Integrated analysis of multimodal single-cell data

Cell, Год журнала: 2021, Номер 184(13), С. 3573 - 3587.e29

Опубликована: Май 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.

Язык: Английский

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

Nature Protocols, Год журнала: 2020, Номер 15(4), С. 1484 - 1506

Опубликована: Фев. 26, 2020

Язык: Английский

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RNA sequencing: the teenage years

Nature Reviews Genetics, Год журнала: 2019, Номер 20(11), С. 631 - 656

Опубликована: Июль 24, 2019

Язык: Английский

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NicheNet: modeling intercellular communication by linking ligands to target genes

Nature Methods, Год журнала: 2019, Номер 17(2), С. 159 - 162

Опубликована: Дек. 9, 2019

Язык: Английский

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Fibrosis: from mechanisms to medicines

Nature, Год журнала: 2020, Номер 587(7835), С. 555 - 566

Опубликована: Ноя. 25, 2020

Язык: Английский

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Exploring tissue architecture using spatial transcriptomics

Nature, Год журнала: 2021, Номер 596(7871), С. 211 - 220

Опубликована: Авг. 11, 2021

Язык: Английский

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Eleven grand challenges in single-cell data science

Genome biology, Год журнала: 2020, Номер 21(1)

Опубликована: Фев. 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.

Язык: Английский

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High-definition spatial transcriptomics for in situ tissue profiling

Nature Methods, Год журнала: 2019, Номер 16(10), С. 987 - 990

Опубликована: Сен. 9, 2019

Язык: Английский

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

Nature Biotechnology, Год журнала: 2020, Номер 39(3), С. 313 - 319

Опубликована: Дек. 7, 2020

Язык: Английский

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Deciphering cell–cell interactions and communication from gene expression

Nature Reviews Genetics, Год журнала: 2020, Номер 22(2), С. 71 - 88

Опубликована: Ноя. 9, 2020

Язык: Английский

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