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Integrative analysis of single-cell genomics data by coupled nonnegative matrix factorizations
Duren, Zhana1,2; Chen, Xi1,2; Zamanighomi, Mahdi1,2,3; Zeng, Wanwen1,2,4,5; Satpathy, Ansuman T.3; Chang, Howard Y.3; Wang, Yong6,7; Wong, Wing Hung1,2,3
2018-07-24
Source PublicationPROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
ISSN0027-8424
Volume115Issue:30Pages:7723-7728
AbstractWhen 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.
Keywordcoupled clustering NMF single-cell genomic data
DOI10.1073/pnas.1805681115
Language英语
Funding ProjectNational 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 Research AreaScience & Technology - Other Topics
WOS SubjectMultidisciplinary Sciences
WOS IDWOS:000439574700050
PublisherNATL ACAD SCIENCES
Citation statistics
Cited Times:6[WOS]   [WOS Record]     [Related Records in WOS]
Document Type期刊论文
Identifierhttp://ir.amss.ac.cn/handle/2S8OKBNM/33386
Collection应用数学研究所
Affiliation1.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
Recommended Citation
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.
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