ArticleCell systems2017
PROBer Provides a General Toolkit for Analyzing Sequencing-Based Toeprinting Assays.
Article in Cell systems, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 12 papers.
What it found
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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.
The trial behind it
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
12 citing papers in PubMed.
- Isoform-specific RNA structure determination using Nano-DMS-MaP.Nature protocols · 2024Review
- RNA Structure Determination by High-Throughput Structural Analysis.Methods in molecular biology (Clifton, N.J.) · 2023Article
- Mobile genomics: tools and techniques for tackling transposons.Philosophical transactions of the Royal Society of London. Series B, Biological sciences · 2020Review
- 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
- Detecting RNA G-Quadruplexes (rG4s) in the Transcriptome.Cold Spring Harbor perspectives in biology · 2018Review
- Article
- PATTERNA: transcriptome-wide search for functional RNA elements via structural data signatures.Genome biology · 2018Article
- Statistical modeling of RNA structure profiling experiments enables parsimonious reconstruction of structure landscapes.Nature communications · 2018Article
- Next-generation sequencing technologies for detection of modified nucleotides in RNAs.RNA biology · 2017Review
- Comparative and integrative analysis of RNA structural profiling data: current practices and emerging questions.Quantitative biology (Beijing, China) · 2017Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
4 authors.
Funding
Abstract
A number of sequencing-based transcriptase drop-off assays have recently been developed to probe post-transcriptional dynamics of RNA-protein interaction, RNA structure, and RNA modification. Although these assays survey a diverse set of epitranscriptomic marks, we use the term toeprinting assays since they share methodological similarities. Their interpretation is predicated on addressing a similar computational challenge: how to learn isoform-specific chemical modification profiles in the face of complex read multi-mapping. We introduce PROBer, a statistical model and associated software, that addresses this challenge for the analysis of toeprinting assays. PROBer takes sequencing data as input and outputs estimated transcript abundances and isoform-specific modification profiles. Results on both simulated and biological data demonstrate that PROBer significantly outperforms individual methods tailored for specific toeprinting assays. Since the space of toeprinting assays is ever expanding and these assays are likely to be performed and analyzed together, we believe PROBer's unified data analysis solution will be valuable to the RNA community.
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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.