ArticleBriefings in bioinformatics2023
Integrated mRNA sequence optimization using deep learning.
Article in Briefings in bioinformatics, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 22 papers.
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Who cites it
22 citing papers in PubMed.
- ContiTE: continuous manifold MoE for few-shot cross-tissue mRNA translation efficiency prediction.Briefings in bioinformatics · 2026Article
- RNARL: reinforcement learning-driven unified generative framework for multi-objective RNA codon design.Genome biology · 2026Article
- VaxLab: integrated platform for rapid multistrategy mRNA vaccine design.Experimental & molecular medicine · 2026Article
- Accelerate the Highly Efficient Development of mRNA Vaccines Through Advanced Computational Methods.MedComm · 2026Review
- mRNA vaccines in cancer immunotherapy: current progress and perspectives in solid tumors and hematologic malignancies.MedScience · 2026Review
- Rewiring the immune response in lung cancer: current progress in bispecific antibodies, CAR-T therapy, and the rise ofFrontiers in immunology · 2026Review
- mRNA therapeutics: Transforming medicine through innovation in design, delivery, and disease treatment.Molecular therapy. Nucleic acids · 2025Review
- The strategies and advances of mRNA translation booster.Asian journal of pharmaceutical sciences · 2025Review
- Enhancing mRNA translation efficiency with discriminative and generative artificial intelligence by optimizing 5' UTR sequences.iScience · 2025Article
- Genome-wide molecular characterization and expression profiling of the cysteine protease gene family in maize.BMC genomics · 2025Article
- Review
- Non-Viral RNA Therapies for Non-Small Cell Lung Cancer and Their Corresponding Clinical Trials.Molecular pharmaceutics · 2025Review
- Advances in Therapeutic Cancer Vaccines, Their Obstacles, and Prospects Toward Tumor Immunotherapy.Molecular biotechnology · 2025Review
- mRNA-LM: full-length integrated SLM for mRNA analysis.Nucleic acids research · 2025Article
- NeoDesign: a computational tool for optimal selection of polyvalent neoantigen combinations.Bioinformatics (Oxford, England) · 2024Article
- mRNA vaccine development and applications: A special focus on tumors (Review).International journal of oncology · 2024Review
- Challenges in LncRNA Biology: Views and Opinions.Non-coding RNA · 2024Article
- Advances in non-viral mRNA delivery to the spleen.Biomaterials science · 2024Review
- Therapeutic cancer vaccines: advancements, challenges, and prospects.Signal transduction and targeted therapy · 2023Review
- mRNA vaccines in disease prevention and treatment.Signal transduction and targeted therapy · 2023Review
Corrections and comments
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Authors and funding
7 authors.
Funding
Abstract
The coronavirus disease of 2019 pandemic has catalyzed the rapid development of mRNA vaccines, whereas, how to optimize the mRNA sequence of exogenous gene such as severe acute respiratory syndrome coronavirus 2 spike to fit human cells remains a critical challenge. A new algorithm, iDRO (integrated deep-learning-based mRNA optimization), is developed to optimize multiple components of mRNA sequences based on given amino acid sequences of target protein. Considering the biological constraints, we divided iDRO into two steps: open reading frame (ORF) optimization and 5' untranslated region (UTR) and 3'UTR generation. In ORF optimization, BiLSTM-CRF (bidirectional long-short-term memory with conditional random field) is employed to determine the codon for each amino acid. In UTR generation, RNA-Bart (bidirectional auto-regressive transformer) is proposed to output the corresponding UTR. The results show that the optimized sequences of exogenous genes acquired the pattern of human endogenous gene sequence. In experimental validation, the mRNA sequence optimized by our method, compared with conventional method, shows higher protein expression. To the best of our knowledge, this is the first study by introducing deep-learning methods to integrated mRNA sequence optimization, and these results may contribute to the development of mRNA therapeutics.
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Registered trials
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.