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COMPUTATIONAL BIOLOGY

Automated sequence-based annotation and interpretation of the human genome

Nature Genetics volume 54, pages 916–917 (2022)Cite this article

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A machine-learning model produces summarized sequence representations of genomic regulatory activity, and provides a functional view of regulatory DNA variation in the human genome, with the aim of better understanding the role of sequence variation in health and disease.

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Fig. 1: Conceptual overview of the Sei framework.

References

  1. Roadmap Epigenomics Consortium. Nature 518, 317–330 (2015).

    Article  Google Scholar 

  2. ENCODE Project Consortium. Nature 583, 699–710 (2020).

    Article  Google Scholar 

  3. Zheng, R. et al. Nucleic Acids Res. 47, D729–D735 (2019).

    Article  CAS  Google Scholar 

  4. Meuleman, W. et al. Nature 584, 244–251 (2020).

    Article  CAS  Google Scholar 

  5. Chen, K. M., Wong, A. K., Troyanskaya, O. G. & Zhou, J. Nat. Genet. https://doi.org/10.1038/s41588-022-01102-2 (2022).

    Article  PubMed  PubMed Central  Google Scholar 

  6. Zentner, G. E. & Henikoff, S. Nat. Rev. Genet. 15, 814–827 (2014).

    Article  CAS  Google Scholar 

  7. Avsec, Ž. et al. Nat. Genet. 53, 354–366 (2021).

    Article  CAS  Google Scholar 

  8. Avsec, Ž. et al. Nat. Methods 18, 1196–1203 (2021).

    Article  CAS  Google Scholar 

  9. Zhou, J. & Troyanskaya, O. G. Nat. Methods 12, 931–934 (2015).

    Article  CAS  Google Scholar 

  10. Zhou, J. et al. Nat. Genet. 50, 1171–1179 (2018).

    Article  CAS  Google Scholar 

  11. Janssens, J. et al. Nature 601, 630–636 (2022).

    Article  CAS  Google Scholar 

  12. Stenson, P. D. et al. Hum. Genet. 139, 1197–1207 (2020).

    Article  Google Scholar 

  13. Maslova, A. et al. Proc. Natl Acad. Sci. USA 117, 25655–25666 (2020).

    Article  CAS  Google Scholar 

  14. Alipanahi, B., Delong, A., Weirauch, M. T. & Frey, B. J. Nat. Biotechnol. 33, 831–838 (2015).

    Article  CAS  Google Scholar 

  15. Ching, T. et al. J. R. Soc. Interface 15, 20170387 (2018).

    Article  Google Scholar 

  16. Zhou, J. Nat. Genet. 54, 725–734 (2022).

    Article  CAS  Google Scholar 

Download references

Author information

Authors and Affiliations

  1. Department of Genetics, Stanford University, Palo Alto, CA, USA

    Anshul Kundaje

  2. Department of Computer Science, Stanford University, Palo Alto, CA, USA

    Anshul Kundaje

  3. Altius Institute for Biomedical Sciences, Seattle, WA, USA

    Wouter Meuleman

  4. Paul G. Allen School of Computer Science & Engineering, University of Washington, Seattle, WA, USA

    Wouter Meuleman

Authors
  1. Anshul Kundaje
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  2. Wouter Meuleman
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Corresponding authors

Correspondence to Anshul Kundaje or Wouter Meuleman.

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Competing interests

A.K. is scientific co-founder of Ravel Biotechnology, is on the scientific advisory board of PatchBio, SerImmune, AINovo, TensorBio and OpenTargets, is a consultant with Illumina and owns shares in DeepGenomics, Immuni and Freenome. W.M. has no competing interests.

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Kundaje, A., Meuleman, W. Automated sequence-based annotation and interpretation of the human genome. Nat Genet 54, 916–917 (2022). https://doi.org/10.1038/s41588-022-01123-x

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