ArticleJournal of computational biology : a journal of computational molecular cell biology2017
Accurate Recovery of Ribosome Positions Reveals Slow Translation of Wobble-Pairing Codons in Yeast.
Article in Journal of computational biology : a journal of computational molecular cell biology, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 16 papers.
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Who cites it
16 citing papers in PubMed, 32 citations in OpenAlex.
- The regulation, function and disease relevance of cytoplasmic tRNAs.Nature reviews. Molecular cell biology · 2026Review
- Advancing codon language modeling with synonymous codon constrained masking.Nucleic acids research · 2026Article
- Variation in the fitness impact of translationally optimal codons among animals.Genome research · 2025Article
- Genome-wide impact of codon usage bias on translation optimization in Drosophila melanogaster.Nature communications · 2024Article
- Article
- Mechanisms governing codon usage bias and the implications for protein expression in the chloroplast of Chlamydomonas reinhardtii.The Plant journal : for cell and molecular biology · 2022Review
- CONCUR: quick and robust calculation of codon usage from ribosome profiling data.Bioinformatics (Oxford, England) · 2021Article
- RiboA: a web application to identify ribosome A-site locations in ribosome profiling data.BMC bioinformatics · 2021Article
- RiboDiPA: a novel tool for differential pattern analysis in Ribo-seq data.Nucleic acids research · 2020Article
- What determines eukaryotic translation elongation: recent molecular and quantitative analyses of protein synthesis.Open biology · 2020Review
- Ribosome Pausing at Inefficient Codons at the End of the Replicase Coding Region Is Important for Hepatitis C Virus Genome Replication.International journal of molecular sciences · 2020Article
- Identifying A- and P-site locations on ribosome-protected mRNA fragments using Integer Programming.Scientific reports · 2019Article
- riboWaltz: Optimization of ribosome P-site positioning in ribosome profiling data.PLoS computational biology · 2018Article
- Using the Ribodeblur pipeline to recover A-sites from yeast ribosome profiling data.Methods (San Diego, Calif.) · 2018Article
- Scikit-ribo Enables Accurate Estimation and Robust Modeling of Translation Dynamics at Codon Resolution.Cell systems · 2018Article
- Using mitoribosomal profiling to investigate human mitochondrial translation.Wellcome open research · 2017Article
Corrections and comments
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Authors and funding
3 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Ribosome profiling quantitatively captures ribosome locations during translation. The resulting profiles of ribosome locations are widely used to study translational speed. However, an accurate estimation of the ribosome location depends on identifying the A-site from ribosome profiling reads, a problem that was previously unsolved. Here, we propose a novel method to estimate the ribosome A-site positions from high-coverage ribosome profiling reads. Our model allows more reads to be used, accurately explains the 3-nt periodicity of ribosome profiling reads from various lengths, and recovers consistent ribosome positions across different lengths. Our recovered ribosome positions are correctly highly skewed toward a single frame within a codon. They retain subcodon resolution and enable detection of off-frame translational events, such as frameshifts. Our method improves the correlation with other estimates of codon decoding time. Furthermore, the refined profiles show that yeast wobble-pairing codons are translated slower than their synonymous Watson-Crick-pairing codons. These results provide evidence that protein synthetic rate can be tuned by codon usage bias.
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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.