ArticleCell systems2018
Scikit-ribo Enables Accurate Estimation and Robust Modeling of Translation Dynamics at Codon Resolution.
Article in Cell systems, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 30 papers.
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Who cites it
30 citing papers in PubMed.
- ANYI: The ANnotated Yeast Interactome.bioRxiv : the preprint server for biology · 2026Article
- Near-cognate tRNAs dominate codon decoding times in simulated ribosomes.Nucleic acids research · 2025Article
- Comparative CRISPRi screens reveal a human stem cell dependence on mRNA translation-coupled quality control.Nature structural & molecular biology · 2025Article
- Ageing-related decline of translation as a consequence of transcription dysregulation.Journal of the Royal Society, Interface · 2025Article
- Interpreting ribosome dynamics during mRNA translation.The Journal of biological chemistry · 2025Review
- Multi-objective computational optimization of human 5' UTR sequences.Briefings in bioinformatics · 2025Article
- The dynamics and functional impact of tRNA repertoires during early embryogenesis in zebrafish.The EMBO journal · 2024Article
- Riboformer: a deep learning framework for predicting context-dependent translation dynamics.Nature communications · 2024Article
- Ribosome profiling: a powerful tool in oncological research.Biomarker research · 2024Review
- Selective gene expression maintains human tRNA anticodon pools during differentiation.Nature cell biology · 2024Article
- A critical period of translational control during brain development at codon resolution.Nature structural & molecular biology · 2022Article
- The relationship of mRNA with protein expression in CD8+ T cells associates with gene class and gene characteristics.PloS one · 2022Article
- Introduction to Bioinformatics Resources for Post-transcriptional Regulation of Gene Expression.Methods in molecular biology (Clifton, N.J.) · 2022Article
- Sequence determinants as key regulators in gene expression of T cells.Immunological reviews · 2021Review
- Natural variation of the cardiac transcriptome in humans.RNA biology · 2021Article
- Article
- RiboA: a web application to identify ribosome A-site locations in ribosome profiling data.BMC bioinformatics · 2021Article
- Quantitative Modeling of Protein Synthesis Using Ribosome Profiling Data.Frontiers in molecular biosciences · 2021Review
- Genome-Wide Analysis of Actively Translated Open Reading Frames Using RiboTaper/ORFquant.Methods in molecular biology (Clifton, N.J.) · 2021Article
- RiboDiPA: a novel tool for differential pattern analysis in Ribo-seq data.Nucleic acids research · 2020Article
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6 authors.
Funding
Abstract
Ribosome profiling (Ribo-seq) is a powerful technique for measuring protein translation; however, sampling errors and biological biases are prevalent and poorly understood. Addressing these issues, we present Scikit-ribo (https://github.com/schatzlab/scikit-ribo), an open-source analysis package for accurate genome-wide A-site prediction and translation efficiency (TE) estimation from Ribo-seq and RNA sequencing data. Scikit-ribo accurately identifies A-site locations and reproduces codon elongation rates using several digestion protocols (r = 0.99). Next, we show that the commonly used reads per kilobase of transcript per million mapped reads-derived TE estimation is prone to biases, especially for low-abundance genes. Scikit-ribo introduces a codon-level generalized linear model with ridge penalty that correctly estimates TE, while accommodating variable codon elongation rates and mRNA secondary structure. This corrects the TE errors for over 2,000 genes in S. cerevisiae, which we validate using mass spectrometry of protein abundances (r = 0.81), and allows us to determine the Kozak-like sequence directly from Ribo-seq. We conclude with an analysis of coverage requirements needed for robust codon-level analysis and quantify the artifacts that can occur from cycloheximide treatment.
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