ArticleBioinformatics (Oxford, England)2017
Motif independent identification of potential RNA G-quadruplexes by G4RNA screener.
Article in Bioinformatics (Oxford, England), 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 67 papers.
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Who cites it
67 citing papers in PubMed.
- RNA G-quadruplex-protein interactions: from nuclear RNA processing to cytoplasmic stress response and neurodegeneration.RNA biology · 2026Review
- G-quadruplex structures affect the immune response to bacterial infection in mouse macrophages.Nature communications · 2026Article
- Discovery of a G-rich ultra stable human ncRNA G-quadruplex that binds ATP.Non-coding RNA research · 2026Article
- Systematic identification of variant-specific RNA structure-small molecule interactions exemplified by RNA G-quadruplexes.Nature communications · 2026Article
- A deep learning framework for comprehensive prediction of human RNA G-quadruplex-binding proteins.Bioinformatics (Oxford, England) · 2026Article
- Non-B DNA structures and their contributions to genetic diversity, aging, and disease.Nucleic acids research · 2026Review
- Computational Analysis Uncovering Contrasts in G-Quadruplex Propensity and Aptamer Enrichment in SELEX-Derived Libraries.Chembiochem : a European journal of chemical biology · 2026Article
- G4mer: An RNA language model for transcriptome-wide identification of G-quadruplexes and disease variants from population-scale genetic data.Nature communications · 2025Article
- Quadrupia provides a comprehensive catalog of G-quadruplexes across genomes from the tree of life.Genome research · 2025Article
- Perspectives on NcRNAs in HBV/cccDNA-driven HCC progression.Cancer cell international · 2025Review
- RNA G‑Quadruplex Reprogramming with Guanine-Rich Antisense Oligonucleotides Inhibits Monoamine Oxidase B's Translation.ACS bio & med chem Au · 2025Article
- A Dataset Curated for the Assessment of G4s in the LncRNAs Dysregulated in Various Human Cancers.Scientific data · 2025Article
- Value of Bioinformatics Models for Predicting Translational Control of Angiogenesis.Circulation research · 2025Review
- Specific Targeting and Imaging of RNA G-Quadruplex (rG4) Structure Using Non-G4-Containing l-RNA Aptamer and Fluorogenic l-Aptamer.Small methods · 2025Article
- A novel L-RNA aptamer to regulate the pUG fold RNA-induced gene expression in vivo.Nucleic acids research · 2025Article
- 5'-UTR G-Quadruplex-Mediated Translation Regulation in Eukaryotes: Current Understanding and Methodological Challenges.International journal of molecular sciences · 2025Review
- Asymmetric distribution of G-quadruplex forming sequences in genomes of retroviruses.Scientific reports · 2025Article
- Machine learning-based prediction of DNA G-quadruplex folding topology with G4ShapePredictor.Scientific reports · 2024Article
- The G4 resolvase Dhx36 modulates cardiomyocyte differentiation and ventricular conduction system development.Nature communications · 2024Article
- Tyrosine 1-phosphorylated RNA polymerase II transcribes PROMPTs to facilitate proximal promoter pausing and induce global transcriptional repression in response to DNA damage.Genome research · 2024Article
7 more citing papers are in PubMed but not listed here.
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Authors and funding
3 authors.
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No grant is acknowledged in the PubMed record.
Abstract
motivationG-quadruplex structures in RNA molecules are known to have regulatory impacts in cells but are difficult to locate in the genome. The minimal requirements for G-quadruplex folding in RNA (G≥3N1-7 G≥3N1-7 G≥3N1-7 G≥3) is being challenged by observations made on specific examples in recent years. The definition of potential G-quadruplex sequences has major repercussions on the observation of the structure since it introduces a bias. The canonical motif only describes a sub-population of the reported G-quadruplexes. To address these issues, we propose an RNA G-quadruplex prediction strategy that does not rely on a motif definition.
resultsWe trained an artificial neural network with sequences of experimentally validated G-quadruplexes from the G4RNA database encoded using an abstract definition of their sequence. This artificial neural network, G4NN, evaluates the similarity of a given sequence to known G-quadruplexes and reports it as a score. G4NN has a predictive power comparable to the reported G richness and G/C skewness evaluations that are the current state-of-the-art for the identification of potential RNA G-quadruplexes. We combined these approaches in the G4RNA screener, a program designed to manage and evaluate the sequences to identify potential G-quadruplexes. AVAILABILITY AND IMPLEMENTATION: G4RNA screener is available for download at http://gitlabscottgroup.med.usherbrooke.ca/J-Michel/g4rna_screener. CONTACT: jean-michel.garant@usherbrooke.ca or jean-pierre.perreault@usherbrooke.ca or michelle.scott@usherbrooke.ca. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
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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.