ArticleNucleic acids research2024
RNAvigate: efficient exploration of RNA chemical probing datasets.
Article in Nucleic acids research, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 19 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
19 citing papers in PubMed.
- InteRRact: a web server for the interactive exploration and comparison of transcriptome-wide RNA-RNA interactions.NAR genomics and bioinformatics · 2026Article
- Comparative analysis of flavivirus sfRNA dynamics and secondary structure.Journal of virology · 2026Article
- R3DCID: circular interaction diagrams for RNA and DNA 3D structures of all sizes.RNA (New York, N.Y.) · 2026Article
- Sequence and structure of protein binding sites in RNA impact biomolecular condensates.Molecular biology of the cell · 2026Article
- Comparative analysis of flavivirus sfRNA dynamics and secondary structure.bioRxiv : the preprint server for biology · 2026Article
- Sequence and structure of protein binding sites in RNA impact biomolecular condensates.bioRxiv : the preprint server for biology · 2026Article
- Article
- RNA Structural Ensemble Determinants of -1 Programmed Ribosomal Frameshifting Efficiency Across Coronavirus Evolution.Journal of molecular biology · 2025Article
- A small cationic probe for accurate, punctate discovery of RNA tertiary structure.bioRxiv : the preprint server for biology · 2025Article
- Compensatory tRNA Modification by DUS3L Confers Resistance to METTL1 Loss in Oesophageal Cancer.bioRxiv : the preprint server for biology · 2025Article
- Functional Proximity across an mRNA.Biochemistry · 2025Article
- Structural determinants of inverted Alu-mediated backsplicing revealed by -MaP and -JuMP.Nucleic acids research · 2025Article
- Ligand-binding pockets in RNA and where to find them.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- Article
- R2DT: a comprehensive platform for visualizing RNA secondary structure.Nucleic acids research · 2025Article
- Abolished frameshifting for predicted structure-stabilizing SARS-CoV-2 mutants: implications to alternative conformations and their statistical structural analyses.RNA (New York, N.Y.) · 2024Article
- Fingerprinting Tertiary Structure in Complex RNAs Using Single-Molecule Correlated Chemical Probing.Biochemistry · 2024Article
- R2DT: A COMPREHENSIVE PLATFORM FOR VISUALISING RNA SECONDARY STRUCTURE.bioRxiv : the preprint server for biology · 2024Article
- Structural Modifications and Novel Protein-Binding Sites in Pre-miR-675-Explaining Its Regulatory Mechanism in Carcinogenesis.Non-coding RNA · 2023Article
Corrections and comments
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2 authors.
Funding
Abstract
Chemical probing technologies enable high-throughput examination of diverse structural features of RNA, including local nucleotide flexibility, RNA secondary structure, protein and ligand binding, through-space interaction networks, and multistate structural ensembles. Deep understanding of RNA structure-function relationships typically requires evaluating a system under structure- and function-altering conditions, linking these data with additional information, and visualizing multilayered relationships. Current platforms lack the broad accessibility, flexibility and efficiency needed to iterate on integrative analyses of these diverse, complex data. Here, we share the RNA visualization and graphical analysis toolset RNAvigate, a straightforward and flexible Python library that automatically parses 21 standard file formats (primary sequence annotations, per- and internucleotide data, and secondary and tertiary structures) and outputs 18 plot types. RNAvigate enables efficient exploration of nuanced relationships between multiple layers of RNA structure information and across multiple experimental conditions. Compatibility with Jupyter notebooks enables nonburdensome, reproducible, transparent and organized sharing of multistep analyses and data visualization strategies. RNAvigate simplifies and accelerates discovery and characterization of RNA-centric functions in biology.
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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.