ArticleQuantitative biology (Beijing, China)2017
Comparative and integrative analysis of RNA structural profiling data: current practices and emerging questions.
Article in Quantitative biology (Beijing, China), 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 26 papers.
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Who cites it
26 citing papers in PubMed.
- A Workflow for Identifying Helicase-Dependent RNA Structural Changes in Transcriptional Termination: From DMS Sequencing Analysis to Reporter Assay-Based Validation.Methods in molecular biology (Clifton, N.J.) · 2027Article
- 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
- Evaluation of novel computational methods to identify RNA-binding protein footprints from structural data.RNA (New York, N.Y.) · 2025Article
- Reliable method for predicting the binding affinity of RNA-small molecule interactions using machine learning.Briefings in bioinformatics · 2024Article
- RNA Structure Determination by High-Throughput Structural Analysis.Methods in molecular biology (Clifton, N.J.) · 2023Article
- Differential analysis of RNA structure probing experiments at nucleotide resolution: uncovering regulatory functions of RNA structure.Nature communications · 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
- Sieving RNA 3D Structures with SHAPE and Evaluating Mechanisms Driving Sequence-Dependent Reactivity Bias.The journal of physical chemistry. B · 2021Article
- Generation of Sequencing Libraries for Structural Analysis of Bacterial 5' UTRs.STAR protocols · 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
- Carbodiimide reagents for the chemical probing of RNA structure in cells.RNA (New York, N.Y.) · 2019Article
- Article
- A k-mer based transcriptomics approach for antisense drug discovery targeting the Ewing's family of tumors.Oncotarget · 2018Article
- Detecting RNA G-Quadruplexes (rG4s) in the Transcriptome.Cold Spring Harbor perspectives in biology · 2018Review
Corrections and comments
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Authors and funding
3 authors.
Funding
Abstract
backgroundStructure profiling experiments provide single-nucleotide information on RNA structure. Recent advances in chemistry combined with application of high-throughput sequencing have enabled structure profiling at transcriptome scale and in living cells, creating unprecedented opportunities for RNA biology. Propelled by these experimental advances, massive data with ever-increasing diversity and complexity have been generated, which give rise to new challenges in interpreting and analyzing these data.
resultsWe review current practices in analysis of structure profiling data with emphasis on comparative and integrative analysis as well as highlight emerging questions. Comparative analysis has revealed structural patterns across transcriptomes and has become an integral component of recent profiling studies. Additionally, profiling data can be integrated into traditional structure prediction algorithms to improve prediction accuracy.
conclusionsTo keep pace with experimental developments, methods to facilitate, enhance and refine such analyses are needed. Parallel advances in analysis methodology will complement profiling technologies and help them reach their full potential.
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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 Socratic graph.