ArticleBioinformatics advances2025
UTRGAN: learning to generate 5' UTR sequences for optimized translation efficiency and gene expression.
Article in Bioinformatics advances, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 14 papers.
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Who cites it
14 citing papers in PubMed.
- Two Classes of Protein Therapeutics: Why Dose-Response Architecture Defines the Boundary of mRNA Medicines.Pharmaceutics · 2026Review
- From Structure to Function of Promoters and 5'UTRs in Maize.International journal of molecular sciences · 2026Review
- mRNA vaccines in oncology: personalized cancer immunization and neoantigen targeting.Molecular & cellular oncology · 2026Review
- Recent Progress in Sequence Optimization of mRNA Vaccine: Biological Mechanism, Quantitative Metrics, and Computational Model.Bioinformatics and biology insights · 2026Review
- mRNA therapeutics: Transforming medicine through innovation in design, delivery, and disease treatment.Molecular therapy. Nucleic acids · 2025Review
- Engineering Anti-Tumor Immunity: An Immunological Framework for mRNA Cancer Vaccines.Vaccines · 2025Review
- Generating functional plasmid origins with OriGen.Nucleic acids research · 2025Article
- RNAtranslator: Modeling protein-conditional RNA design as sequence-to-sequence natural language translation.PLoS computational biology · 2025Article
- Artificial intelligence-driven circRNA vaccine development: multimodal collaborative optimization and a new paradigm for biomedical applications.Briefings in bioinformatics · 2025Article
- Improving the generalization of protein expression models with mechanistic sequence information.Nucleic acids research · 2025Article
- Optimization of regulatory DNA with active learning.Computational and structural biotechnology journal · 2025Article
- mRNA vaccine sequence and structure design and optimization: Advances and challenges.The Journal of biological chemistry · 2025Review
- A generative framework for enhanced cell-type specificity in rationally designed mRNAs.bioRxiv : the preprint server for biology · 2024Article
- A 5' UTR Language Model for Decoding Untranslated Regions of mRNA and Function Predictions.Nature machine intelligence · 2024Article
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Authors and funding
5 authors.
Funding
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Abstract
Motivation: The 5' untranslated region (5' UTR) of mRNA is crucial for the molecule's translatability and stability, making it essential for designing synthetic biological circuits for high and stable protein expression. Several UTR sequences are patented and widely used in laboratories. This paper presents UTRGAN, a Generative Adversarial Network (GAN)-based model for generating 5' UTR sequences, coupled with an optimization procedure to ensure high expression for target gene sequences or high ribosome load and translation efficiency. Results: The model generates sequences mimicking various properties of natural UTR sequences and optimizes them to achieve (i) up to five-fold higher average predicted expression on target genes, (ii) up to two-fold higher predicted mean ribosome load, and (iii) a 34-fold higher average predicted translation efficiency compared to initial UTR sequences. UTRGAN-generated sequences also exhibit higher similarity to known regulatory motifs in regions such as internal ribosome entry sites, upstream open reading frames, G-quadruplexes, and Kozak and initiation start codon regions. Availability and Implementation: The source code, including the model implementation and the optimization are released at http://github.com/ciceklab/UTRGAN. We downloaded the dataset from the UTRdb 2.0 database and available within the GitHub repository.
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Registered trials
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