ArticleNucleic acids research2020
RiboVIEW: a computational framework for visualization, quality control and statistical analysis of ribosome profiling data.
Article in Nucleic acids research, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. An erratum has been issued. Cited by 12 papers.
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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.
- Multi-omic assessment of mRNA translation dynamics in liver cancer cell lines.Scientific data · 2025Article
- A review of Ribosome profiling and tools used in Ribo-seq data analysis.Computational and structural biotechnology journal · 2024Review
- Exploring the potential of large language model-based chatbots in challenges of ribosome profiling data analysis: a review.Briefings in bioinformatics · 2024Review
- Ribosomal protein RPL39L is an efficiency factor in the cotranslational folding of a subset of proteins with alpha helical domains.Nucleic acids research · 2024Article
- Ribosome Profiling of Plants.Methods in molecular biology (Clifton, N.J.) · 2024Article
- Queuosine-tRNA promotes sex-dependent learning and memory formation by maintaining codon-biased translation elongation speed.The EMBO journal · 2023Article
- Ribo-uORF: a comprehensive data resource of upstream open reading frames (uORFs) based on ribosome profiling.Nucleic acids research · 2023Article
- Review
- Analysis of Ribosome Profiling Data.Methods in molecular biology (Clifton, N.J.) · 2022Article
- ORFik: a comprehensive R toolkit for the analysis of translation.BMC bioinformatics · 2021Article
- RiboA: a web application to identify ribosome A-site locations in ribosome profiling data.BMC bioinformatics · 2021Article
- RiboToolkit: an integrated platform for analysis and annotation of ribosome profiling data to decode mRNA translation at codon resolution.Nucleic acids research · 2020Article
Corrections and comments
- Erratum issued
Authors and funding
2 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Recently, newly developed ribosome profiling methods based on high-throughput sequencing of ribosome-protected mRNA footprints allow to study genome-wide translational changes in detail. However, computational analysis of the sequencing data still represents a bottleneck for many laboratories. Further, specific pipelines for quality control and statistical analysis of ribosome profiling data, providing high levels of both accuracy and confidence, are currently lacking. In this study, we describe automated bioinformatic and statistical diagnoses to perform robust quality control of ribosome profiling data (RiboQC), to efficiently visualize ribosome positions and to estimate ribosome speed (RiboMine) in an unbiased way. We present an R pipeline to setup and undertake the analyses that offers the user an HTML page to scan own data regarding the following aspects: periodicity, ligation and digestion of footprints; reproducibility and batch effects of replicates; drug-related artifacts; unbiased codon enrichment including variability between mRNAs, for A, P and E sites; mining of some causal or confounding factors. We expect our pipeline to allow an optimal use of the wealth of information provided by ribosome profiling experiments.
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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 OpenQuestion graph.