Integrated analysis of multimodal single-cell data

Cell, Journal Year: 2021, Volume and Issue: 184(13), P. 3573 - 3587.e29

Published: May 31, 2021

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, unsupervised framework to learn the relative utility each data type in cell, enabling integrative analysis modalities. We apply our procedure a CITE-seq dataset 211,000 human peripheral blood mononuclear cells (PBMCs) with panels extending 228 antibodies construct reference atlas circulating immune system. Multimodal substantially improves ability resolve cell states, allowing us identify validate previously unreported lymphoid subpopulations. Moreover, demonstrate how leverage this rapidly map new datasets interpret responses vaccination coronavirus disease 2019 (COVID-19). Our approach broadly applicable strategy analyze look beyond transcriptome toward unified definition identity.

Language: Английский

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CellPhoneDB: inferring cell–cell communication from combined expression of multi-subunit ligand–receptor complexes

Nature Protocols, Journal Year: 2020, Volume and Issue: 15(4), P. 1484 - 1506

Published: Feb. 26, 2020

Language: Английский

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RNA sequencing: the teenage years

Nature Reviews Genetics, Journal Year: 2019, Volume and Issue: 20(11), P. 631 - 656

Published: July 24, 2019

Language: Английский

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NicheNet: modeling intercellular communication by linking ligands to target genes

Nature Methods, Journal Year: 2019, Volume and Issue: 17(2), P. 159 - 162

Published: Dec. 9, 2019

Language: Английский

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Fibrosis: from mechanisms to medicines

Nature, Journal Year: 2020, Volume and Issue: 587(7835), P. 555 - 566

Published: Nov. 25, 2020

Language: Английский

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Exploring tissue architecture using spatial transcriptomics

Nature, Journal Year: 2021, Volume and Issue: 596(7871), P. 211 - 220

Published: Aug. 11, 2021

Language: Английский

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Eleven grand challenges in single-cell data science

Genome biology, Journal Year: 2020, Volume and Issue: 21(1)

Published: Feb. 7, 2020

Abstract The recent boom in microfluidics and combinatorial indexing strategies, combined with low sequencing costs, has empowered single-cell technology. Thousands—or even millions—of cells analyzed a single experiment amount to data revolution biology pose unique science problems. Here, we outline eleven challenges that will be central bringing this emerging field of forward. For each challenge, highlight motivating research questions, review prior work, formulate open This compendium is for established researchers, newcomers, students alike, highlighting interesting rewarding problems the coming years.

Language: Английский

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High-definition spatial transcriptomics for in situ tissue profiling

Nature Methods, Journal Year: 2019, Volume and Issue: 16(10), P. 987 - 990

Published: Sept. 9, 2019

Language: Английский

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Highly sensitive spatial transcriptomics at near-cellular resolution with Slide-seqV2

Nature Biotechnology, Journal Year: 2020, Volume and Issue: 39(3), P. 313 - 319

Published: Dec. 7, 2020

Language: Английский

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Deciphering cell–cell interactions and communication from gene expression

Nature Reviews Genetics, Journal Year: 2020, Volume and Issue: 22(2), P. 71 - 88

Published: Nov. 9, 2020

Language: Английский

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