ArticleNature communications2022
SHAPE-guided RNA structure homology search and motif discovery.
Article in Nature communications, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 16 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
16 citing papers in PubMed.
- A telomere-to-telomere gapfree genome assembly of Triplophysa stoliczkae (Tibetan stone loach, family Nemacheilidae).Scientific data · 2026Article
- Identification of conserved RNA regulatory switches in living cells using RNA secondary structure ensemble mapping and covariation analysis.Nature biotechnology · 2026Article
- The LARP6 La module fromRNA biology · 2025Article
- A conserved RNA structure at the capsid-coding sequence of Zika virus genome is required for viral replication in a host-dependent manner.Journal of virology · 2025Article
- Enhanced Generalizability of RNA Secondary Structure Prediction via Convolutional Block Attention Network and Ensemble Learning.Molecules (Basel, Switzerland) · 2025Article
- Deep generalizable prediction of RNA secondary structure via base pair motif energy.Nature communications · 2025Article
- Article
- The role of structure in regulatory RNA elements.Bioscience reports · 2024Review
- Identification of RNA structures and their roles in RNA functions.Nature reviews. Molecular cell biology · 2024Review
- The regulatory landscape of interacting RNA and protein pools in cellular homeostasis and cancer.Human genomics · 2024Review
- SHAPEwarp-web: sequence-agnostic search for structurally homologous RNA regions across databases of chemical probing data.Nucleic acids research · 2024Article
- Deep Conservation and Unexpected Evolutionary History of Neighboring lncRNAs MALAT1 and NEAT1.Journal of molecular evolution · 2024Article
- An intronic RNA element modulates Factor VIII exon-16 splicing.Nucleic acids research · 2024Article
- Chemical RNA Cross-Linking: Mechanisms, Computational Analysis, and Biological Applications.JACS Au · 2023Review
- The Metabolome Weakens RNA Thermodynamic Stability and Strengthens RNA Chemical Stability.Biochemistry · 2022Article
- News from around the RNA world: new avenues in RNA biology, biotechnology and therapeutics from the 2022 SIBBM meeting.Biology open · 2022Article
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
No grant is acknowledged in the PubMed record.
Abstract
The rapidly growing popularity of RNA structure probing methods is leading to increasingly large amounts of available RNA structure information. This demands the development of efficient tools for the identification of RNAs sharing regions of structural similarity by direct comparison of their reactivity profiles, hence enabling the discovery of conserved structural features. We here introduce SHAPEwarp, a largely sequence-agnostic SHAPE-guided algorithm for the identification of structurally-similar regions in RNA molecules. Analysis of Dengue, Zika and coronavirus genomes recapitulates known regulatory RNA structures and identifies novel highly-conserved structural elements. This work represents a preliminary step towards the model-free search and identification of shared and conserved RNA structural features within transcriptomes.
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.