ArticleBMC systems biology2012
Computational codon optimization of synthetic gene for protein expression.
Article in BMC systems biology, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 34 papers.
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Who cites it
34 citing papers in PubMed.
- A multi-objective sequence engineering framework for rational genetic vaccine design.Journal of the Royal Society, Interface · 2026Article
- Pichia-CLM: A language model-based codon optimization pipeline forProceedings of the National Academy of Sciences of the United States of America · 2026Article
- Designing a multi-epitope vaccine against dengue virus-2 usingBioImpacts : BI · 2026Article
- codonGPT: reinforcement learning on a generative language model enables scalable mRNA design.Nucleic acids research · 2025Article
- Comparative Analysis of Codon Optimization Tools: Advancing toward a Multi-Criteria Framework for Synthetic Gene Design.Journal of microbiology and biotechnology · 2025Article
- Screening of novel therapeutic targets and chimeric vaccine construction against antibiotic-resistantFrontiers in immunology · 2025Article
- Differentially used codons among essential genes in bacteria identified by machine learning-based analysis.Molecular genetics and genomics : MGG · 2024Article
- mRNAid, an open-source platform for therapeutic mRNA design and optimization strategies.NAR genomics and bioinformatics · 2024Article
- Article
- Gene recoding by synonymous mutations creates promiscuous intragenic transcription initiation in mycobacteria.bioRxiv : the preprint server for biology · 2023Article
- Computer-aided genomic data analysis of drug-resistantFrontiers in cellular and infection microbiology · 2023Article
- Nanomedicine for the Delivery of RNA in Cancer.Cancers · 2022Review
- Overcoming the Solubility Problem in E. coli: Available Approaches for Recombinant Protein Production.Methods in molecular biology (Clifton, N.J.) · 2022Review
- Codon pair optimization (CPO): a software tool for synthetic gene design based on codon pair bias to improve the expression of recombinant proteins in Pichia pastoris.Microbial cell factories · 2021Article
- Analysis of 11,430 recombinant protein production experiments reveals that protein yield is tunable by synonymous codon changes of translation initiation sites.PLoS computational biology · 2021Article
- Review
- mRNA codon optimization with quantum computers.PloS one · 2021Article
- Article
- Engineering Biology to Construct Microbial Chassis for the Production of Difficult-to-Express Proteins.International journal of molecular sciences · 2020Review
- Computational Tools for Discovering and Engineering Natural Product Biosynthetic Pathways.iScience · 2020Review
Corrections and comments
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Authors and funding
2 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundThe construction of customized nucleic acid sequences allows us to have greater flexibility in gene design for recombinant protein expression. Among the various parameters considered for such DNA sequence design, individual codon usage (ICU) has been implicated as one of the most crucial factors affecting mRNA translational efficiency. However, previous works have also reported the significant influence of codon pair usage, also known as codon context (CC), on the level of protein expression.
resultsIn this study, we have developed novel computational procedures for evaluating the relative importance of optimizing ICU and CC for enhancing protein expression. By formulating appropriate mathematical expressions to quantify the ICU and CC fitness of a coding sequence, optimization procedures based on genetic algorithm were employed to maximize its ICU and/or CC fitness. Surprisingly, the in silico validation of the resultant optimized DNA sequences for Escherichia coli, Lactococcus lactis, Pichia pastoris and Saccharomyces cerevisiae suggests that CC is a more relevant design criterion than the commonly considered ICU.
conclusionsThe proposed CC optimization framework can complement and enhance the capabilities of current gene design tools, with potential applications to heterologous protein production and even vaccine development in synthetic biotechnology.
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