ArticleInternational journal of molecular sciences2024
Link Between Individual Codon Frequencies and Protein Expression: Going Beyond Codon Adaptation Index.
Article in International journal of molecular sciences, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 5 papers.
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5 citing papers in PubMed.
- Transfer learning with pre-trained language models for protein expression level prediction inSynthetic and systems biotechnology · 2026Article
- Evolution and Functional Implications of Codon Usage Bias in Eukaryotes.Journal of molecular evolution · 2026Review
- ColiFormer: A Transformer-Based Codon Optimization Model Balancing Multiple Objectives for EnhancedBioengineering (Basel, Switzerland) · 2026Article
- Multidimensional Gene Space as an Approach for Analyzing the Organization of Genomes.International journal of molecular sciences · 2025Article
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3 authors.
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Abstract
An important role of a particular synonymous codon composition of a gene in its expression level is well known. There are a number of algorithms optimizing codon usage of recombinant genes to maximize their expression in host cells. Nevertheless, the underlying mechanism remains unsolved and is of significant relevance. In the realm of modern biotechnology, directing protein production to a specific level is crucial for metabolic engineering, genome rewriting and a growing number of other applications. In this study, we propose two new simple statistical and empirical methods for predicting the protein expression level from the nucleotide sequence of the corresponding gene: Codon Expression Index Score (CEIS) and Codon Productivity Score (CPS). Both of these methods are based on the influence of each individual codon in the gene on the overall expression level of the encoded protein and the frequencies of isoacceptors in the species. Our predictions achieve a correlation level of up to r = 0.7 with experimentally measured quantitative proteome data of
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