ArticleNature machine intelligence2024
A 5' UTR Language Model for Decoding Untranslated Regions of mRNA and Function Predictions.
Article in Nature machine intelligence, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 69 papers.
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Who cites it
69 citing papers in PubMed.
- Functional analysis ofMolecular therapy. Nucleic acids · 2026Article
- AI foundation models for RNA biology.RNA biology · 2026Review
- mRNA lipid nanoparticle vaccines: current status, challenges and future prospects.Molecular biomedicine · 2026Review
- From rules to foundation models: a comprehensive review of machine learning approaches for siRNA design.NAR genomics and bioinformatics · 2026Review
- Deciphering the comprehensive relationship between 5' UTR and 3' UTR sequences with deep learning.Bioinformatics (Oxford, England) · 2026Article
- Functional Variants of the RAD51 Gene Contribute to Susceptibility to Non-Syndromic Orofacial Clefts in a Han Chinese Population.Orthodontics & craniofacial research · 2026Article
- Advancing bioinformatics with language models: components, applications, and perspectives.Briefings in bioinformatics · 2026Review
- The Use of Deep Learning in RNA Therapeutic Development.ACS nano · 2026Review
- Evaluating DNA Function Understanding in Genomic Language Models Using Evolutionarily Implausible Sequences.ACS synthetic biology · 2026Article
- Engineered mRNA backbones for gene expression in human T cells.Molecular therapy. Nucleic acids · 2026Article
- Enhancement of Therapeutic mRNA Translation in Cellular Stress Conditions.International journal of molecular sciences · 2026Review
- Bridging sequence-structure motifs and genetic variants for genome-wide dynamic RNA-protein interaction profiling.Nature communications · 2026Article
- Detecting and quantifying overparametrization in RNA language models with REDIAL.bioRxiv : the preprint server for biology · 2026Article
- IRES-TrAPPr reveals novel insights into viral and cellular mRNA translation.bioRxiv : the preprint server for biology · 2026Article
- In vivo CAR-T therapy: from molecular design to precision delivery.Journal of nanobiotechnology · 2026Review
- "More" Artificial mRNAs: Beyond the Art of Nature.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Review
- AI-guided multi-omics analysis identifies NPC1-modulated susceptibility to SARS-CoV-2 infection under PMNature communications · 2026Article
- UTR-DynaPro: a CNN-transformer multimodal language model for decoding 5'UTR regulatory mechanisms.Scientific reports · 2026Article
- Fine-tuning ERK activity enables proliferation-differentiation balance during lineage specification of human embryonic stem cells.PLoS biology · 2026Article
- The DNA dialect: a comprehensive guide to pretrained genomic language models.Molecular systems biology · 2026Review
9 more citing papers are in PubMed but not listed here.
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8 authors.
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Abstract
The 5' UTR, a regulatory region at the beginning of an mRNA molecule, plays a crucial role in regulating the translation process and impacts the protein expression level. Language models have showcased their effectiveness in decoding the functions of protein and genome sequences. Here, we introduced a language model for 5' UTR, which we refer to as the UTR-LM. The UTR-LM is pre-trained on endogenous 5' UTRs from multiple species and is further augmented with supervised information including secondary structure and minimum free energy. We fine-tuned the UTR-LM in a variety of downstream tasks. The model outperformed the best known benchmark by up to 5% for predicting the Mean Ribosome Loading, and by up to 8% for predicting the Translation Efficiency and the mRNA Expression Level. The model also applies to identifying unannotated Internal Ribosome Entry Sites within the untranslated region and improves the AUPR from 0.37 to 0.52 compared to the best baseline. Further, we designed a library of 211 novel 5' UTRs with high predicted values of translation efficiency and evaluated them via a wet-lab assay. Experiment results confirmed that our top designs achieved a 32.5% increase in protein production level relative to well-established 5' UTR optimized for therapeutics.
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