ArticleBioinformatics (Oxford, England)2012
RIsearch: fast RNA-RNA interaction search using a simplified nearest-neighbor energy model.
Article in Bioinformatics (Oxford, England), 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 64 papers.
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Who cites it
64 citing papers in PubMed, 94 citations in OpenAlex.
- Small RNA Transcriptome of the Oral Microbiome during Periodontitis Progression.Applied and environmental microbiology · 2015Trial
- Cross-Virus RNA Language Models for Within-Family RNA-RNA Interaction Prediction in SARS-CoV-2 and Porcine Deltacoronavirus.International journal of molecular sciences · 2026Article
- Small Regulatory RNAs in Prokaryotes: Key Features, Identification, Environmental Roles, and Applications.Microorganisms · 2026Review
- Exploitation of Biocomputational Approaches for siRNA-Mediated Gene Silencing of HPV: A Novel Therapeutic Strategy for Cervical Cancer.Cancer reports (Hoboken, N.J.) · 2025Article
- Predict SARS-CoV-2 genome interactions based on RNA language models.Biosafety and health · 2025Article
- Mesenchymal stromal cell extracellular vesicles reduceAmerican journal of physiology. Lung cellular and molecular physiology · 2025Article
- Modeling RNA duplex dynamics with Gibbs sampling enhances base-pair prediction accuracy and reveals structural activity profiles.NAR genomics and bioinformatics · 2025Article
- Benchmarking the methods for predicting base pairs in RNA-RNA interactions.Bioinformatics (Oxford, England) · 2025Article
- Let-7b-5p loaded Mesenchymal Stromal Cell Extracellular Vesicles reducebioRxiv : the preprint server for biology · 2025Article
- Construction of a Dataset for All Expressed Transcripts for Alzheimer's Disease Research.Brain sciences · 2024Article
- UID-Dual Transcriptome Sequencing Analysis of the Molecular Interactions betweenAnimals : an open access journal from MDPI · 2024Article
- Elucidating the Functional Roles of Long Non-Coding RNAs in Alzheimer's Disease.International journal of molecular sciences · 2024Article
- Genome-wide transcriptional profiling and functional analysis of long noncoding RNAs and mRNAs in chicken macrophages associated with the infection of avian pathogenic E. coli.BMC veterinary research · 2024Article
- How to do RNA-RNA Interaction Prediction? A Use-Case Driven Handbook Using IntaRNA.Methods in molecular biology (Clifton, N.J.) · 2024Review
- Gene silencing of Helicobacter pylori through newly designed siRNA convenes the treatment of gastric cancer.Cancer medicine · 2023Article
- A Hitchhiker's guide to RNA-RNA structure and interaction prediction tools.Briefings in bioinformatics · 2023Review
- Whole-Transcriptome RNA Sequencing Uncovers the Global Expression Changes and RNA Regulatory Networks in Duck Embryonic Myogenesis.International journal of molecular sciences · 2023Article
- lncRNA and circRNA expression profiles in the hippocampus of AβExperimental and therapeutic medicine · 2023Article
- Fast RNA-RNA Interaction Prediction Methods for Interaction Analysis of Transcriptome-Scale Large Datasets.Methods in molecular biology (Clifton, N.J.) · 2023Review
- Review
4 more citing papers are in PubMed but not listed here.
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Authors and funding
3 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
motivationRegulatory, non-coding RNAs often function by forming a duplex with other RNAs. It is therefore of interest to predict putative RNA-RNA duplexes in silico on a genome-wide scale. Current computational methods for predicting these interactions range from fast complementary-based searches to those that take intramolecular binding into account. Together these methods constitute a trade-off between speed and accuracy, while leaving room for improvement within the context of genome-wide screens. A fast pre-filtering of putative duplexes would therefore be desirable.
resultsWe present RIsearch, an implementation of a simplified Turner energy model for fast computation of hybridization, which significantly reduces runtime while maintaining accuracy. Its time complexity for sequences of lengths m and n is with a much smaller pre-factor than other tools. We show that this energy model is an accurate approximation of the full energy model for near-complementary RNA-RNA duplexes. RIsearch uses a Smith-Waterman-like algorithm using a dinucleotide scoring matrix which approximates the Turner nearest-neighbor energies. We show in benchmarks that we achieve a speed improvement of at least 2.4× compared with RNAplex, the currently fastest method for searching near-complementary regions. RIsearch shows a prediction accuracy similar to RNAplex on two datasets of known bacterial short RNA (sRNA)-messenger RNA (mRNA) and eukaryotic microRNA (miRNA)-mRNA interactions. Using RIsearch as a pre-filter in genome-wide screens reduces the number of binding site candidates reported by miRNA target prediction programs, such as TargetScanS and miRanda, by up to 70%. Likewise, substantial filtering was performed on bacterial RNA-RNA interaction data. AVAILABILITY: The source code for RIsearch is available at: http://rth.dk/resources/risearch.
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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.