Robust integration of multiple single-cell RNA sequencing datasets using a single reference space von Liu, Yang, Wang, Tao, Zhou, Bin, Zheng, Deyou

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

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The immune checkpoint B7x expands tumor-infiltrating Tregs and promotes resistance to anti-CTLA-4 therapy von John, Peter, Pulanco, Marc C., Galbo, Phillip M., Wei, Yao, Ohaegbulam, Kim C., Zheng, Deyou, Zang, Xingxing

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In vivo transcriptional governance of hair follicle stem cells by canonical Wnt regulators von Lien, Wen-Hui, Polak, Lisa, Lin, Mingyan, Lay, Kenneth, Zheng, Deyou, Fuchs, Elaine

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

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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 von Ferrena, Alexander, Zhang, Xusheng, Shrestha, Rupendra, Zheng, Deyou, Liu, Wei

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A comprehensive spatial-temporal transcriptomic analysis of differentiating nascent mouse lens epithelial and fiber cells von Zhao, Yilin, Zheng, Deyou, Cvekl, Ales

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Significant expansion of the REST/NRSF cistrome in human versus mouse embryonic stem cells: potential implications for neural development von Rockowitz, Shira, Zheng, Deyou

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

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Perinatal angiogenesis from pre-existing coronary vessels via DLL4–NOTCH1 signalling von Lu, Pengfei, Wang, Yidong, Liu, Yang, Wang, Yifeng, Wu, Bingruo, Zheng, Deyou, Harvey, Richard P., Zhou, Bin

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

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Glucocorticoid Receptor Confers Resistance to Antiandrogens by Bypassing Androgen Receptor Blockade von Arora, Vivek K., Schenkein, Emily, Murali, Rajmohan, Subudhi, Sumit K., Wongvipat, John, Balbas, Minna D., Shah, Neel, Cai, Ling, Efstathiou, Eleni, Logothetis, Chris, Zheng, Deyou, Sawyers, Charles L.

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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 von Wang, Ping, Mokhtari, Ryan, Pedrosa, Erika, Kirschenbaum, Michael, Bayrak, Can, Zheng, Deyou, Lachman, Herbert M

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SMARTcleaner: identify and clean off-target signals in SMART ChIP-seq analysis von Zhao, Dejian, Zheng, Deyou

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Six3 and Six6 Are Jointly Required for the Maintenance of Multipotent Retinal Progenitors through Both Positive and Negative Regulation von Diacou, Raven, Zhao, Yilin, Zheng, Deyou, Cvekl, Ales, Liu, Wei

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PRC1 preserves epidermal tissue integrity independently of PRC2 von Cohen, Idan, Zhao, Dejian, Menon, Gopinathan, Nakayama, Manabu, Koseki, Haruhiko, Zheng, Deyou, Ezhkova, Elena

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Identification and Initial Functional Characterization of a Human Vascular Cell–Enriched Long Noncoding RNA von Bell, Robert D, Long, Xiaochun, Lin, Mingyan, Bergmann, Jan H, Nanda, Vivek, Cowan, Sarah L, Zhou, Qian, Han, Yu, Spector, David L, Zheng, Deyou, Miano, Joseph M

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Single-cell transcriptomics uncovers a non-autonomous Tbx1-dependent genetic program controlling cardiac neural crest cell development von De Bono, Christopher, Liu, Yang, Ferrena, Alexander, Valentine, Aneesa, Zheng, Deyou, Morrow, Bernice E.

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

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The DNA dioxygenase Tet1 regulates H3K27 modification and embryonic stem cell biology independent of its catalytic activity von Chrysanthou, Stephanie, Tang, Qin, Lee, Joun, Taylor, Samuel J, Zhao, Yilin, Steidl, Ulrich, Zheng, Deyou, Dawlaty, Meelad M

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