Genomic language models could transform medicine but not yet
M. E. Consens, B. Li, A. R. Poetsch, and S. Gilbert. Genomic language models could transform medicine but not yet. npj Digital Medicine, 8:1–4, 12 2025. ISSN 23986352. doi: 10.1038/S41746-025-01603-4;SUBJMETA=1538,692,700;KWRD=HEALTH+CARE, HEALTH+POLICY. URL https://www.nature.com/articles/s41746-025-01603-4.
References
Brixi, G. et al. Genome modeling and design across all domains of life with Evo 2. 2025.02.18.638918. Preprint at https://doi.org/10.1101/2025.02.18.638918 (2025).
Callaway, E. Biggest-ever AI biology model writes DNA on demand. Nature 638, 868–869 (2025).
Park, E. G. et al. Genomic analyses of non-coding RNAs overlapping transposable elements and its implication to human diseases. Int. J. Mol. Sci. 23, 8950 (2022).
Alonso, M.E., Pernaute, B., Crespo, M., Gómez-Skarmeta, J.L. & Manzanares, M. Understanding the regulatory genome. Int. J. Develop. Biol. https://ijdb.ehu.eus/article/072428ma (2009).
Consens, M. E. et al. Transformers and genome language models. Nat. Machine Intell. https://www.nature.com/articles/s42256-025-01007-9 (2025).
Dalla-Torre, H. et al. Nucleotide transformer: building and evaluating robust foundation models for human genomics. Nat. Methods 22, 287–297 (2025).
Nguyen, E. et al. Sequence modeling and design from molecular to genome scale with Evo. Science 386, eado9336 (2024).
Comfort, N. Genetics: we are the 98%. Nature 520, 615–616 (2015).
Benegas, G., Albors, C., Aw, A.J. et al. A DNA language model based on multispecies alignment predicts the effects of genome-wide variants. Nat Biotechnol. https://doi.org/10.1038/s41587-024-02511-w (2025).
Health (US), N. I. of & Study, B. S. C. Understanding Human Genetic Variation. in NIH Curriculum Supplement Series [Internet] (National Institutes of Health, 2007).
Gresova, K., Martinek, V., Cechak, D., Simecek, P. & Alexiou, P. Genomic benchmarks: a collection of datasets for genomic sequence classification. BMC Genomic Data 24, 25 (2023).
Marin, F. I. et al. BEND: Benchmarking DNA language models on biologically meaningful tasks. Preprint at https://doi.org/10.48550/arXiv.2311.12570 (2024).
Ji, Y., Zhou, Z., Liu, H. & Davuluri, R. V. DNABERT: pre-trained bidirectional encoder representations from transformers model for DNA-language in genome. Bioinformatics 37, 2112–2120 (2021).
Sanabria, M., Hirsch, J. & Poetsch, A. R. Distinguishing word identity and sequence context in DNA language models. BMC Bioinformatics 25, 301 (2024).
Sanabria, M., Hirsch, J., Joubert, P. M. & Poetsch, A. R. DNA language model GROVER learns sequence context in the human genome. Nat. Mach. Intell. 6, 911–923 (2024).
Bloomfield, D. et al. AI and biosecurity: the need for governance. Science 385, 831–833 (2024).
Riedemann, L., Labonne, M. & Gilbert, S. The path forward for large language models in medicine is open. Npj Digit. Med. 7, 1–5 (2024).
Poetsch, A. R. KI-Modell analysiert und generiert DNA-Strukturen (SMC, 2024).
Derraz, B. et al. New regulatory thinking is needed for AI-based personalised drug and cell therapies in precision oncology. Npj Precis. Oncol. 8, 1–11 (2024).
Harishbhai Tilala, M. et al. Ethical considerations in the use of artificial intelligence and machine learning in health care: a comprehensive review. Cureus 16, e62443 (2024).
Zhou, Z. et al. DNABERT-2: Efficient Foundation Model and Benchmark For Multi-Species Genome. (2023).
Nguyen, E. et al. HyenaDNA: Long-Range Genomic Sequence Modeling at Single Nucleotide Resolution. (2023).
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