefings in bioinformatics · 2025Article
- Biomolecules Interacting with Long Noncoding RNAs.Biology · 2025Review
- DuplexDiscoverer: a computational method for the analysis of experimental duplex RNA-RNA interaction data.Nucleic acids research · 2025Article
- A Comprehensive Benchmark of Tools for Efficient Genomic Interval Querying.bioRxiv : the preprint server for biology · 2025Article
- ChimericFragments: computation, analysis and visualization of global RNA networks.NAR genomics and bioinformatics · 2024Article
- CheRRI-Accurate classification of the biological relevance of putative RNA-RNA interaction sites.GigaScience · 2024Article
- Limits of experimental evidence in RNA secondary structure prediction.Frontiers in bioinformatics · 2024Article
- A Hitchhiker's guide to RNA-RNA structure and interaction prediction tools.Briefings in bioinformatics · 2023Review
- RNA interaction format: a general data format for RNA interactions.Bioinformatics (Oxford, England) · 2023Article
- Chemical RNA Cross-Linking: Mechanisms, Computational Analysis, and Biological Applications.JACS Au · 2023Review
Corrections and comments
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Authors and funding
2 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
RNA-RNA inter- and intramolecular interactions are fundamental for numerous biological processes. While there are reasonable approaches to map RNA secondary structures genome-wide, understanding how different RNAs interact to carry out their regulatory functions requires mapping of intermolecular base pairs. Recently, different strategies to detect RNA-RNA duplexes in living cells, so called direct duplex detection (DDD) methods, have been developed. Common to all is the Psoralen-mediated in vivo RNA crosslinking followed by RNA Proximity Ligation to join the two interacting RNA strands. Sequencing of the RNA via classical RNA-seq and subsequent specialised bioinformatic analyses the result in the prediction of inter- and intramolecular RNA-RNA interactions. Existing approaches adapt standard RNA-seq analysis pipelines, but often neglect inherent features of RNA-RNA interactions that are useful for filtering and statistical assessment. Here we present RNAnue, a general pipeline for the inference of RNA-RNA interactions from DDD experiments that takes into account hybridisation potential and statistical significance to improve prediction accuracy. We applied RNAnue to data from different DDD studies and compared our results to those of the original methods. This showed that RNAnue performs better in terms of quantity and quality of predictions.
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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.