ArticleMethods (San Diego, Calif.)2020
Mapping the RNA structural landscape of viral genomes.
Article in Methods (San Diego, Calif.), 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 26 papers.
What it found
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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
26 citing papers in PubMed.
- RNAStructuromeDB: a transcriptome-wide database of predicted RNA secondary structures with integrated APIs for functional annotation and RNA-targeted drug discovery.NAR genomics and bioinformatics · 2026Article
- Precursor RNA structural patterns at SF3B1 mutation sensitive cryptic 3' splice sites.RNA biology · 2025Article
- Identification of a conserved RNA structure in thebioRxiv : the preprint server for biology · 2025Article
- Unraveling unbreakable hairpins: characterizing RNA secondary structures that are persistent after dinucleotide shuffling.RNA (New York, N.Y.) · 2025Article
- Transcriptome-wide prediction of heat-sensitive RNA structures inFrontiers in plant science · 2025Article
- The RNA secondary structure of androgen receptor-FL and V7 transcripts reveals novel regulatory regions.Nucleic acids research · 2024Article
- Discovery of RNA secondary structural motifs using sequence-ordered thermodynamic stability and comparative sequence analysis.MethodsX · 2023Article
- Broad-spectrum metastasis suppressing compounds and therapeutic uses thereof in human tumors.Scientific reports · 2023Article
- Strategic construction of mRNA vaccine derived from conserved and experimentally validated epitopes of avian influenza type A virus: a reverse vaccinology approach.Clinical and experimental vaccine research · 2023Article
- Thermodynamic and structural characterization of an EBV infected B-cell lymphoma transcriptome.NAR genomics and bioinformatics · 2022Article
- Expansion of the RNAStructuromeDB to include secondary structural data spanning the human protein-coding transcriptome.Scientific reports · 2022Article
- Prediction and analysis of functional RNA structures within the integrative genomics viewer.NAR genomics and bioinformatics · 2022Article
- In silico analysis of local RNA secondary structure in influenza virus A, B and C finds evidence of widespread ordered stability but little evidence of significant covariation.Scientific reports · 2022Article
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- Analysis of key genes inFrontiers in tropical diseases · 2022Article
- Systematically Studying the Effect of Small Molecules Interacting with RNA in Cellular and Preclinical Models.ACS chemical biology · 2021Review
- Article
- A map of the SARS-CoV-2 RNA structurome.NAR genomics and bioinformatics · 2021Article
- The global and local distribution of RNA structure throughout the SARS-CoV-2 genome.Journal of virology · 2021Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
3 authors.
Funding
Abstract
Functional RNA structures are prevalent in viral genomes, and have been shown to play roles in almost every aspect of their biology. However, the majority of viral RNA remains structurally uncharacterized. This is likely to remain true as the cost of sequencing decreases much faster than the cost of structural characterizations. Because of this, there is a need for rapid, inexpensive methods to highlight regions of viral RNA which are ideal candidates for structure-function analyses. The ScanFold method was developed as a single sequence alternative to traditional RNA structural motif discovery pipelines, which rely heavily on well curated sequence alignments to identify conserved RNA structures. ScanFold focuses on identifying (based on their more stable than expected folding energies) the most likely functional structures encoded within a single large RNA sequence, while allowing predicted motifs to be tested for evidence of structural conservation later. Decoupling these processes can be a benefit to researchers studying viruses lacking the ideal phylogenetic depth to yield evidence of structural conservation. Here, we demonstrate how the most significant ScanFold predicted structures correspond to higher base pairing probabilities, SHAPE reactivities, and predict known functional structures within the ZIKV and HIV-1 genomes with accuracy. Best practices and examples are also shown to aid users in utilizing ScanFold for their own systems of interest. ScanFold is available as a Webserver (https://mosslabtools.bb.iastate.edu/scanfold) or can be downloaded (https://github.com/moss-lab/ScanFold) and run locally.
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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.