ArticleNature communications2025
CodonTransformer: a multispecies codon optimizer using context-aware neural networks.
Article in Nature communications, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 27 papers.
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Who cites it
27 citing papers in PubMed.
- Enhancing protein expression in humans through codon optimization with transformer and contrastive learning.Molecular therapy. Nucleic acids · 2026Article
- VeloHARMO: a deep learning framework for mRNA coding sequence generation and design via translation velocity harmonization.Briefings in bioinformatics · 2026Article
- CasY7: An optimized Cas12i system for enhanced genome editing in monocot crops.Journal of integrative plant biology · 2026Article
- Toward Rational Design of Precision-Fermented Milk Proteins: Integrating Cross-Species Selection, Post-Translational Modification, and AI Optimization.Comprehensive reviews in food science and food safety · 2026Review
- Foundation Models for Microbiome Research: From Sequence Semantics to Community Dynamics and Multimodal World Models.Advanced genetics (Hoboken, N.J.) · 2026Review
- RNARL: reinforcement learning-driven unified generative framework for multi-objective RNA codon design.Genome biology · 2026Article
- Biosynthesis of Sciadonic Acid Derived from Gymnosperms with Anti-Colitis Activity.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Article
- Beyond Starch: Towards a Scalable Potato Platform for Molecular Farming.Plant biotechnology journal · 2026Review
- Recombinant Protein Drugs: A 2025 Update.BioDrugs : clinical immunotherapeutics, biopharmaceuticals and gene therapy · 2026Review
- Deep Learning-Guided Reverse Translation Enhances Soluble Expression of Recombinant Proteins inInternational journal of molecular sciences · 2026Article
- Is the molecular microenvironment of the latent HIV reservoir predictable using deep learning approaches?Journal of virology · 2026Review
- Molecular engineering of Komagataella phaffii for venom toxin production.Applied microbiology and biotechnology · 2026Review
- AI-enabled protein design facilitates future plant research and crop breeding.Plant physiology · 2026Review
- VaxLab: integrated platform for rapid multistrategy mRNA vaccine design.Experimental & molecular medicine · 2026Article
- Unintended Creation or Insertion of Antisense Promoter Motifs During Codon Optimization: A Cyber-Biosecurity Risk.Microorganisms · 2026Article
- Cross-species gene redesign leveraging ortholog information and generative modeling.Nature communications · 2026Article
- Advancing codon language modeling with synonymous codon constrained masking.Nucleic acids research · 2026Article
- Pichia-CLM: A language model-based codon optimization pipeline forProceedings of the National Academy of Sciences of the United States of America · 2026Article
- CodonRL: Multi-Objective Codon Sequence Optimization Using Demonstration-Guided Reinforcement Learning.bioRxiv : the preprint server for biology · 2026Article
- ColiFormer: A Transformer-Based Codon Optimization Model Balancing Multiple Objectives for EnhancedBioengineering (Basel, Switzerland) · 2026Article
Corrections and comments
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Authors and funding
5 authors.
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No grant is acknowledged in the PubMed record.
Abstract
Degeneracy in the genetic code allows many possible DNA sequences to encode the same protein. Optimizing codon usage within a sequence to meet organism-specific preferences faces combinatorial explosion. Nevertheless, natural sequences optimized through evolution provide a rich source of data for machine learning algorithms to explore the underlying rules. Here, we introduce CodonTransformer, a multispecies deep learning model trained on over 1 million DNA-protein pairs from 164 organisms spanning all domains of life. The model demonstrates context-awareness thanks to its Transformers architecture and to our sequence representation strategy that combines organism, amino acid, and codon encodings. CodonTransformer generates host-specific DNA sequences with natural-like codon distribution profiles and with minimum negative cis-regulatory elements. This work introduces the strategy of Shared Token Representation and Encoding with Aligned Multi-masking (STREAM) and provides a codon optimization framework with a customizable open-access model and a user-friendly Google Colab interface.
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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.