ArticleNucleic acids research2011
Simplified RNA secondary structure mapping by automation of SHAPE data analysis.
Article in Nucleic acids research, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 28 papers.
What it found
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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.
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Who cites it
28 citing papers in PubMed, 43 citations in OpenAlex.
- IPANEMAP Suite: a pipeline for probing-informed RNA structure modeling.NAR genomics and bioinformatics · 2025Article
- RNA Secondary Structure Modeling Following the IPANEMAP Workflow.Methods in molecular biology (Clifton, N.J.) · 2024Article
- Programmable antivirals targeting critical conserved viral RNA secondary structures from influenza A virus and SARS-CoV-2.Nature medicine · 2022Article
- Review
- Hepatitis C Virus Translation Regulation.International journal of molecular sciences · 2020Review
- Article
- New windows into retroviral RNA structures.Retrovirology · 2018Review
- RiboCAT: a new capillary electrophoresis data analysis tool for nucleic acid probing.RNA (New York, N.Y.) · 2017Article
- Establishment and Application of a High Throughput Screening System Targeting the Interaction between HCV Internal Ribosome Entry Site and Human Eukaryotic Translation Initiation Factor 3.Frontiers in microbiology · 2017Article
- Fingerprinting the junctions of RNA structure by an open-paddlewheel diruthenium compound.RNA (New York, N.Y.) · 2016Article
- Automated band annotation for RNA structure probing experiments with numerous capillary electrophoresis profiles.Bioinformatics (Oxford, England) · 2015Article
- Conserved RNA secondary structures and long-range interactions in hepatitis C viruses.RNA (New York, N.Y.) · 2015Article
- Computational analysis of RNA structures with chemical probing data.Methods (San Diego, Calif.) · 2015Review
- In virio SHAPE analysis of tRNA(Lys3) annealing to HIV-1 genomic RNA in wild type and protease-deficient virus.Retrovirology · 2015Article
- Article
- A magnesium-induced RNA conformational switch at the internal ribosome entry site of hepatitis C virus genome visualized by atomic force microscopy.Nucleic acids research · 2015Article
- High-throughput mutate-map-rescue evaluates SHAPE-directed RNA structure and uncovers excited states.RNA (New York, N.Y.) · 2014Article
- Hepatitis delta antigen requires a flexible quasi-double-stranded RNA structure to bind and condense hepatitis delta virus RNA in a ribonucleoprotein complex.Journal of virology · 2014Article
- Computational analysis of conserved RNA secondary structure in transcriptomes and genomes.Annual review of biophysics · 2014Review
- Annealing to sequences within the primer binding site loop promotes an HIV-1 RNA conformation favoring RNA dimerization and packaging.RNA (New York, N.Y.) · 2013Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
4 authors at 1 institution in 1 country.
Funding
Abstract
SHAPE (Selective 2'-hydroxyl acylation analysed by primer extension) technology has emerged as one of the leading methods of determining RNA secondary structure at the nucleotide level. A significant bottleneck in using SHAPE is the complex and time-consuming data processing that is required. We present here a modified data collection method and a series of algorithms, embodied in a program entitled Fast Analysis of SHAPE traces (FAST), which significantly reduces processing time. We have used this method to resolve the secondary structure of the first ~900 nt of the hepatitis C virus (HCV) genome, including the entire core gene. We have also demonstrated the ability of SHAPE/FAST to detect the binding of a small molecule inhibitor to the HCV internal ribosomal entry site (IRES). In conclusion, FAST allows for high-throughput data processing to match the current high-throughput generation of data possible with SHAPE, reducing the barrier to determining the structure of RNAs of interest.
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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.