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ArticlesPeer ReviewedFull Text
Sci-fate characterizes the dynamics of gene expression in single cells
Author / Creator:Cao, Junyue ; Zhou, Wei ; Steemers, Frank ; Trapnell, Cole ; Shendure, Jay
Publisher:New York: Nature Publishing Group US
Journal title:Nature biotechnology, 2020-08, Vol.38 (8), p.980-988
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ArticlesPeer ReviewedFull Text
Joint profiling of chromatin accessibility and gene expression in thousands of single cells
Author / Creator:Cao, Junyue ; Cusanovich, Darren A. ; Ramani, Vijay ; Aghamirzaie, Delasa ; Pliner, Hannah A. ; Hill, Andrew J. ; Daza, Riza M. ; McFaline-Figueroa, Jose L. ; Packer, Jonathan S. ; Christiansen, Lena ; Steemers, Frank J. ; Adey, Andrew C. ; Trapnell, Cole ; Shendure, Jay
Publisher:United States: The American Association for the Advancement of Science
Journal title:Science (American Association for the Advancement of Science), 2018-09, Vol.361 (6409), p.1380-1385
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ArticlesPeer ReviewedFull Text
The single-cell transcriptional landscape of mammalian organogenesis
Author / Creator:Cao, Junyue ; Spielmann, Malte ; Qiu, Xiaojie ; Huang, Xingfan ; Ibrahim, Daniel M. ; Hill, Andrew J. ; Zhang, Fan ; Mundlos, Stefan ; Christiansen, Lena ; Steemers, Frank J. ; Trapnell, Cole ; Shendure, Jay
Publisher:London: Nature Publishing Group UK
Journal title:Nature (London), 2019-02, Vol.566 (7745), p.496-502
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ArticlesPeer ReviewedFull Text
Comprehensive single-cell transcriptional profiling of a multicellular organism
Author / Creator:Cao, Junyue ; Packer, Jonathan S. ; Ramani, Vijay ; Cusanovich, Darren A. ; Huynh, Chau ; Daza, Riza ; Qiu, Xiaojie ; Lee, Choli ; Furlan, Scott N. ; Steemers, Frank J. ; Adey, Andrew ; Waterston, Robert H. ; Trapnell, Cole ; Shendure, Jay
Publisher:United States: American Association for the Advancement of Science
Journal title:Science (American Association for the Advancement of Science), 2017-08, Vol.357 (6352), p.661-667
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Newsletter articlesFull Text
INTERNATIONAL PATENT: ILLUMINA, INC. , UNIVERSITY OF WASHINGTON , SRIVATSAN, SANJAY , MCFALINE-FIGUEROA, JOSE , RAMANI, VIJAY , CAO, JUNYUE , BOOTH, GREGORY , SHENDURE, JAY , TRAPNELL, COLE , STEEMERS...
Publisher:Washington, D.C: HT Digital Streams Limited
Journal title:US Fed News Service, Including US State News, 2020
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ArticlesPeer ReviewedFull Text
Systematic reconstruction of cellular trajectories across mouse embryogenesis
Author / Creator:Qiu, Chengxiang ; Cao, Junyue ; Martin, Beth K. ; Li, Tony ; Welsh, Ian C. ; Srivatsan, Sanjay ; Huang, Xingfan ; Calderon, Diego ; Noble, William Stafford ; Disteche, Christine M. ; Murray, Stephen A. ; Spielmann, Malte ; Moens, Cecilia B. ; Trapnell, Cole ; Shendure, Jay
Publisher:New York: Nature Publishing Group US
Journal title:Nature genetics, 2022-03, Vol.54 (3), p.328-341
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ArticlesPeer ReviewedFull Text
Expanding the binding specificity for RNA recognition by a PUF domain
Author / Creator:Zhou, Wei ; Melamed, Daniel ; Banyai, Gabor ; Meyer, Cindy ; Tuschl, Thomas ; Wickens, Marvin ; Cao, Junyue ; Fields, Stanley
Publisher:London: Nature Publishing Group UK
Journal title:Nature communications, 2021-08, Vol.12 (1), p.5107-15, Article 5107
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ArticlesPeer ReviewedFull Text
HSF1 critically attunes proteotoxic stress sensing by mTORC1 to combat stress and promote growth
Author / Creator:Su, Kuo-Hui ; Cao, Junyue ; Tang, Zijian ; Dai, Siyuan ; He, Yishu ; Sampson, Stephen Byers ; Benjamin, Ivor J. ; Dai, Chengkai
Publisher:London: Nature Publishing Group UK
Journal title:Nature cell biology, 2016-05, Vol.18 (5), p.527-539
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ArticlesPeer ReviewedFull Text
Structural and kinetic analysis of the COP9-Signalosome activation and the cullin-RING ubiquitin ligase deneddylation cycle
Author / Creator:Mosadeghi, Ruzbeh ; Reichermeier, Kurt M ; Winkler, Martin ; Schreiber, Anne ; Reitsma, Justin M ; Zhang, Yaru ; Stengel, Florian ; Cao, Junyue ; Kim, Minsoo ; Sweredoski, Michael J ; Hess, Sonja ; Leitner, Alexander ; Aebersold, Ruedi ; Peter, Matthias ; Deshaies, Raymond J ; Enchev, Radoslav I
Publisher:England: eLife Science Publications, Ltd
Journal title:eLife, 2016-03, Vol.5
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ArticlesPeer ReviewedFull Text
Publisher Correction: Expanding the binding specificity for RNA recognition by a PUF domain
Author / Creator:Zhou, Wei ; Melamed, Daniel ; Banyai, Gabor ; Meyer, Cindy ; Tuschl, Thomas ; Wickens, Marvin ; Cao, Junyue ; Fields, Stanley
Publisher:London: Nature Publishing Group UK
Journal title:Nature communications, 2022-06, Vol.13 (1), p.3693-3693, Article 3693
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ArticlesPeer ReviewedFull Text
Transformer-Based Single-Cell Language Model: A Survey
Author / Creator:Lan, Wei ; He, Guohang ; Liu, Mingyang ; Chen, Qingfeng ; Cao, Junyue ; Peng, Wei
Publisher:Beijing: Tsinghua University Press
Journal title:Big Data Mining and Analytics, 2024-12, Vol.7 (4), p.1169-1186
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ArticlesPeer ReviewedFull Text
Aging- and Alzheimer’s disease-related rare cell type dynamics in the mammalian brain unveiled
Author / Creator:Cao, Junyue
Publisher:New York: Nature Publishing Group US
Journal title:Nature genetics, 2023-12, Vol.55 (12), p.2027-2028
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ArticlesPeer ReviewedFull Text
949 Flexible control of T cell memory and self-renewal by a reversible epigenetic switch
Author / Creator:Abadie, Kathleen ; Clark, Elisa C ; Valanparambil, Rajesh ; Ukogu, Obinna ; Yang, Wei ; Daza, Riza ; Ng, Kenneth ; Fathima, Jumana ; Wang, Allan ; Bhandoola, Avinash ; Nourmohammad, Hao ; Ahmed, Rafi ; Shendure, Jay ; Cao, Junyue ; Kueh, Hao Yuan
Publisher:London: BMJ Publishing Group Ltd
Journal title:Journal for immunotherapy of cancer, 2023-11, Vol.11 (Suppl 1), p.A1052-A1052
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ArticlesPeer ReviewedFull Text
Detecting protein and post-translational modifications in single cells with iDentification and qUantification sEparaTion (DUET)
Author / Creator:Zhang, Yandong ; Sohn, Changho ; Lee, Seoyeon ; Ahn, Heejeong ; Seo, Jinyoung ; Cao, Junyue ; Cai, Long
Publisher:London: Nature Publishing Group UK
Journal title:Communications biology, 2020-08, Vol.3 (1), p.420-420, Article 420
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ArticlesPeer ReviewedFull Text
Author Correction: Detecting protein and post-translational modifications in single cells with iDentification and qUantification sEparaTion (DUET)
Author / Creator:Zhang, Yandong ; Sohn, Changho ; Lee, Seoyeon ; Ahn, Heejeong ; Seo, Jinyoung ; Cao, Junyue ; Cai, Long
Publisher:London: Nature Publishing Group UK
Journal title:Communications biology, 2020-08, Vol.3 (1), p.463-463, Article 463
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ArticlesPeer ReviewedFull Text
Optimized single-nucleus transcriptional profiling by combinatorial indexing
Author / Creator:Martin, Beth K. ; Qiu, Chengxiang ; Nichols, Eva ; Phung, Melissa ; Green-Gladden, Rula ; Srivatsan, Sanjay ; Blecher-Gonen, Ronnie ; Beliveau, Brian J. ; Trapnell, Cole ; Cao, Junyue ; Shendure, Jay
Publisher:London: Nature Publishing Group UK
Journal title:Nature protocols, 2023-01, Vol.18 (1), p.188-207
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ArticlesPeer ReviewedFull Text
NGCN: Drug‐target interaction prediction by integrating information and feature learning from heterogeneous network
Author / Creator:Cao, Junyue ; Chen, Qingfeng ; Qiu, Junlai ; Wang, Yiming ; Lan, Wei ; Du, Xiaojing ; Tan, Kai
Publisher:England: John Wiley & Sons, Inc
Journal title:Journal of cellular and molecular medicine, 2024-04, Vol.28 (7), p.e18224-n/a
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ArticlesPeer ReviewedFull Text
A global view of aging and Alzheimer’s pathogenesis-associated cell population dynamics and molecular signatures in human and mouse brains
Author / Creator:Sziraki, Andras ; Lu, Ziyu ; Lee, Jasper ; Banyai, Gabor ; Anderson, Sonya ; Abdulraouf, Abdulraouf ; Metzner, Eli ; Liao, Andrew ; Banfelder, Jason ; Epstein, Alexander ; Schaefer, Chloe ; Xu, Zihan ; Zhang, Zehao ; Gan, Li ; Nelson, Peter T. ; Zhou, Wei ; Cao, Junyue
Publisher:New York: Nature Publishing Group US
Journal title:Nature genetics, 2023-12, Vol.55 (12), p.2104-2116
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ArticlesPeer ReviewedFull Text
A Descent Conjugate Gradient Algorithm for Optimization Problems and Its Applications in Image Restoration and Compression Sensing
Author / Creator:Cao, Junyue ; Wu, Jinzhao
Publisher:Cairo, Egypt: Hindawi Publishing Corporation
Journal title:Mathematical problems in engineering, 2020, Vol.2020 (2020), p.1-9
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ArticlesPeer ReviewedFull Text
A single-cell time-lapse of mouse prenatal development from gastrula to birth
Author / Creator:Qiu, Chengxiang ; Martin, Beth K. ; Welsh, Ian C. ; Daza, Riza M. ; Le, Truc-Mai ; Huang, Xingfan ; Nichols, Eva K. ; Taylor, Megan L. ; Fulton, Olivia ; O’Day, Diana R. ; Gomes, Anne Roshella ; Ilcisin, Saskia ; Srivatsan, Sanjay ; Deng, Xinxian ; Disteche, Christine M. ; Noble, William Stafford ; Hamazaki, Nobuhiko ; Moens, Cecilia B. ; Kimelman, David ; Cao, Junyue ; Schier, Alexander F. ; Spielmann, Malte ; Murray, Stephen A. ; Trapnell, Cole ; Shendure, Jay
Publisher:London: Nature Publishing Group UK
Journal title:Nature (London), 2024-02, Vol.626 (8001), p.1084-1093
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Sci-fate characterizes the dynamics of gene expression in single cells

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Joint profiling of chromatin accessibility and gene expression in thousands of single cells

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The single-cell transcriptional landscape of mammalian organogenesis

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Comprehensive single-cell transcriptional profiling of a multicellular organism

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INTERNATIONAL PATENT: ILLUMINA, INC. , UNIVERSITY OF WASHINGTON , SRIVATSAN, SANJAY , MCFALINE-FIGUEROA, JOSE , RAMANI, VIJAY , CAO, JUNYUE , BOOTH, GREGORY , SHENDURE, JAY , TRAPNELL, COLE , STEEMERS...

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Systematic reconstruction of cellular trajectories across mouse embryogenesis

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Expanding the binding specificity for RNA recognition by a PUF domain

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HSF1 critically attunes proteotoxic stress sensing by mTORC1 to combat stress and promote growth

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Structural and kinetic analysis of the COP9-Signalosome activation and the cullin-RING ubiquitin ligase deneddylation cycle

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Publisher Correction: Expanding the binding specificity for RNA recognition by a PUF domain

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Transformer-Based Single-Cell Language Model: A Survey

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Aging- and Alzheimer’s disease-related rare cell type dynamics in the mammalian brain unveiled

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949 Flexible control of T cell memory and self-renewal by a reversible epigenetic switch

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Detecting protein and post-translational modifications in single cells with iDentification and qUantification sEparaTion (DUET)

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Author Correction: Detecting protein and post-translational modifications in single cells with iDentification and qUantification sEparaTion (DUET)

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Optimized single-nucleus transcriptional profiling by combinatorial indexing

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NGCN: Drug‐target interaction prediction by integrating information and feature learning from heterogeneous network

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A global view of aging and Alzheimer’s pathogenesis-associated cell population dynamics and molecular signatures in human and mouse brains

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A Descent Conjugate Gradient Algorithm for Optimization Problems and Its Applications in Image Restoration and Compression Sensing

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A single-cell time-lapse of mouse prenatal development from gastrula to birth

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