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Yuhan Hao, Stephanie Hao, Erica Andersen‐Nissen, William M. Mauck, Shiwei Zheng, Andrew Butler, Madeline J. Lee, Aaron J. Wilk, Charlotte A. Darby, Michael A. Zager and 15 more
The simultaneous measurement of multiple modalities represents an exciting frontier for single-cell genomics and necessitates computational methods that can define cellular states based on multimodal data. Here, we introduce "weighted-nearest neighbor" analysis, an unsupervised framework to learn the relative utility of each data type in each cell, enabling an integrative analysis of multiple modalities. We apply our procedure to a CITE-seq dataset of 211,000 human peripheral blood mononuclear cells (PBMCs) with panels extending to 228 antibodies to construct a multimodal reference atlas of the circulating immune system. Multimodal analysis substantially improves our ability to resolve cell states, allowing us to identify and validate previously unreported lymphoid subpopulations. Moreover, we demonstrate how to leverage this reference to rapidly map new datasets and to interpret immune responses to vaccination and coronavirus disease 2019 (COVID-19). Our approach represents a broadly applicable strategy to analyze single-cell multimodal datasets and to look beyond the transcriptome toward a unified and multimodal definition of cellular identity.
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Hao, Y., Hao, S., Andersen‐Nissen, E., Mauck, W. M., Zheng, S., Butler, A., Lee, M. J., Wilk, A. J., Darby, C. A., Zager, M. A., Hoffman, P., Stoeckius, M., Papalexi, E., Mimitou, E. P., Jain, J., Srivastava, A., Stuart, T., Ballweber-Fleming, L., Yeung, B. Z., … Satija, R. (2021). Integrated analysis of multimodal single-cell data. Cell, 184(13), 3573–3587.e29. https://doi.org/10.1016/j.cell.2021.04.048
Hao, Yuhan, et al. "Integrated analysis of multimodal single-cell data." Cell, vol. 184, no. 13, 2021, pp. 3573–3587.e29, https://doi.org/10.1016/j.cell.2021.04.048.
Hao, Yuhan, Stephanie Hao, Erica Andersen‐Nissen, William M. Mauck, Shiwei Zheng, Andrew Butler, Madeline J. Lee, et al. "Integrated analysis of multimodal single-cell data." Cell 184, no. 13 (2021): 3573–3587.e29. https://doi.org/10.1016/j.cell.2021.04.048.
Hao Y., Hao S., Andersen‐Nissen E. [и др.] Integrated analysis of multimodal single-cell data // Cell. — 2021. — Vol. 184, № 13. — P. 3573–3587.e29. — URL: https://doi.org/10.1016/j.cell.2021.04.048
@article{hao2021integrated,
title = {{Integrated analysis of multimodal single-cell data}},
author = {Yuhan Hao and Stephanie Hao and Erica Andersen‐Nissen and William M. Mauck and Shiwei Zheng and Andrew Butler and Madeline J. Lee and Aaron J. Wilk and Charlotte A. Darby and Michael A. Zager and Paul Hoffman and Marlon Stoeckius and Efthymia Papalexi and Eleni P. Mimitou and Jaison Jain and Avi Srivastava and Tim Stuart and Lamar Ballweber-Fleming and Bertrand Z. Yeung and Angela J. Rogers and M. Juliana McElrath and Catherine A. Blish and Raphaël Gottardo and Peter Smibert and Rahul Satija},
journal = {Cell},
year = {2021},
volume = {184},
number = {13},
pages = {3573--3587.e29},
doi = {10.1016/j.cell.2021.04.048},
url = {https://doi.org/10.1016/j.cell.2021.04.048}
}TY - JOUR AU - Hao, Yuhan AU - Hao, Stephanie AU - Andersen‐Nissen, Erica AU - Mauck, William M. AU - Zheng, Shiwei AU - Butler, Andrew AU - Lee, Madeline J. AU - Wilk, Aaron J. AU - Darby, Charlotte A. AU - Zager, Michael A. AU - Hoffman, Paul AU - Stoeckius, Marlon AU - Papalexi, Efthymia AU - Mimitou, Eleni P. AU - Jain, Jaison AU - Srivastava, Avi AU - Stuart, Tim AU - Ballweber-Fleming, Lamar AU - Yeung, Bertrand Z. AU - Rogers, Angela J. AU - McElrath, M. Juliana AU - Blish, Catherine A. AU - Gottardo, Raphaël AU - Smibert, Peter AU - Satija, Rahul TI - Integrated analysis of multimodal single-cell data JO - Cell VL - 184 IS - 13 SP - 3573 EP - 3587.e29 PY - 2021 DA - 2021/05/31 DO - 10.1016/j.cell.2021.04.048 UR - https://doi.org/10.1016/j.cell.2021.04.048 ER -
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