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A wider field of view to predict expression

A gene sequence-to-expression machine learning model achieves improved accuracy by incorporating information about potential long-range interactions.

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Fig. 1: Prediction of gene expression by Enformer.


  1. 1.

    Avsec, Z. et al. Nat. Methods (2021).

    Article  Google Scholar 

  2. 2.

    Kelley, D. R. et al. Genome Res. 28, 739–750 (2018).

    CAS  Article  Google Scholar 

  3. 3.

    Ouyang, Z., Zhou, Q. & Wong, W. H. Proc. Natl Acad. Sci. USA 106, 21521–21526 (2009).

    CAS  Article  Google Scholar 

  4. 4.

    Karlić, R. et al. Proc. Natl Acad. Sci. USA 107, 2926–2931 (2010).

    Article  Google Scholar 

  5. 5.

    Kelley, D. R., Snoek, J. & Rinn, J. L. Genome Res. 26, 990–999 (2016).

    CAS  Article  Google Scholar 

  6. 6.

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

    CAS  Article  Google Scholar 

  7. 7.

    Waswani, A. et al. in Advances in Neural Information Processing Systems 30 (NIPS2017) 6000–6010 (2017).

  8. 8.

    Gasperini, M., Tome, J. M. & Shendure, J. Nat. Rev. Genet. 21, 292–310 (2020).

    CAS  Article  Google Scholar 

  9. 9.

    Fudenberg, G., Kelley, D. R. & Pollard, K. S. Nat. Methods 17, 1111–1117 (2020).

    Article  Google Scholar 

  10. 10.

    Schreiber, J.M., Lu, Y.Y. & Noble, W.S. in ICML Workshop on Computational Biology (2020).

Download references


This work was supported by NIH award U01 HG009395.

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Correspondence to William Stafford Noble.

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The authors declare no competing interests.

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Lu, Y.Y., Noble, W.S. A wider field of view to predict expression. Nat Methods 18, 1155–1156 (2021).

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