ArticleG3 (Bethesda, Md.)2014
Mean of the typical decoding rates: a new translation efficiency index based on the analysis of ribosome profiling data.
Article in G3 (Bethesda, Md.), 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 33 papers.
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Who cites it
33 citing papers in PubMed.
- Synonymous codon usage regulates translation initiation.Cell reports · 2023Article
- eIF3 mRNA selectivity profiling reveals eIF3k as a cancer-relevant regulator of ribosome content.The EMBO journal · 2023Article
- Translation in the cell under fierce competition for shared resources: a mathematical model.Journal of the Royal Society, Interface · 2022Article
- Article
- Comparison of rRNA depletion methods for efficient bacterial mRNA sequencing.Scientific reports · 2022Article
- Identification of conserved slow codons that are important for protein expression and function.RNA biology · 2021Article
- Quantitative Modeling of Protein Synthesis Using Ribosome Profiling Data.Frontiers in molecular biosciences · 2021Review
- Codon-based indices for modeling gene expression and transcript evolution.Computational and structural biotechnology journal · 2021Review
- Whole cell biophysical modeling of codon-tRNA competition reveals novel insights related to translation dynamics.PLoS computational biology · 2020Article
- Codon bias confers stability to human mRNAs.EMBO reports · 2019Article
- The Critical Role of Codon Composition on the Translation Efficiency Robustness of the Hepatitis A Virus Capsid.Genome biology and evolution · 2019Article
- Quantitative principles of cis-translational control by general mRNA sequence features in eukaryotes.Genome biology · 2019Article
- A chemical kinetic basis for measuring translation initiation and elongation rates from ribosome profiling data.PLoS computational biology · 2019Article
- Quantification and discovery of sequence determinants of protein-per-mRNA amount in 29 human tissues.Molecular systems biology · 2019Article
- Networks of ribosome flow models for modeling and analyzing intracellular traffic.Scientific reports · 2019Article
- Structural Basis of the Subcellular Topology Landscape ofFrontiers in microbiology · 2019Article
- Novel insights into gene expression regulation during meiosis revealed by translation elongation dynamics.NPJ systems biology and applications · 2019Article
- Cells alter their tRNA abundance to selectively regulate protein synthesis during stress conditions.Science signaling · 2018Article
- riboWaltz: Optimization of ribosome P-site positioning in ribosome profiling data.PLoS computational biology · 2018Article
- Shoelaces: an interactive tool for ribosome profiling processing and visualization.BMC genomics · 2018Article
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2 authors.
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No grant is acknowledged in the PubMed record.
Abstract
Gene translation modeling and prediction is a fundamental problem that has numerous biomedical implementations. In this work we present a novel, user-friendly tool/index for calculating the mean of the typical decoding rates that enables predicting translation elongation efficiency of protein coding genes for different tissue types, developmental stages, and experimental conditions. The suggested translation efficiency index is based on the analysis of the organism's ribosome profiling data. This index could be used for example to predict changes in translation elongation efficiency of lowly expressed genes that usually have relatively low and/or biased ribosomal densities and protein levels measurements, or can be used for example for predicting translation efficiency of new genetically engineered genes. We demonstrate the usability of this index via the analysis of six organisms in different tissues and developmental stages. Distributable cross platform application and guideline are available for download at: http://www.cs.tau.ac.il/~tamirtul/MTDR/MTDR_Install.html.
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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.