Integrative analysis of single-cell genomics data by coupled nonnegative matrix factorizations

doi:10.1073/pnas.1805681115

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	Integrative analysis of single-cell genomics data by coupled nonnegative matrix factorizations
	Duren, Zhana 1,2; Chen, Xi 1,2; Zamanighomi, Mahdi 1,2,3; Zeng, Wanwen 1,2,4,5; Satpathy, Ansuman T.3; Chang, Howard Y.3; Wang, Yong6,7 ; Wong, Wing Hung 1,2,3
	2018-07-24
发表期刊	PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
ISSN	0027-8424
卷号	115 期号:30 页码:7723-7728
摘要	When different types of functional genomics data are generated on single cells from different samples of cells from the same heterogeneous population, the clustering of cells in the different samples should be coupled. We formulate this "coupled clustering" problem as an optimization problem and propose the method of coupled nonnegative matrix factorizations (coupled NMF) for its solution. The method is illustrated by the integrative analysis of single-cell RNA-sequencing (RNA-seq) and single-cell ATAC-sequencing (ATAC-seq) data.
关键词	coupled clustering NMF single-cell genomic data
DOI	10.1073/pnas.1805681115
语种	英语
资助项目	National Institutes of Health[R01HG007834] ; National Institutes of Health[R01GM109836] ; National Institutes of Health[P50HG007735] ; Strategic Priority Research Program of the Chinese Academy of Sciences[XDB13000000]
WOS研究方向	Science & Technology - Other Topics
WOS类目	Multidisciplinary Sciences
WOS记录号	WOS:000439574700050
出版者	NATL ACAD SCIENCES
引用统计
文献类型	期刊论文
条目标识符	http://ir.amss.ac.cn/handle/2S8OKBNM/33386
专题	应用数学研究所
通讯作者	Wong, Wing Hung
作者单位	1.Stanford Univ, Dept Stat, Stanford, CA 94305 USA 2.Stanford Univ, Dept Biomed Data Sci, Stanford, CA 94305 USA 3.Stanford Univ, Ctr Personal Dynam Regulomes, Stanford, CA 94305 USA 4.Tsinghua Univ, Key Lab Bioinformat, Bioinformat Div, Minist Educ, Beijing 100080, Peoples R China 5.Tsinghua Univ, Ctr Synthet & Syst Biol, Dept Automat, Beijing 100080, Peoples R China 6.Chinese Acad Sci, Acad Math & Syst Sci, Beijing 100080, Peoples R China 7.Chinese Acad Sci, Ctr Excellence Anim Evolut & Genet, Kunming 650223, Yunnan, Peoples R China
推荐引用方式 GB/T 7714	Duren, Zhana,Chen, Xi,Zamanighomi, Mahdi,et al. Integrative analysis of single-cell genomics data by coupled nonnegative matrix factorizations[J]. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA,2018,115(30):7723-7728.
APA	Duren, Zhana.,Chen, Xi.,Zamanighomi, Mahdi.,Zeng, Wanwen.,Satpathy, Ansuman T..,...&Wong, Wing Hung.(2018).Integrative analysis of single-cell genomics data by coupled nonnegative matrix factorizations.PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA,115(30),7723-7728.
MLA	Duren, Zhana,et al."Integrative analysis of single-cell genomics data by coupled nonnegative matrix factorizations".PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA 115.30(2018):7723-7728.