New computational method uses convolutional neural networks for cis-regulatory sequence analysis to analyze and cluster scATAC-seq data.
This is a preview of subscription content, access via your institution
Access options
Access Nature and 54 other Nature Portfolio journals
Get Nature+, our best-value online-access subscription
$32.99 / 30 days
cancel any time
Subscribe to this journal
Receive 12 print issues and online access
$259.00 per year
only $21.58 per issue
Rent or buy this article
Prices vary by article type
from$1.95
to$39.95
Prices may be subject to local taxes which are calculated during checkout
References
Avsec, Ž. et al. Nat. Genet. 53, 354–366 (2021).
Janssens, J. et al. Nature 601, 630–636 (2022).
Cusanovich, D. A. et al. Cell 174, 1309–1324.e18 (2018).
Kelley, D. R., Snoek, J. & Rinn, J. L. Genome Res. 26, 990–999 (2016).
de Almeida, B. P., Reiter, F., Pagani, M. & Stark, A. Nat. Genet. 54, 613–624 (2022).
Avsec, Ž. et al. Nat. Methods 18, 1196–1203 (2021).
Shrikumar, A., Greenside, P. & Kundaje, A. Preprint at https://doi.org/10.48550/arXiv.1704.02685 (2019).
Wasserman, W. W. & Sandelin, A. Nat. Rev. Genet. 5, 276–287 (2004).
Minnoye, L. et al. Nat. Rev. Methods Primer 1, 10 (2021).
Lareau, C. A. et al. Nat. Biotechnol. 37, 916–924 (2019).
Yuan, H. & Kelly, D. R. Nat. Methods https://doi.org/10.1038/s41592-022-01562-8 (2022).
Stuart, T., Srivastava, A., Madad, S., Lareau, C. A. & Satija, R. Nat. Methods 18, 1333–1341 (2021).
Bravo González-Blas, C. et al. Nat. Methods 16, 397–400 (2019).
Xiong, L. et al. Nat. Commun. 10, 4576 (2019).
Schep, A. N., Wu, B., Buenrostro, J. D. & Greenleaf, W. J. Nat. Methods 14, 975–978 (2017).
Acknowledgements
I am grateful to Niklas Kempynck, Nikolai Hecker, Gabriele Partel, Ibrahim Ihsan Taskiran, Carmen Bravo González-Blas, Harold O. F. Snyers d'Attenhoven, and Ioannis Sarropoulous for critical comments and advice on the text and to Duygu Koldere Vilain for her help with the figure design.
Author information
Authors and Affiliations
Corresponding author
Ethics declarations
Competing interests
The author declares no competing interests.
Rights and permissions
About this article
Cite this article
Aerts, S. How regulatory sequences learn cell representations. Nat Methods 19, 1041–1043 (2022). https://doi.org/10.1038/s41592-022-01570-8
Published:
Version of record:
Issue date:
DOI: https://doi.org/10.1038/s41592-022-01570-8
