ArticleNucleic acids research2017
A high-throughput approach to profile RNA structure.
Article in Nucleic acids research, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 35 papers.
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Who cites it
35 citing papers in PubMed.
- Decoding the Structural Complexity of Viral RNAs with SHAPE to Guide Antiviral Therapeutics.Viruses · 2026Review
- The role of low-complexity repeats in RNA-RNA interactions and a deep learning framework for duplex prediction.Nature communications · 2026Article
- Decoding the lncRNA World: Comprehensive Approaches to lncRNA Structure and Interactome Studies.Cells · 2026Review
- The Use of Enhanced Analytical Pipelines for the Characterization of Poly(A) and Poly(A)-LNP Formulation Critical Quality Attributes.Molecular pharmaceutics · 2025Article
- Xist condensates: perspectives for therapeutic intervention.Genome biology · 2025Review
- Deep generalizable prediction of RNA secondary structure via base pair motif energy.Nature communications · 2025Article
- The role of RNA in the nanoscale organization of α-synuclein phase separation.NAR molecular medicine · 2025Article
- Subgenomic flaviviral RNAs and human proteins:Computational and structural biotechnology journal · 2024Article
- ALS-associated FUS mutation reshapes the RNA and protein composition of stress granules.Nucleic acids research · 2024Article
- Long noncoding RNA study: Genome-wide approaches.Genes & diseases · 2023Review
- Article
- The PRALINE database: protein and Rna humAn singLe nucleotIde variaNts in condEnsates.Bioinformatics (Oxford, England) · 2023Article
- RNA secondary structure packages evaluated and improved by high-throughput experiments.Nature methods · 2022Article
- Computational and Experimental Approaches to Study the RNA Secondary Structures of RNA Viruses.Viruses · 2022Review
- Deep learning models for RNA secondary structure prediction (probably) do not generalize across families.Bioinformatics (Oxford, England) · 2022Article
- RNA editing increases the nucleotide diversity of SARS-CoV-2 in human host cells.PLoS genetics · 2022Article
- Predicting RNA Secondary Structure Using In Vitro and In Vivo Data.Methods in molecular biology (Clifton, N.J.) · 2022Article
- Phase Separation Drives SARS-CoV-2 Replication: A Hypothesis.Frontiers in molecular biosciences · 2022Article
- Article
- Structural landscape of the complete genomes of dengue virus serotypes and other viral hemorrhagic fevers.BMC genomics · 2021Article
Corrections and comments
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Authors and funding
4 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Here we introduce the Computational Recognition of Secondary Structure (CROSS) method to calculate the structural profile of an RNA sequence (single- or double-stranded state) at single-nucleotide resolution and without sequence length restrictions. We trained CROSS using data from high-throughput experiments such as Selective 2΄-Hydroxyl Acylation analyzed by Primer Extension (SHAPE; Mouse and HIV transcriptomes) and Parallel Analysis of RNA Structure (PARS; Human and Yeast transcriptomes) as well as high-quality NMR/X-ray structures (PDB database). The algorithm uses primary structure information alone to predict experimental structural profiles with >80% accuracy, showing high performances on large RNAs such as Xist (17 900 nucleotides; Area Under the ROC Curve AUC of 0.75 on dimethyl sulfate (DMS) experiments). We integrated CROSS in thermodynamics-based methods to predict secondary structure and observed an increase in their predictive power by up to 30%.
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