Scalable analysis of cell-type composition from single-cell transcriptomics using deep recurrent learning

被引：120

作者：

Deng, Yue ^{[1
]}

Bao, Feng ^{[2
]}

Dai, Qionghai ^{[2
]}

Wu, Lani F. ^{[1
]}

Altschuler, Steven J. ^{[1
]}

机构：

[1] Univ Calif San Francisco, Dept Pharmaceut Chem, San Francisco, CA 94143 USA

[2] Tsinghua Univ, Tsinghua Natl Lab Informat Sci & Technol, Dept Automat, Beijing, Peoples R China

来源：

NATURE METHODS | 2019年 / 16卷 / 04期

关键词：

NETWORK;

D O I：

10.1038/s41592-019-0353-7

中图分类号：

Q5 [生物化学];

学科分类号：

071010 ; 081704 ;

摘要：

Recent advances in large-scale single-cell RNA-seq enable fine-grained characterization of phenotypically distinct cellular states in heterogeneous tissues. We present scScope, a scalable deep-learning-based approach that can accurately and rapidly identify cell-type composition from millions of noisy single-cell gene-expression profiles.

引用

页码：311 / +

页数：7

共 27 条

[1] Integrating single-cell transcriptomic data across different conditions, technologies, and species [J].

Butler, Andrew ;

Hoffman, Paul ;

Smibert, Peter ;

Papalexi, Efthymia ;

Satija, Rahul .

NATURE BIOTECHNOLOGY, 2018, 36 (05) :411-+

[2] Efficient Generation of Transcriptomic Profiles by Random Composite Measurements [J].

Cleary, Brian ;

Le Cong ;

Cheung, Anthea ;

Lander, Eric S. ;

Regev, Aviv .

CELL, 2017, 171 (06) :1424-+

[3] Single-cell RNA-seq denoising using a deep count autoencoder [J].

Eraslan, Goekcen ;

Simon, Lukas M. ;

Mircea, Maria ;

Mueller, Nikola S. ;

Theis, Fabian J. .

NATURE COMMUNICATIONS, 2019, 10 (1)

[4] Reconstruction of a functional human gene network, with an application for prioritizing positional candidate genes [J].

Franke, Lude ;

van Bakel, Harm ;

Fokkens, Like ;

de Jong, Edwin D. ;

Egmont-Petersen, Michael ;

Wijmenga, Cisca .

AMERICAN JOURNAL OF HUMAN GENETICS, 2006, 78 (06) :1011-1025

[5] Single-cell genome sequencing: current state of the science [J].

Gawad, Charles ;

Koh, Winston ;

Quake, Stephen R. .

NATURE REVIEWS GENETICS, 2016, 17 (03) :175-188

[6] A single-cell survey of the small intestinal epithelium [J].

Haber, Adam L. ;

Biton, Moshe ;

Rogel, Noga ;

Herbst, Rebecca H. ;

Shekhar, Karthik ;

Smillie, Christopher ;

Burgin, Grace ;

Delorey, Toni M. ;

Howitt, Michael R. ;

Katz, Yarden ;

Tirosh, Itay ;

Beyaz, Semir ;

Dionne, Danielle ;

Zhang, Mei ;

Raychowdhury, Raktima ;

Garrett, Wendy S. ;

Rozenblatt-Rosen, Orit ;

Shi, Hai Ning ;

Yilmaz, Omer ;

Xavier, Ramnik J. ;

Regev, Aviv .

NATURE, 2017, 551 (7680) :333-+

[7] Batch effects in single-cell RNA-sequencing data are corrected by matching mutual nearest neighbors [J].

Haghverdi, Laleh ;

Lun, Aaron T. L. ;

Morgan, Michael D. ;

Marioni, John C. .

NATURE BIOTECHNOLOGY, 2018, 36 (05) :421-+

[8] Mapping the Mouse Cell Atlas by Microwell-Seq [J].

Han, Xiaoping ;

Wang, Renying ;

Zhou, Yincong ;

Fei, Lijiang ;

Sun, Huiyu ;

Lai, Shujing ;

Saadatpour, Assieh ;

Zhou, Zimin ;

Chen, Haide ;

Ye, Fang ;

Huang, Daosheng ;

Xu, Yang ;

Huang, Wentao ;

Jiang, Mengmeng ;

Jiang, Xinyi ;

Mao, Jie ;

Chen, Yao ;

Lu, Chenyu ;

Xie, Jin ;

Fang, Qun ;

Wang, Yibin ;

Yue, Rui ;

Li, Tiefeng ;

Huang, He ;

Orkin, Stuart H. ;

Yuan, Guo-Cheng ;

Chen, Ming ;

Guo, Guoji .

CELL, 2018, 172 (05) :1091-+

[9] COMPARING PARTITIONS [J].

HUBERT, L ;

ARABIE, P .

JOURNAL OF CLASSIFICATION, 1985, 2 (2-3) :193-218

[10]

Jeon CJ, 1998, J NEUROSCI, V18, P8936

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