ArticleDNA research : an international journal for rapid publication of reports on genes and genomes2014
Modelling the efficiency of codon-tRNA interactions based on codon usage bias.
Article in DNA research : an international journal for rapid publication of reports on genes and genomes, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 86 papers, 1 of them a synthesis that pooled it.
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Who cites it
86 citing papers in PubMed, 1 synthesis or guideline pooled it, 141 citations in OpenAlex.
- Synonymous but Not Silent: The Codon Usage Code for Gene Expression and Protein Folding.Annual review of biochemistry · 2021Pooled it
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- Complete mitochondrial genome of Laetiporus ailaoshanensis (Laetiporaceae, Basidiomycota): features, evolution, and phylogeny.BMC genomics · 2026Article
- Mapping the inter- and intra-genic codon-usage landscape inNAR genomics and bioinformatics · 2026Article
- Advancing codon language modeling with synonymous codon constrained masking.Nucleic acids research · 2026Article
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- Codon usage bias is presumably affected by tRNA selection effects in Actinidia polyploidization events.BMC genomics · 2025Article
- Macroevolutionary changes in natural selection on codon usage reflect evolution of the tRNA pool across a budding yeast subphylum.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
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- A deep learning model trained on expressed transcripts across different tissue types reveals cell-type codon-optimization preferences.Nucleic acids research · 2025Article
- Effective Gene Expression Prediction and Optimization from Protein Sequences.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2025Article
- Over time analysis of the codon usage of SARS-CoV-2 and its variants.Computational and structural biotechnology journal · 2025Article
- Computational Analysis of MDR1 Variants Predicts Effect on Cancer Cells via their Effect on mRNA Folding.PLoS computational biology · 2024Article
26 more citing papers are in PubMed but not listed here.
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Authors and funding
2 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The tRNA adaptation index (tAI) is a widely used measure of the efficiency by which a coding sequence is recognized by the intra-cellular tRNA pool. This index includes among others weights that represent wobble interactions between codons and tRNA molecules. Currently, these weights are based only on the gene expression in Saccharomyces cerevisiae. However, the efficiencies of the different codon-tRNA interactions are expected to vary among different organisms. In this study, we suggest a new approach for adjusting the tAI weights to any target model organism without the need for gene expression measurements. Our method is based on optimizing the correlation between the tAI and a measure of codon usage bias. Here, we show that in non-fungal the new tAI weights predict protein abundance significantly better than the traditional tAI weights. The unique tRNA-codon adaptation weights computed for 100 different organisms exhibit a significant correlation with evolutionary distance. The reported results demonstrate the usefulness of the new measure in future genomic studies.
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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.