Prompt-based bioinformatics redefines how scientists interact with biological data, enabling natural language queries across multi-omics layers. By removing coding barriers and streamlining integration, this paradigm facilitates accessible, hypothesis-driven discovery. We call for community standards, educational adoption and collaborative development to realize its full potential in research and clinical settings.
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References
Auffarth, B. Generative AI with LangChain: Build Large Language Model (LLM) Apps with Python, ChatGPT, and other LLMs (Packt Publishing, 2023).
Sahoo, P. et al. A systematic survey of prompt engineering in large language models: Techniques and applications. Preprint at https://doi.org/10.48550/arXiv.2402.07927 (2024).
Iperi, C. et al. BiomiX, a user-friendly bioinformatic tool for democratized analysis and integration of multiomics data. BMC Bioinformatics 26, 8 (2025).
Argelaguet, R. et al. Multi-Omics factor analysis-a framework for unsupervised integration of multi-omics data sets. Mol. Syst. Biol. 14, e8124 (2018).
Yang, X. et al. PromptBio: a multi-agent AI platform for bioinformatics data analysis. Preprint at bioRxiv https://doi.org/10.1101/2025.07.05.663295 (2025).
Zhou, J. et al. An AI agent for fully automated multi‐omic analyses. Adv. Sci. (Weinh.) 11, e2407094 (2024).
Martinek, V. et al. Agentomics-ML: autonomous machine learning experimentation agent for genomic and transcriptomic data. Preprint at https://doi.org/10.48550/arXiv.2506.05542 (2025).
Liu, W. et al. DrBioRight 2.0: an LLM-powered bioinformatics chatbot for large-scale cancer functional proteomics analysis. Nat. Commun. 16, 2256 (2025).
Lobentanzer, S. et al. A platform for the biomedical application of large language models. Nat. Biotechnol. 43, 166–169 (2025).
Luo, Y. et al. BioMedGPT: open multimodal generative pre-trained transformer for biomedicine. Preprint at https://doi.org/10.48550/arXiv.2308.09442 (2023).
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Awan, A.R., Oveisi, M. & Karimi, M.M. Prompt-based bioinformatics: a new interface for multi-omics analysis. Nat Rev Genet (2025). https://doi.org/10.1038/s41576-025-00889-0
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DOI: https://doi.org/10.1038/s41576-025-00889-0
