High-Codon: A Deep Learning-Based Codon Optimization Tool for Enhanced Heterologous Protein Expression in Escherichia coli

Li, J.; Dong, X.; Liu, J.

doi:10.1101/2025.05.30.656984

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bioRxiv · 10.1101/2025.05.30.656984

High-Codon: A Deep Learning-Based Codon Optimization Tool for Enhanced Heterologous Protein Expression in Escherichia coli

Li, J.·Dong, X.·Liu, J.

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Abstract

High-Codon is a deep learning-based codon optimization tool designed to enhance the expression levels of heterologous proteins in Escherichia coli. This approach employs a BERT pre-trained model to construct a sequence labeling framework for predicting optimal codons. Additionally, an expression-level weighted loss function is introduced to strengthen the models ability to learn from highly expressed proteins. Evaluation using 100 protein sequences from 34 species demonstrates that High-Codon outperforms traditional optimization methods.

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Li, J., Dong, X., Liu, J.. 2025-06-02. High-Codon: A Deep Learning-Based Codon Optimization Tool for Enhanced Heterologous Protein Expression in Escherichia coli. https://doi.org/10.1101/2025.05.30.656984

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