ArticleProceedings of the National Academy of Sciences of the United States of America2011
Modeling and automation of sequencing-based characterization of RNA structure.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 70 papers.
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Who cites it
70 citing papers in PubMed.
- Two riboswitch classes that share a common ligand-binding fold show major differences in the ability to accommodate mutations.Nucleic acids research · 2024Article
- Identification of RNA structures and their roles in RNA functions.Nature reviews. Molecular cell biology · 2024Review
- Isoform-specific RNA structure determination using Nano-DMS-MaP.Nature protocols · 2024Review
- txtools: an R package facilitating analysis of RNA modifications, structures, and interactions.Nucleic acids research · 2024Article
- Molecular Dynamics Simulations with Grand-Canonical Reweighting Suggest Cooperativity Effects in RNA Structure Probing Experiments.Journal of chemical theory and computation · 2023Article
- A riboswitch separated from its ribosome-binding site still regulates translation.Nucleic acids research · 2023Article
- RNA Structure Determination by High-Throughput Structural Analysis.Methods in molecular biology (Clifton, N.J.) · 2023Article
- Molecular dynamics analysis of biomolecular systems including nucleic acids.Biophysics and physicobiology · 2022Article
- Accurate detection of RNA stem-loops in structurome data reveals widespread association with protein binding sites.RNA biology · 2021Article
- Rapid structure-function insights via hairpin-centric analysis of big RNA structure probing datasets.NAR genomics and bioinformatics · 2021Article
- Computationally reconstructing cotranscriptional RNA folding from experimental data reveals rearrangement of non-native folding intermediates.Molecular cell · 2021Article
- Analysis of a preQ1-I riboswitch in effector-free and bound states reveals a metabolite-programmed nucleobase-stacking spine that controls gene regulation.Nucleic acids research · 2020Article
- Genome-Wide Discovery of DEAD-Box RNA Helicase Targets Reveals RNA Structural Remodeling in Transcription Termination.Genetics · 2019Article
- reactIDR: evaluation of the statistical reproducibility of high-throughput structural analyses towards a robust RNA structure prediction.BMC bioinformatics · 2019Article
- dStruct: identifying differentially reactive regions from RNA structurome profiling data.Genome biology · 2019Article
- High-throughput determination of RNA structures.Nature reviews. Genetics · 2018Review
- RNA Framework: an all-in-one toolkit for the analysis of RNA structures and post-transcriptional modifications.Nucleic acids research · 2018Article
- Article
- Probing of RNA structures in a positive sense RNA virus reveals selection pressures for structural elements.Nucleic acids research · 2018Article
- PATTERNA: transcriptome-wide search for functional RNA elements via structural data signatures.Genome biology · 2018Article
10 more citing papers are in PubMed but not listed here.
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9 authors.
Funding
Abstract
Sequence census methods reduce molecular measurements such as transcript abundance and protein-nucleic acid interactions to counting problems via DNA sequencing. We focus on a novel assay utilizing this approach, called selective 2'-hydroxyl acylation analyzed by primer extension sequencing (SHAPE-Seq), that can be used to characterize RNA secondary and tertiary structure. We describe a fully automated data analysis pipeline for SHAPE-Seq analysis that includes read processing, mapping, and structural inference based on a model of the experiment. Our methods rely on the solution of a series of convex optimization problems for which we develop efficient and effective numerical algorithms. Our results can be easily extended to other chemical probes of RNA structure, and also generalized to modeling polymerase drop-off in other sequence census-based experiments.
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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.