ArticleRNA (New York, N.Y.)2011
Sharing and archiving nucleic acid structure mapping data.
Article in RNA (New York, N.Y.), 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 20 papers.
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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.
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Who cites it
20 citing papers in PubMed, 37 citations in OpenAlex.
- High-throughput determination of RNA structures.Nature reviews. Genetics · 2018Review
- Structural divergence creates new functional features in alphavirus genomes.Nucleic acids research · 2018Article
- Updates to the RNA mapping database (RMDB), version 2.Nucleic acids research · 2018Article
- Impact of RNA structure on ZFP36L2 interaction with luteinizing hormone receptor mRNA.RNA (New York, N.Y.) · 2017Article
- Classification of RNA structure change by 'gazing' at experimental data.Bioinformatics (Oxford, England) · 2017Article
- Structure-Function Model for Kissing Loop Interactions That Initiate Dimerization of Ty1 RNA.Viruses · 2017Article
- Studying RNA Homology and Conservation with Infernal: From Single Sequences to RNA Families.Current protocols in bioinformatics · 2016Article
- Rich RNA Structure Landscapes Revealed by Mutate-and-Map Analysis.PLoS computational biology · 2015Article
- RNA-Puzzles Round II: assessment of RNA structure prediction programs applied to three large RNA structures.RNA (New York, N.Y.) · 2015Article
- Standardization of RNA chemical mapping experiments.Biochemistry · 2014Article
- Computational modeling of RNA 3D structures, with the aid of experimental restraints.RNA biology · 2014Review
- The mutate-and-map protocol for inferring base pairs in structured RNA.Methods in molecular biology (Clifton, N.J.) · 2014Article
- Accurate SHAPE-directed RNA secondary structure modeling, including pseudoknots.Proceedings of the National Academy of Sciences of the United States of America · 2013Article
- Principles for understanding the accuracy of SHAPE-directed RNA structure modeling.Biochemistry · 2013Article
- An RNA Mapping DataBase for curating RNA structure mapping experiments.Bioinformatics (Oxford, England) · 2012Article
- Evaluating our ability to predict the structural disruption of RNA by SNPs.BMC genomics · 2012Article
- The mechanisms of RNA SHAPE chemistry.Journal of the American Chemical Society · 2012Article
- Toward interoperable bioscience data.Nature genetics · 2012Article
- Structural effects of linkage disequilibrium on the transcriptome.RNA (New York, N.Y.) · 2012Article
- Meeting report of the RNA Ontology Consortium January 8-9, 2011.Standards in genomic sciences · 2011Article
Corrections and comments
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Authors and funding
17 authors at 8 institutions in 2 countries.
Funding
Abstract
Nucleic acids are particularly amenable to structural characterization using chemical and enzymatic probes. Each individual structure mapping experiment reveals specific information about the structure and/or dynamics of the nucleic acid. Currently, there is no simple approach for making these data publically available in a standardized format. We therefore developed a standard for reporting the results of single nucleotide resolution nucleic acid structure mapping experiments, or SNRNASMs. We propose a schema for sharing nucleic acid chemical probing data that uses generic public servers for storing, retrieving, and searching the data. We have also developed a consistent nomenclature (ontology) within the Ontology of Biomedical Investigations (OBI), which provides unique identifiers (termed persistent URLs, or PURLs) for classifying the data. Links to standardized data sets shared using our proposed format along with a tutorial and links to templates can be found at http://snrnasm.bio.unc.edu.
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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.