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ArticlesPeer ReviewedFull Text
Robust integration of multiple single-cell RNA sequencing datasets using a single reference space
Author / Creator:Liu, Yang ; Wang, Tao ; Zhou, Bin ; Zheng, Deyou
Publisher:New York: Nature Publishing Group US
Journal title:Nature biotechnology, 2021-07, Vol.39 (7), p.877-884
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NFI transcription factors provide chromatin access to maintain stem cell identity while preventing unintended lineage fate choices
Author / Creator:Adam, Rene C. ; Yang, Hanseul ; Ge, Yejing ; Infarinato, Nicole R. ; Gur-Cohen, Shiri ; Miao, Yuxuan ; Wang, Ping ; Zhao, Yilin ; Lu, Catherine P. ; Kim, Jeong E. ; Ko, Joo Y. ; Paik, Seung S. ; Gronostajski, Richard M. ; Kim, Jaehwan ; Krueger, James G. ; Zheng, Deyou ; Fuchs, Elaine
Publisher:London: Nature Publishing Group UK
Journal title:Nature cell biology, 2020-06, Vol.22 (6), p.640-650
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ArticlesPeer ReviewedFull Text
Six3 and Six6 jointly control diverse target genes in multiple cell populations over developmental trajectories of mouse embryonic retinal progenitor cells
Author / Creator:Ferrena, Alexander ; Zhang, Xusheng ; Shrestha, Rupendra ; Zheng, Deyou ; Liu, Wei
Publisher:United States: Public Library of Science
Journal title:PloS one, 2024-10, Vol.19 (10), p.e0308839
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The immune checkpoint B7x expands tumor-infiltrating Tregs and promotes resistance to anti-CTLA-4 therapy
Author / Creator:John, Peter ; Pulanco, Marc C. ; Galbo, Phillip M. ; Wei, Yao ; Ohaegbulam, Kim C. ; Zheng, Deyou ; Zang, Xingxing
Publisher:London: Nature Publishing Group UK
Journal title:Nature communications, 2022-05, Vol.13 (1), p.2506-15, Article 2506
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Pioneer factors govern super-enhancer dynamics in stem cell plasticity and lineage choice
Author / Creator:Adam, Rene C. ; Yang, Hanseul ; Rockowitz, Shira ; Larsen, Samantha B. ; Nikolova, Maria ; Oristian, Daniel S. ; Polak, Lisa ; Kadaja, Meelis ; Asare, Amma ; Zheng, Deyou ; Fuchs, Elaine
Publisher:London: Nature Publishing Group UK
Journal title:Nature (London), 2015-05, Vol.521 (7552), p.366-370
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Regulation of the glucocorticoid receptor via a BET-dependent enhancer drives antiandrogen resistance in prostate cancer
Author / Creator:Shah, Neel ; Wang, Ping ; Wongvipat, John ; Karthaus, Wouter R ; Abida, Wassim ; Armenia, Joshua ; Rockowitz, Shira ; Drier, Yotam ; Bernstein, Bradley E ; Long, Henry W ; Freedman, Matthew L ; Arora, Vivek K ; Zheng, Deyou ; Sawyers, Charles L
Publisher:England: eLife Science Publications, Ltd
Journal title:eLife, 2017-09, Vol.6
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ArticlesPeer ReviewedFull Text
Perinatal angiogenesis from pre-existing coronary vessels via DLL4–NOTCH1 signalling
Author / Creator:Lu, Pengfei ; Wang, Yidong ; Liu, Yang ; Wang, Yifeng ; Wu, Bingruo ; Zheng, Deyou ; Harvey, Richard P. ; Zhou, Bin
Publisher:London: Nature Publishing Group UK
Journal title:Nature cell biology, 2021-09, Vol.23 (9), p.967-977
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Single cell multi-omic analysis identifies a Tbx1-dependent multilineage primed population in murine cardiopharyngeal mesoderm
Author / Creator:Nomaru, Hiroko ; Liu, Yang ; De Bono, Christopher ; Righelli, Dario ; Cirino, Andrea ; Wang, Wei ; Song, Hansoo ; Racedo, Silvia E. ; Dantas, Anelisa G. ; Zhang, Lu ; Cai, Chen-Leng ; Angelini, Claudia ; Christiaen, Lionel ; Kelly, Robert G. ; Baldini, Antonio ; Zheng, Deyou ; Morrow, Bernice E.
Publisher:London: Nature Publishing Group UK
Journal title:Nature communications, 2021-11, Vol.12 (1), p.6645-19, Article 6645
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In vivo transcriptional governance of hair follicle stem cells by canonical Wnt regulators
Author / Creator:Lien, Wen-Hui ; Polak, Lisa ; Lin, Mingyan ; Lay, Kenneth ; Zheng, Deyou ; Fuchs, Elaine
Publisher:London: Nature Publishing Group UK
Journal title:Nature cell biology, 2014-02, Vol.16 (2), p.179-190
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CRISPR/Cas9-mediated heterozygous knockout of the autism gene CHD8 and characterization of its transcriptional networks in cerebral organoids derived from iPS cells
Author / Creator:Wang, Ping ; Mokhtari, Ryan ; Pedrosa, Erika ; Kirschenbaum, Michael ; Bayrak, Can ; Zheng, Deyou ; Lachman, Herbert M.
Publisher:England: BioMed Central Ltd
Journal title:Molecular autism, 2017-03, Vol.8 (1), p.11-11, Article 11
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SMARTcleaner: identify and clean off-target signals in SMART ChIP-seq analysis
Author / Creator:Zhao, Dejian ; Zheng, Deyou
Publisher:England: BioMed Central Ltd
Journal title:BMC bioinformatics, 2018-12, Vol.19 (1), p.544-544, Article 544
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Single-cell transcriptomics uncovers a non-autonomous Tbx1-dependent genetic program controlling cardiac neural crest cell development
Author / Creator:De Bono, Christopher ; Liu, Yang ; Ferrena, Alexander ; Valentine, Aneesa ; Zheng, Deyou ; Morrow, Bernice E.
Publisher:London: Nature Publishing Group UK
Journal title:Nature communications, 2023-03, Vol.14 (1), p.1551-1551, Article 1551
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PRC2 is recurrently inactivated through EED or SUZ12 loss in malignant peripheral nerve sheath tumors
Author / Creator:Lee, William ; Teckie, Sewit ; Wiesner, Thomas ; Ran, Leili ; Prieto Granada, Carlos N ; Lin, Mingyan ; Zhu, Sinan ; Cao, Zhen ; Liang, Yupu ; Sboner, Andrea ; Tap, William D ; Fletcher, Jonathan A ; Huberman, Kety H ; Qin, Li-Xuan ; Viale, Agnes ; Singer, Samuel ; Zheng, Deyou ; Berger, Michael F ; Chen, Yu ; Antonescu, Cristina R ; Chi, Ping
Publisher:New York: Nature Publishing Group US
Journal title:Nature genetics, 2014-11, Vol.46 (11), p.1227-1232
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Metacell-based differential expression analysis identifies cell type specific temporal gene response programs in COVID-19 patient PBMCs
Author / Creator:O’Leary, Kevin ; Zheng, Deyou
Publisher:London: Nature Publishing Group UK
Journal title:NPJ systems biology and applications, 2024-04, Vol.10 (1), p.36-36, Article 36
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ETS factors reprogram the androgen receptor cistrome and prime prostate tumorigenesis in response to PTEN loss
Author / Creator:Chen, Yu ; Chi, Ping ; Rockowitz, Shira ; Iaquinta, Phillip J ; Shamu, Tambudzai ; Shukla, Shipra ; Gao, Dong ; Sirota, Inna ; Carver, Brett S ; Wongvipat, John ; Scher, Howard I ; Zheng, Deyou ; Sawyers, Charles L
Publisher:New York: Nature Publishing Group US
Journal title:Nature medicine, 2013-08, Vol.19 (8), p.1023-1029
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ArticlesPeer ReviewedFull Text
ZMYND11-MBTD1 induces leukemogenesis through hijacking NuA4/TIP60 acetyltransferase complex and a PWWP-mediated chromatin association mechanism
Author / Creator:Li, Jie ; Galbo, Phillip M. ; Gong, Weida ; Storey, Aaron J. ; Tsai, Yi-Hsuan ; Yu, Xufen ; Ahn, Jeong Hyun ; Guo, Yiran ; Mackintosh, Samuel G. ; Edmondson, Ricky D. ; Byrum, Stephanie D. ; Farrar, Jason E. ; He, Shenghui ; Cai, Ling ; Jin, Jian ; Tackett, Alan J. ; Zheng, Deyou ; Wang, Gang Greg
Publisher:London: Nature Publishing Group UK
Journal title:Nature communications, 2021-02, Vol.12 (1), p.1045-18, Article 1045
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Profiling of chromatin accessibility and identification of general cis-regulatory mechanisms that control two ocular lens differentiation pathways
Author / Creator:Zhao, Yilin ; Zheng, Deyou ; Cvekl, Ales
Publisher:England: BioMed Central Ltd
Journal title:Epigenetics & chromatin, 2019-05, Vol.12 (1), p.27-27, Article 27
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Fine-tuning spatial-temporal dynamics and surface receptor expression support plasma cell-intrinsic longevity
Author / Creator:Jing, Zhixin ; Galbo, Phillip ; Ovando, Luis ; Demouth, Megan ; Welte, Skylar ; Park, Rosa ; Chandran, Kartik ; Wu, Yinghao ; MacCarthy, Thomas ; Zheng, Deyou ; Fooksman, David
Publisher:England: eLife Science Publications, Ltd
Journal title:eLife, 2024-06, Vol.12
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Nfatc1 orchestrates aging in hair follicle stem cells
Author / Creator:Keyes, Brice E. ; Segal, Jeremy P. ; Heller, Evan ; Lien, Wen-Hui ; Chang, Chiung-Ying ; Guo, Xingyi ; Oristian, Dan S. ; Zheng, Deyou ; Fuchs, Elaine
Publisher:United States: National Academy of Sciences
Journal title:Proceedings of the National Academy of Sciences - PNAS, 2013-12, Vol.110 (51), p.E4950-E4959
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Protective effects of macrophage-specific integrin α5 in myocardial infarction are associated with accentuated angiogenesis
Author / Creator:Li, Ruoshui ; Chen, Bijun ; Kubota, Akihiko ; Hanna, Anis ; Humeres, Claudio ; Hernandez, Silvia C. ; Liu, Yang ; Ma, Richard ; Tuleta, Izabela ; Huang, Shuaibo ; Venugopal, Harikrishnan ; Zhu, Fenglan ; Su, Kai ; Li, Jun ; Zhang, Jinghang ; Zheng, Deyou ; Frangogiannis, Nikolaos G.
Publisher:London: Nature Publishing Group UK
Journal title:Nature communications, 2023-11, Vol.14 (1), p.7555-7555, Article 7555
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Showing 1 to 20 of 140 results

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Robust integration of multiple single-cell RNA sequencing datasets using a single reference space

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NFI transcription factors provide chromatin access to maintain stem cell identity while preventing unintended lineage fate choices

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Six3 and Six6 jointly control diverse target genes in multiple cell populations over developmental trajectories of mouse embryonic retinal progenitor cells

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The immune checkpoint B7x expands tumor-infiltrating Tregs and promotes resistance to anti-CTLA-4 therapy

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Pioneer factors govern super-enhancer dynamics in stem cell plasticity and lineage choice

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Regulation of the glucocorticoid receptor via a BET-dependent enhancer drives antiandrogen resistance in prostate cancer

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Perinatal angiogenesis from pre-existing coronary vessels via DLL4–NOTCH1 signalling

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Single cell multi-omic analysis identifies a Tbx1-dependent multilineage primed population in murine cardiopharyngeal mesoderm

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In vivo transcriptional governance of hair follicle stem cells by canonical Wnt regulators

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CRISPR/Cas9-mediated heterozygous knockout of the autism gene CHD8 and characterization of its transcriptional networks in cerebral organoids derived from iPS cells

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SMARTcleaner: identify and clean off-target signals in SMART ChIP-seq analysis

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Single-cell transcriptomics uncovers a non-autonomous Tbx1-dependent genetic program controlling cardiac neural crest cell development

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PRC2 is recurrently inactivated through EED or SUZ12 loss in malignant peripheral nerve sheath tumors

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Metacell-based differential expression analysis identifies cell type specific temporal gene response programs in COVID-19 patient PBMCs

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ETS factors reprogram the androgen receptor cistrome and prime prostate tumorigenesis in response to PTEN loss

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ZMYND11-MBTD1 induces leukemogenesis through hijacking NuA4/TIP60 acetyltransferase complex and a PWWP-mediated chromatin association mechanism

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Profiling of chromatin accessibility and identification of general cis-regulatory mechanisms that control two ocular lens differentiation pathways

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Fine-tuning spatial-temporal dynamics and surface receptor expression support plasma cell-intrinsic longevity

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Nfatc1 orchestrates aging in hair follicle stem cells

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Protective effects of macrophage-specific integrin α5 in myocardial infarction are associated with accentuated angiogenesis

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