ArticleRNA (New York, N.Y.)2017
Visualization of RNA structure models within the Integrative Genomics Viewer.
Article in RNA (New York, N.Y.), 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 22 papers.
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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.
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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
22 citing papers in PubMed.
- dsRNAscan maps human dsRNAome, revealing conservation, intermolecular dsRNA, and correlates of ADAR dependency.Molecular cell · 2026Article
- A conserved long-range RNA interaction in SARS-CoV-2 recruits ADAR1 to enhance virus proliferation.Nature communications · 2025Article
- Article
- Comprehensive Mapping of Human dsRNAome Reveals Conservation, Neuronal Enrichment, and Intermolecular Interactions.bioRxiv : the preprint server for biology · 2025Article
- Alternative splicing of CARM1 regulated by LincGET-guided paraspeckles biases the first cell fate in mammalian early embryos.Nature structural & molecular biology · 2024Article
- RIP-Seq analysis of non-PPR chloroplast editing factors reveals broad RNA interactions and enrichment of less efficiently translated RNAs by OZ1 and ORRM1 complexes.The Plant journal : for cell and molecular biology · 2024Article
- A Method to Quantitatively Examine Heat Stress-Induced Alternative Splicing in Plants by RNA-Seq and RT-PCR.Methods in molecular biology (Clifton, N.J.) · 2024Article
- Structural analysis of MALAT1 long noncoding RNA in cells and in evolution.RNA (New York, N.Y.) · 2023Article
- Structure-first identification of RNA elements that regulate dengue virus genome architecture and replication.Proceedings of the National Academy of Sciences of the United States of America · 2023Article
- RNA G-quadruplex organizes stress granule assembly through DNAPTP6 in neurons.Science advances · 2023Article
- Prediction and analysis of functional RNA structures within the integrative genomics viewer.NAR genomics and bioinformatics · 2022Article
- Comprehensive mapping of SARS-CoV-2 interactions in vivo reveals functional virus-host interactions.Nature communications · 2021Article
- Decoding LncRNAs.Cancers · 2021Review
- SHAPE Directed Discovery of New Functions in Large RNAs.Accounts of chemical research · 2021Review
- Comprehensive in vivo secondary structure of the SARS-CoV-2 genome reveals novel regulatory motifs and mechanisms.Molecular cell · 2021Article
- Visualization of lncRNA and mRNA Structure Models Within the Integrative Genomics Viewer.Methods in molecular biology (Clifton, N.J.) · 2021Article
- Article
- Mapping the RNA structural landscape of viral genomes.Methods (San Diego, Calif.) · 2020Article
- Functional classification of long non-coding RNAs by k-mer content.Nature genetics · 2018Article
- Article
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2 authors.
Funding
Abstract
Analyses of the interrelationships between RNA structure and function are increasingly important components of genomic studies. The SHAPE-MaP strategy enables accurate RNA structure probing and realistic structure modeling of kilobase-length noncoding RNAs and mRNAs. Existing tools for visualizing RNA structure models are not suitable for efficient analysis of long, structurally heterogeneous RNAs. In addition, structure models are often advantageously interpreted in the context of other experimental data and gene annotation information, for which few tools currently exist. We have developed a module within the widely used and well supported open-source Integrative Genomics Viewer (IGV) that allows visualization of SHAPE and other chemical probing data, including raw reactivities, data-driven structural entropies, and data-constrained base-pair secondary structure models, in context with linear genomic data tracks. We illustrate the usefulness of visualizing RNA structure in the IGV by exploring structure models for a large viral RNA genome, comparing bacterial mRNA structure in cells with its structure under cell- and protein-free conditions, and comparing a noncoding RNA structure modeled using SHAPE data with a base-pairing model inferred through sequence covariation analysis.
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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.