Programmable RNA translation by IRES discovery and new generation using deep learning

Machine Learning


  • Komar, AA & Hatzoglou, M. Exploring internal ribosome entry sites as therapeutic targets. front. Oncor. 5233 (2015).

    Article Google Scholar

  • Martinand-Mari, C., Lebleu, B. & Robbins, I. Oligonucleotide-based strategies to inhibit human hepatitis C virus. oligonucleotide 13539–548 (2003).

    Article Google Scholar

  • Nulf, CJ & Corey, D. Intracellular inhibition of hepatitis C virus (HCV) internal ribosome entry site (IRES)-dependent translation by peptide nucleic acids (PNA) and locked nucleic acids (LNA). Nucleic acid research institute 323792–3798 (2004).

    Article Google Scholar

  • Filbin, ME & Kieft, JS Toward a structural understanding of IRES RNA function. car. opinion. structure. Biol. 19267–276 (2009).

    Article Google Scholar

  • Lozano, G., Fernandez, N. & Martinez-Salas, E. Modeling three-dimensional structural motifs of viral IRES. J. Mol. Biol. 428767–776 (2016).

    Article Google Scholar

  • Plank, T.-DM and Kieft, JS Structure of a non-protein-coding RNA that drives internal ribosome entry site function. Wiley Interdisciple. Rev.RNA 3195–212 (2012).

    Article Google Scholar

  • Mailliot, J. & Martin, F. Viral internal ribosome entry sites: four classes for one target. Wiley Interdisciple. Rev.RNA 9e1458 (2018).

    Article Google Scholar

  • Chen, R. et al. Manipulating circular RNA to enhance protein production. nut. biotechnology. 41262–272 (2023).

    Article Google Scholar

  • Choi, S.-W. & Nam, J.-W. Optimal design of synthetic circular RNA. Experience point mole. medicine. 561281–1292 (2024).

    Article Google Scholar

  • Kolekar, P., Pataskar, A., Kulkarni-Kale, U., Pal, J. & Kulkarni, A. Irespred: a web server for predicting internal ribosome entry sites (IRES) in cells and viruses. Science. Member of Parliament 627436 (2016).

    Article Google Scholar

  • Zhao, J. et al. IRESfinder: Identifying RNA internal ribosome entry sites in eukaryotic cells using framed k-mer features. J. Genet. genomics 45403–406 (2018).

    Article Google Scholar

  • Wang, J. & Gribskov, M. IRESpy: an XGBoost model for predicting internal ribosome entry sites. BMC bioinf. 20409 (2019).

    Article Google Scholar

  • Zhou, Y. et al. DeepCIP: A multimodal deep learning method for predicting internal ribosome entry sites of circRNAs. Calculate. Biol. medicine. 164107288 (2023).

    Article Google Scholar

  • Chu, Y. A 5′ UTR language model for decoding untranslated regions of other mRNAs and predicting their functions. Zenodo https://doi.org/10.5281/zenodo.10621605 (2024).

  • Shen, T. et al. Accurate RNA 3D structure prediction using a language model-based deep learning approach. nut. method twenty one2287–2298 (2024).

    Article Google Scholar

  • Weingarten-Gabbay, S. et al. Comparative genetics. Systematic discovery of cap-independent translated sequences in human and viral genomes. science 351aad4939 (2016).

    Article Google Scholar

  • Zhao, J. et al. Iresbase: A comprehensive database of experimentally validated internal ribosome entry sites. Genom. proteome. Bioinform. 18129–139 (2020).

    Article Google Scholar

  • Mokrejs, M. et al. IRESite – a tool for examining internal ribosome entry sites in viruses and cells. Nucleic acid research institute 38D131–D136 (2010).

    Article Google Scholar

  • Calvary, I. et al. Rfam 14: Expanding coverage of metagenomics, viruses, and microRNA families. Nucleic acid research institute 49D192–D200 (2021).

    Article Google Scholar

  • Ho, J., Jain, A., Abbeel, P. Denoising diffusion stochastic model. Preprint available at https://doi.org/10.48550/arxiv.2006.11239 (2020).

  • Zhao, Y., Oono, K., Takizawa, H. & Kotera, M. GenerRNA: Generative pre-trained language models for de novo RNA design. PLoS ONE 19e0310814 (2024).

    Article Google Scholar

  • Thoma, C., Bergamini, G., Galy, B., Hundsdoerfer, P. & Hentze, MW Enhancement of IRES-mediated translation of c-myc and BiP mRNAs by poly(A) tails is independent of intact eIF4G and PABP. Mol. cell 15925–935 (2004).

    Article Google Scholar

  • Lee, H et al. riboCIRC: a comprehensive database of translatable circRNAs. Genome Biol. twenty two79 (2021).

    Article Google Scholar

  • Gritsenko, AA et al. Sequence features of viral and human internal ribosome entry sites predict their activity. PLoS Computing. Biol. 13e1005734 (2017).

    Article Google Scholar

  • Dvir, S. et al. Decoding the rules by which 5′-UTR sequences influence protein expression in yeast. National Academy of Procedures. Science. united states of america 110E2792–E2801 (2013).

    Article Google Scholar

  • Hie, BL et al. Efficient evolution of human antibodies from a general protein language model. nut. biotechnology. 42275–283 (2024).

    Article Google Scholar

  • Ronneberger, O., Fischer, P. & Brox, T. U-net: convolutional networks for biomedical image segmentation. in Medical Image Computing and Computer-Assisted Intervention – MICCAI 2015 234–241 (Springer, 2015).

  • He, K et al. Deep residual learning for image recognition. in IEEE Conference on Procedural Computer Vision and Pattern Recognition 770–778 (IEEE, 2016).

  • Vaswani, A. et al. All you need is attention. in Procedures 31st International Conference on Neural Information Processing Systems 6000–6010 (NiSEN, 2017).

  • Shen, Z., Zhang, M., Zhao, H., Yi, S., Li, H. Efficient attention: Attention with linear complexity. in IEEE/CVF Winter Conference on Applications of Procedure Computer Vision 3531–3539 (IEEE, 2021).

  • Hughes, NW et al. Machine learning-optimized Cas12a barcoding enables single cell lineage and transcriptional profile recovery. Mol. cell 823103–3118 (2022).

    Article Google Scholar

  • Ying, D. et al. Targeting herpes simplex virus with CRISPR-Cas9 cures herpetic stromal keratitis in mice. nut. biotechnology. 39567–577 (2021).

    Article Google Scholar

  • Ying, D. et al. Virus-like particles targeting dendritic cells as potent mRNA vaccine carriers. nut. biomed. engineering 9185–200 (2025).

    Article Google Scholar

  • Chu, Y. a96123155/IRES_Prediction_Design: IRES-AI. Zenodo https://doi.org/10.5281/zenodo.15081323 (2026).



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