Network diffusion for scalable embedding of massive single-cell ATAC-seq data

被引：8

作者：

Dong, Kangning ^{[1
,2
]}

Zhang, Shihua ^{[1
,2
,3
,4
]}

机构：

[1] Chinese Acad Sci, Acad Math & Syst Sci, RCSDS, NCMIS,CEMS, Beijing 100190, Peoples R China

[2] Univ Chinese Acad Sci, Sch Math Sci, Beijing 100049, Peoples R China

[3] Chinese Acad Sci, Ctr Excellence Anim Evolut & Genet, Kunming 650223, Yunnan, Peoples R China

[4] Univ Chinese Acad Sci, Hangzhou Inst Adv Study, Key Lab Syst Biol, Hangzhou 310024, Peoples R China

来源：

SCIENCE BULLETIN | 2021年 / 66卷 / 22期

基金：

国家重点研发计划; 中国国家自然科学基金;

关键词：

ACCESSIBILITY;

D O I：

10.1016/j.scib.2021.05.014

中图分类号：

O [数理科学和化学]; P [天文学、地球科学]; Q [生物科学]; N [自然科学总论];

学科分类号：

07 ; 0710 ; 09 ;

摘要：

[No abstract available]

引用

页码：2271 / 2276

页数：6

共 15 条

[1] Classifying cells with Scasat, a single-cell ATAC-seq analysis tool [J].

Baker, Syed Murtuza ;

Rogerson, Connor ;

Hayes, Andrew ;

Sharrocks, Andrew D. ;

Rattray, Magnus .

NUCLEIC ACIDS RESEARCH, 2019, 47 (02)

[2] T-bet and Eomes Are Differentially Linked to the Exhausted Phenotype of CD8+T Cells in HIV Infection [J].

Buggert, Marcus ;

Tauriainen, Johanna ;

Yamamoto, Takuya ;

Frederiksen, Juliet ;

Ivarsson, Martin A. ;

Michaelsson, Jakob ;

Lund, Ole ;

Hejdeman, Bo ;

Jansson, Marianne ;

Sonnerborg, Anders ;

Koup, Richard A. ;

Betts, Michael R. ;

Karlsson, Annika C. .

PLOS PATHOGENS, 2014, 10 (07)

[3] JunB promotes Th17 cell identity and restrains alternative CD4+ T-cell programs during inflammation [J].

Carr, Tiffany M. ;

Wheaton, Joshua D. ;

Houtz, Geoffrey M. ;

Ciofani, Maria .

NATURE COMMUNICATIONS, 2017, 8

[4] A Single-Cell Atlas of In Vivo Mammalian Chromatin Accessibility [J].

Cusanovich, Darren A. ;

Hill, Andrew J. ;

Aghamirzaie, Delasa ;

Daza, Riza M. ;

Pliner, Hannah A. ;

Berletch, Joel B. ;

Filippova, Galina N. ;

Huang, Xingfan ;

Christiansen, Lena ;

DeWitt, William S. ;

Lee, Choli ;

Regalado, Samuel G. ;

Read, David F. ;

Steemers, Frank J. ;

Disteche, Christine M. ;

Trapnell, Cole ;

Shendure, Jay .

CELL, 2018, 174 (05) :1309-+

[5] Multiplex single-cell profiling of chromatin accessibility by combinatorial cellular indexing [J].

Cusanovich, Darren A. ;

Daza, Riza ;

Adey, Andrew ;

Pliner, Hannah A. ;

Christiansen, Lena ;

Gunderson, Kevin L. ;

Steemers, Frank J. ;

Trapnell, Cole ;

Shendure, Jay .

SCIENCE, 2015, 348 (6237) :910-914

[6] Variable SATB1 Levels Regulate Hematopoietic Stem Cell Heterogeneity with Distinct Lineage Fate [J].

Doi, Yukiko ;

Yokota, Takafumi ;

Satoh, Yusuke ;

Okuzaki, Daisuke ;

Tokunaga, Masahiro ;

Ishibashi, Tomohiko ;

Sudo, Takao ;

Ueda, Tomoaki ;

Shingai, Yasuhiro ;

Ichii, Michiko ;

Tanimura, Akira ;

Ezoe, Sachiko ;

Shibayama, Hirohiko ;

Kohwi-Shigematsu, Terumi ;

Takeda, Junji ;

Oritani, Kenji ;

Kanakura, Yuzuru .

CELL REPORTS, 2018, 23 (11) :3223-3235

[7] Comprehensive analysis of single cell ATAC-seq data with SnapATAC [J].

Fang, Rongxin ;

Preissl, Sebastian ;

Li, Yang ;

Hou, Xiaomeng ;

Lucero, Jacinta ;

Wang, Xinxin ;

Motamedi, Amir ;

Shiau, Andrew K. ;

Zhou, Xinzhu ;

Xie, Fangming ;

Mukamel, Eran A. ;

Zhang, Kai ;

Zhang, Yanxiao ;

Behrens, M. Margarita ;

Ecker, Joseph R. ;

Ren, Bing .

NATURE COMMUNICATIONS, 2021, 12 (01)

[8] cisTopic: cis-regulatory topic modeling on single-cell ATAC-seq data [J].

Gonzalez-Blas, Carmen Bravo ;

Minnoye, Liesbeth ;

Papasokrati, Dafni ;

Aibar, Sara ;

Hulselmans, Gert ;

Christiaens, Valerie ;

Davie, Kristofer ;

Wouters, Jasper ;

Aerts, Stein .

NATURE METHODS, 2019, 16 (05) :397-+

[9] T-bet and GATA3 orchestrate Th1 and Th2 differentiation through lineage-specific targeting of distal regulatory elements [J].

Kanhere, Aditi ;

Hertweck, Arnulf ;

Bhatia, Urvashi ;

Goekmen, M. Refik ;

Perucha, Esperanza ;

Jackson, Ian ;

Lord, Graham M. ;

Jenner, Richard G. .

NATURE COMMUNICATIONS, 2012, 3

[10] Droplet-based combinatorial indexing for massive-scale single-cell chromatin accessibility [J].

Lareau, Caleb A. ;

Duarte, Fabiana M. ;

Chew, Jennifer G. ;

Kartha, Vinay K. ;

Burkett, Zach D. ;

Kohlway, Andrew S. ;

Pokholok, Dmitry ;

Aryee, Martin J. ;

Steemers, Frank J. ;

Lebofsky, Ronald ;

Buenrostro, Jason D. .

NATURE BIOTECHNOLOGY, 2019, 37 (08) :916-+

← 1 2 →