ArticleNucleic acids research2017
RIsearch2: suffix array-based large-scale prediction of RNA-RNA interactions and siRNA off-targets.
Article in Nucleic acids research, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 58 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
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.
The trial behind it
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.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
58 citing papers in PubMed.
- Bacterial small RNAs and extracellular vesicles in inflammatory and osteoimmune diseases: regulatory mechanisms and host-microbe communication.Archives of microbiology · 2026Review
- Computational Analysis of Sequence Editability in the Theophylline RNA Aptamer as a Functional RNA Module.International journal of molecular sciences · 2026Article
- Transcriptional perturbation of LINE-1 elements reveals their cis-regulatory potential.EMBO reports · 2026Article
- rbpCNN: a biophysics-informed deep learning model for predicting piRNA and mRNA interactions.Scientific reports · 2026Article
- The role of low-complexity repeats in RNA-RNA interactions and a deep learning framework for duplex prediction.Nature communications · 2026Article
- Single alkyl phosphonate modification of the siRNA backbone in the seed region enhances specificity and therapeutic profile.Nucleic acids research · 2025Article
- Small interfering RNA: From designing to therapeutic in cancer.Journal, genetic engineering & biotechnology · 2025Review
- Transcriptome analysis of lncRNAs in granulosa cells in follicles of White King pigeons exposed to white and red light during the laying intervals.Journal of animal science · 2025Article
- Construction of a Prognostic Model for Cervical Cancer Related to lncRNA Based on Differential Co-expression Network and Functional Study of Key Gene EGFR-AS1.Journal of Cancer · 2025Article
- Integration analysis ofBiochemistry and biophysics reports · 2024Article
- Identification of lncRNAs regulating seed traits in Brassica juncea and development of a comprehensive seed omics database.Functional & integrative genomics · 2024Article
- 3D feasibility of 2D RNA-RNA interaction paths by stepwise folding simulations.RNA (New York, N.Y.) · 2024Article
- CheRRI-Accurate classification of the biological relevance of putative RNA-RNA interaction sites.GigaScience · 2024Article
- How to do RNA-RNA Interaction Prediction? A Use-Case Driven Handbook Using IntaRNA.Methods in molecular biology (Clifton, N.J.) · 2024Review
- Generation and characterization of a knock-in mouse model for spastic tetraplegia, thin corpus callosum, and progressive microcephaly (SPATCCM).Mammalian genome : official journal of the International Mammalian Genome Society · 2023Article
- A Hitchhiker's guide to RNA-RNA structure and interaction prediction tools.Briefings in bioinformatics · 2023Review
- Aflatoxin B1 affects porcine alveolar macrophage growth through the calcium signaling pathway mediated by the ceRNA regulatory network.Molecular biology reports · 2023Article
- lncRNA and circRNA expression profiles in the hippocampus of AβExperimental and therapeutic medicine · 2023Article
- Article
- HCMV Infection Reduces Nidogen-1 Expression, Contributing to Impaired Neural Rosette Development in Brain Organoids.Journal of virology · 2023Article
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.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Intermolecular interactions of ncRNAs are at the core of gene regulation events, and identifying the full map of these interactions bears crucial importance for ncRNA functional studies. It is known that RNA-RNA interactions are built up by complementary base pairings between interacting RNAs and high level of complementarity between two RNA sequences is a powerful predictor of such interactions. Here, we present RIsearch2, a large-scale RNA-RNA interaction prediction tool that enables quick localization of potential near-complementary RNA-RNA interactions between given query and target sequences. In contrast to previous heuristics which either search for exact matches while including G-U wobble pairs or employ simplified energy models, we present a novel approach using a single integrated seed-and-extend framework based on suffix arrays. RIsearch2 enables fast discovery of candidate RNA-RNA interactions on genome/transcriptome-wide scale. We furthermore present an siRNA off-target discovery pipeline that not only predicts the off-target transcripts but also computes the off-targeting potential of a given siRNA. This is achieved by combining genome-wide RIsearch2 predictions with target site accessibilities and transcript abundance estimates. We show that this pipeline accurately predicts siRNA off-target interactions and enables off-targeting potential comparisons between different siRNA designs. RIsearch2 and the siRNA off-target discovery pipeline are available as stand-alone software packages from http://rth.dk/resources/risearch.
Indexed as
Identifiers
What OpenQuestion holds
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.