ArticleBiology direct2016
Estimation of ribosome profiling performance and reproducibility at various levels of resolution.
Article in Biology direct, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 43 papers.
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Who cites it
43 citing papers in PubMed.
- Ageing-related decline of translation as a consequence of transcription dysregulation.Journal of the Royal Society, Interface · 2025Article
- Evaluation of Eukaryotic mRNA Coding Potential.Methods in molecular biology (Clifton, N.J.) · 2025Article
- A review of Ribosome profiling and tools used in Ribo-seq data analysis.Computational and structural biotechnology journal · 2024Review
- Comprehensive quantitative modeling of translation efficiency in a genome-reduced bacterium.Molecular systems biology · 2023Article
- What Can Ribo-Seq, Immunopeptidomics, and Proteomics Tell Us About the Noncanonical Proteome?Molecular & cellular proteomics : MCP · 2023Article
- What can Ribo-seq and proteomics tell us about the non-canonical proteome?bioRxiv : the preprint server for biology · 2023Article
- Article
- Evaluating data integrity in ribosome footprinting datasets through modelled polysome profiles.Nucleic acids research · 2022Article
- Review
- Modeling the ribosomal small subunit dynamic in Saccharomyces cerevisiae based on TCP-seq data.Nucleic acids research · 2022Article
- Analysis of Ribosome Profiling Data.Methods in molecular biology (Clifton, N.J.) · 2022Article
- Specificity of mRNA Folding and Its Association with Evolutionarily Adaptive mRNA Secondary Structures.Genomics, proteomics & bioinformatics · 2021Article
- Prokaryotic rRNA-mRNA interactions are involved in all translation steps and shape bacterial transcripts.RNA biology · 2021Article
- Genes with 5' terminal oligopyrimidine tracts preferentially escape global suppression of translation by the SARS-CoV-2 Nsp1 protein.RNA (New York, N.Y.) · 2021Article
- Genes with 5' terminal oligopyrimidine tracts preferentially escape global suppression of translation by the SARS-CoV-2 Nsp1 protein.bioRxiv : the preprint server for biology · 2021Article
- RiboA: a web application to identify ribosome A-site locations in ribosome profiling data.BMC bioinformatics · 2021Article
- Variability in mRNA translation: a random matrix theory approach.Scientific reports · 2021Article
- The effects of codon bias and optimality on mRNA and protein regulation.Cellular and molecular life sciences : CMLS · 2021Review
- Codon-based indices for modeling gene expression and transcript evolution.Computational and structural biotechnology journal · 2021Review
- Pairs of amino acids at the P- and A-sites of the ribosome predictably and causally modulate translation-elongation rates.Journal of molecular biology · 2020Article
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2 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundRibosome profiling (or Ribo-seq) is currently the most popular methodology for studying translation; it has been employed in recent years to decipher various fundamental gene expression regulation aspects. The main promise of the approach is its ability to detect ribosome densities over an entire transcriptome in high resolution of single codons. Indeed, dozens of ribo-seq studies have included results related to local ribosome densities in different parts of the transcript; nevertheless, the performance of Ribo-seq has yet to be quantitatively evaluated and reported in a large-scale multi-organismal and multi-protocol study of currently available datasets.
resultsHere we provide the first objective evaluation of Ribo-seq at the resolution of a single nucleotide(s) using clear, interpretable measures, based on the analysis of 15 experiments, 6 organisms, and a total of 612, 961 transcripts. Our major conclusion is that the ability to infer signals of ribosomal densities at nucleotide scale is considerably lower than previously thought, as signals at this level are not reproduced well in experimental replicates. In addition, we provide various quantitative measures that connect the expected error rate with Ribo-seq analysis resolution.
conclusionsThe analysis of Ribo-seq data at the resolution of codons and nucleotides provides a challenging task, calls for task-specific statistical methods and further protocol improvements. We believe that our results are important for every researcher studying translation and specifically for researchers analyzing data generated by the Ribo-seq approach. REVIEWERS: This article was reviewed by Dmitrij Frishman, Eugene Koonin and Frank Eisenhaber.
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