ArticleIUBMB life2023
Thirteen dubious ways to detect conserved structural RNAs.
Article in IUBMB life, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 16 papers.
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Who cites it
16 citing papers in PubMed.
- dsRNAscan maps human dsRNAome, revealing conservation, intermolecular dsRNA, and correlates of ADAR dependency.Molecular cell · 2026Article
- RNA regulation in plants.Science China. Life sciences · 2026Review
- What does it take to learn the rules of RNA base pairing? A lot less than you may think.Communications biology · 2026Article
- Exploring the regulatory potential of RNA structures in 202 cyanobacterial genomes.Nucleic acids research · 2026Article
- All-at-once RNA folding with 3D motif prediction framed by evolutionary information.Nature methods · 2025Article
- Evaluating computational tools for protein-coding sequence detection: Are they up to the task?RNA (New York, N.Y.) · 2025Article
- ECSFinder: optimized prediction of evolutionarily conserved RNA secondary structures from genome sequences.Nucleic acids research · 2025Article
- RNAhub-an automated pipeline to search and align RNA homologs with secondary structure assessment.Nucleic acids research · 2025Article
- Comprehensive Mapping of Human dsRNAome Reveals Conservation, Neuronal Enrichment, and Intermolecular Interactions.bioRxiv : the preprint server for biology · 2025Article
- The regulatory landscape of interacting RNA and protein pools in cellular homeostasis and cancer.Human genomics · 2024Review
- sincFold: end-to-end learning of short- and long-range interactions in RNA secondary structure.Briefings in bioinformatics · 2024Article
- Deep Conservation and Unexpected Evolutionary History of Neighboring lncRNAs MALAT1 and NEAT1.Journal of molecular evolution · 2024Article
- When will RNA get its AlphaFold moment?Nucleic acids research · 2023Article
- RNA covariation at helix-level resolution for the identification of evolutionarily conserved RNA structure.PLoS computational biology · 2023Article
- Exploring the landscape of tools and resources for the analysis of long non-coding RNAs.Computational and structural biotechnology journal · 2023Review
- GERONIMO: A tool for systematic retrieval of structural RNAs in a broad evolutionary context.GigaScience · 2022Article
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3 authors.
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Abstract
Covariation induced by compensatory base substitutions in RNA alignments is a great way to deduce conserved RNA structure, in principle. In practice, success depends on many factors, importantly the quality and depth of the alignment and the choice of covariation statistic. Measuring covariation between pairs of aligned positions is easy. However, using covariation to infer evolutionarily conserved RNA structure is complicated by other extraneous sources of covariation such as that resulting from homologous sequences having evolved from a common ancestor. In order to provide evidence of evolutionarily conserved RNA structure, a method to distinguish covariation due to sources other than RNA structure is necessary. Moreover, there are several sorts of artifactually generated covariation signals that can further confound the analysis. Additionally, some covariation signal is difficult to detect due to incomplete comparative data. Here, we investigate and critically discuss the practice of inferring conserved RNA structure by comparative sequence analysis. We provide new methods on how to approach and decide which of the numerous long non-coding RNAs (lncRNAs) have biologically relevant structures.
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