ArticleNucleic acids research2018
RNA Framework: an all-in-one toolkit for the analysis of RNA structures and post-transcriptional modifications.
Article in Nucleic acids research, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 77 papers.
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77 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
- Gapmers targeting conserved SARS-CoV-2 single-stranded regions reduce viral load and reshape inflammatory macrophage responses.iScience · 2026Article
- MERGE-RNA: a physics-based model to predict RNA secondary structure ensembles with chemical probing.Nucleic acids research · 2026Article
- Interdependent RNA structural motifs at the 3'-terminus of the West Nile virus genome regulate viral growth.Nucleic acids research · 2026Article
- Modtector: ultra-fast modification signal mining on mapped sequencing reads.Bioinformatics (Oxford, England) · 2026Article
- Expression of conjugation genes is controlled by a novel zipper-type transcriptional attenuation mechanism.Nucleic acids research · 2026Article
- Rational design of hammerhead ribozymes as CD93 silencing tools for vascular diseases.Molecular therapy. Nucleic acids · 2026Article
- Identification of conserved RNA regulatory switches in living cells using RNA secondary structure ensemble mapping and covariation analysis.Nature biotechnology · 2026Article
- RNAStructuromeDB: a transcriptome-wide database of predicted RNA secondary structures with integrated APIs for functional annotation and RNA-targeted drug discovery.NAR genomics and bioinformatics · 2026Article
- FIRST-seq: a nanopore-based cDNA sequencing platform for RNA modification and structure profiling.Genome biology · 2026Article
- VIRSE: a variational Bayesian framework for RNA structural ensemble inference.Briefings in bioinformatics · 2026Article
- RNA functional modulation by Mitoxantrone via RNA structural ensemble repartitioning.Nature communications · 2026Article
- Enhancing plant antiviral responses and productivity through the elimination of mScience advances · 2026Article
- RiboBright reveals cell-type-specific differences in ribosome organization and movement.Nature communications · 2026Article
- Site-Selective Ligand Selection by Mutational Profiling for Covalent RNA Targeting.Angewandte Chemie (International ed. in English) · 2026Article
- DMS-informed secondary structure modeling of Epstein-Barr Virus LMP-1 pre-mRNA defines novel elements spanning introns.PloS one · 2026Article
- RNA Structure and Its Function.Methods in molecular biology (Clifton, N.J.) · 2026Article
- Identification of conserved RNA secondary structures in human respiratory syncytial virus A (hRSV A).NAR genomics and bioinformatics · 2025Article
- RNA switch model for localization and translation of the myelin basic protein mRNA.bioRxiv : the preprint server for biology · 2025Article
- Control of gene output by intron RNA structure.bioRxiv : the preprint server for biology · 2025Article
17 more citing papers are in PubMed but not listed here.
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Authors and funding
4 authors.
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No grant is acknowledged in the PubMed record.
Abstract
RNA is emerging as a key regulator of a plethora of biological processes. While its study has remained elusive for decades, the recent advent of high-throughput sequencing technologies provided the unique opportunity to develop novel techniques for the study of RNA structure and post-transcriptional modifications. Nonetheless, most of the required downstream bioinformatics analyses steps are not easily reproducible, thus making the application of these techniques a prerogative of few laboratories. Here we introduce RNA Framework, an all-in-one toolkit for the analysis of most NGS-based RNA structure probing and post-transcriptional modification mapping experiments. To prove the extreme versatility of RNA Framework, we applied it to both an in-house generated DMS-MaPseq dataset, and to a series of literature available experiments. Notably, when starting from publicly available datasets, our software easily allows replicating authors' findings. Collectively, RNA Framework provides the most complete and versatile toolkit to date for a rapid and streamlined analysis of the RNA epistructurome. RNA Framework is available for download at: http://www.rnaframework.com.
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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.