ReviewWiley interdisciplinary reviews. RNA2017
Transcending the prediction paradigm: novel applications of SHAPE to RNA function and evolution.
Review in Wiley interdisciplinary reviews. RNA, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 32 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
32 citing papers in PubMed.
- Markov models of SHAPE data improve secondary structure prediction.bioRxiv : the preprint server for biology · 2026Article
- Deep learning for RNA secondary structure determination: gauging generalizability and broadening the scope of traditional methods.RNA (New York, N.Y.) · 2026Review
- Deep Learning for RNA Secondary Structure Determination: Gauging Generalizability and Broadening the Scope of Traditional Methods.bioRxiv : the preprint server for biology · 2025Article
- The molecular dissection of TRIM25's RNA-binding mechanism provides key insights into its antiviral activity.Nature communications · 2024Article
- Towards parsimonious generative modeling of RNA families.Nucleic acids research · 2024Article
- Led-Seq: ligation-enhanced double-end sequence-based structure analysis of RNA.Nucleic acids research · 2023Article
- Structural analysis of MALAT1 long noncoding RNA in cells and in evolution.RNA (New York, N.Y.) · 2023Article
- Differential analysis of RNA structure probing experiments at nucleotide resolution: uncovering regulatory functions of RNA structure.Nature communications · 2022Article
- Alternative poly-adenylation modulates α1-antitrypsin expression in chronic obstructive pulmonary disease.PLoS genetics · 2021Article
- Geometric deep learning of RNA structure.Science (New York, N.Y.) · 2021Article
- An exon-biased biophysical approach and NMR spectroscopy define the secondary structure of a conserved helical element within the HOTAIR long non-coding RNA.Journal of structural biology · 2021Article
- Characteristic chemical probing patterns of loop motifs improve prediction accuracy of RNA secondary structures.Nucleic acids research · 2021Article
- In vivo structure of the Ty1 retrotransposon RNA genome.Nucleic acids research · 2021Article
- Using SHAPE-MaP To Model RNA Secondary Structure and Identify 3'UTR Variation in Chikungunya Virus.Journal of virology · 2020Article
- The chemistry and applications of RNA 2'-OH acylation.Nature reviews. Chemistry · 2020Article
- GraphClust2: Annotation and discovery of structured RNAs with scalable and accessible integrative clustering.GigaScience · 2019Article
- Integration of accessibility data from structure probing into RNA-RNA interaction prediction.Bioinformatics (Oxford, England) · 2019Article
- ShaKer: RNA SHAPE prediction using graph kernel.Bioinformatics (Oxford, England) · 2019Article
- dStruct: identifying differentially reactive regions from RNA structurome profiling data.Genome biology · 2019Article
- Nucleotide and structural label identification in single RNA molecules with quantum tunneling spectroscopy.Chemical science · 2019Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
2 authors.
Funding
Abstract
Selective 2'-hydroxyl acylation analyzed by primer extension (SHAPE) provides information on RNA structure at single-nucleotide resolution. It is most often used in conjunction with RNA secondary structure prediction algorithms as a probabilistic or thermodynamic restraint. With the recent advent of ultra-high-throughput approaches for collecting SHAPE data, the applications of this technology are extending beyond structure prediction. In this review, we discuss recent applications of SHAPE data in the transcriptomic context and how this new experimental paradigm is changing our understanding of these experiments and RNA folding in general. SHAPE experiments probe both the secondary and tertiary structure of an RNA, suggesting that model-free approaches for within and comparative RNA structure analysis can provide significant structural insight without the need for a full structural model. New methods incorporating SHAPE at different nucleotide resolutions are required to parse these transcriptomic data sets to transcend secondary structure modeling with global structural metrics. These 'multiscale' approaches provide deeper insights into RNA global structure, evolution, and function in the cell. WIREs RNA 2017, 8:e1374. doi: 10.1002/wrna.1374 For further resources related to this article, please visit the WIREs website.
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.