Skip to main content

Thank you for visiting nature.com. You are using a browser version with limited support for CSS. To obtain the best experience, we recommend you use a more up to date browser (or turn off compatibility mode in Internet Explorer). In the meantime, to ensure continued support, we are displaying the site without styles and JavaScript.

  • Comment
  • Published:

Programmable biology through artificial intelligence: from nucleic acids to proteins to cells

Nature Methods volume 21, pages 1384–1386 (2024)Cite this article

Subjects

Artificial intelligence-enabled computational tools not only help us to elucidate biological processes but also facilitate the programming of biology through molecular and cellular engineering.

This is a preview of subscription content, access via your institution

Relevant articles

Open Access articles citing this article.

Access options

Buy this article

  • Purchase on SpringerLink
  • Instant access to the full article PDF.

USD 39.95

Prices may be subject to local taxes which are calculated during checkout

Fig. 1: Applications of AI-based methods for programming biology.

References

  1. Villiger, L. et al. Nat. Rev. Mol. Cell Biol. 25, 464–487 (2024).

    Article  CAS  PubMed  Google Scholar 

  2. Wang, J. Y. & Doudna, J. A. Science 379, eadd8643 (2023).

    Article  CAS  PubMed  Google Scholar 

  3. Shmakov, S. et al. Mol. Cell 60, 385–397 (2015).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  4. Altae-Tran, H. et al. Science 382, eadi1910 (2023).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  5. Hwang, Y., Cornman, A. L., Kellogg, E. H., Ovchinnikov, S. & Girguis, P. R. Nat. Commun. 15, 2880 (2024).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  6. Boger, R. et al. In 2023 ICML Workshop on Computational Biology https://icml-compbio.github.io/2023/papers/WCBICML2023_paper138.pdf (2023).

  7. Alley, E. C., Khimulya, G., Biswas, S., AlQuraishi, M. & Church, G. M. Nat. Methods 16, 1315–1322 (2019).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  8. Ruffolo, J. A. et al. Preprint at bioRxiv https://doi.org/10.1101/2024.04.22.590591 (2024).

  9. Nguyen, E. et al. Preprint at bioRxiv https://doi.org/10.1101/2024.02.27.582234 (2024).

  10. Krishna, R. et al. Science 384, eadl2528 (2024).

    Article  CAS  PubMed  Google Scholar 

  11. Joung, J. et al. Cell 186, 209–229.e26 (2023).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  12. Replogle, J. M. et al. Cell 185, 2559–2575.e28 (2022).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  13. Theodoris, C. V. et al. Nature 618, 616–624 (2023).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  14. Lotfollahi, M., Wolf, F. A. & Theis, F. J. Nat. Methods 16, 715–721 (2019).

    Article  CAS  PubMed  Google Scholar 

  15. Kedzierska, K. Z., Crawford, L., Amini, A. P. & Lu, A. X. Preprint at bioRxiv https://doi.org/10.1101/2023.10.16.561085 (2023).

Download references

Author information

Author notes

  1. These authors contributed equally: Omar O. Abudayyeh, Jonathan S. Gootenberg.

Authors and Affiliations

  1. Harvard Medical School, Harvard University, Boston, MA, USA

    Omar O. Abudayyeh & Jonathan S. Gootenberg

  2. Division of Engineering in Medicine, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Cambridge, MA, USA

    Omar O. Abudayyeh & Jonathan S. Gootenberg

  3. Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Boston, MA, USA

    Omar O. Abudayyeh & Jonathan S. Gootenberg

  4. Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA

    Omar O. Abudayyeh & Jonathan S. Gootenberg

Authors
  1. Omar O. Abudayyeh
    View author publications

    Search author on:PubMed Google Scholar

  2. Jonathan S. Gootenberg
    View author publications

    Search author on:PubMed Google Scholar

Corresponding authors

Correspondence to Omar O. Abudayyeh or Jonathan S. Gootenberg.

Ethics declarations

Competing interests

J.S.G. and O.O.A. are co-founders of Sherlock Biosciences, Tome Biosciences, Doppler Bio and Circle Labs.

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Abudayyeh, O.O., Gootenberg, J.S. Programmable biology through artificial intelligence: from nucleic acids to proteins to cells. Nat Methods 21, 1384–1386 (2024). https://doi.org/10.1038/s41592-024-02338-y

Download citation

  • Published:

  • Version of record:

  • Issue date:

  • DOI: https://doi.org/10.1038/s41592-024-02338-y

This article is cited by

Search

Advanced search

Quick links

Nature Briefing: Translational Research

Sign up for the Nature Briefing: Translational Research newsletter — top stories in biotechnology, drug discovery and pharma.

Get what matters in translational research, free to your inbox weekly. Sign up for Nature Briefing: Translational Research