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

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Metacell-based differential expression analysis identifies cell type specific temporal gene response programs in COVID-19 patient PBMCs by Kevin O’Leary, Deyou Zheng

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Profiling of chromatin accessibility and identification of general cis-regulatory mechanisms that control two ocular lens differentiation pathways by Yilin Zhao, Deyou Zheng, Ales Cvekl

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Characterization of cell-cell communication in autistic brains with single-cell transcriptomes by Maider Astorkia, Herbert M. Lachman, Deyou Zheng

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Small RNAs originated from pseudogenes: cis- or trans-acting? by Xingyi Guo, Zhaolei Zhang, Mark B Gerstein, Deyou Zheng

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Transcriptomic analysis and novel insights into lens fibre cell differentiation regulated by Gata3 by Elena Martynova, Yilin Zhao, Qing Xie, Deyou Zheng, Ales Cvekl

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Characteristics of allelic gene expression in human brain cells from single-cell RNA-seq data analysis by Dejian Zhao, Mingyan Lin, Erika Pedrosa, Herbert M. Lachman, Deyou Zheng

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Characterization of human pseudogene-derived non-coding RNAs for functional potential. by Xingyi Guo, Mingyan Lin, Shira Rockowitz, Herbert M Lachman, Deyou Zheng

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Mammalian TBX1 preferentially binds and regulates downstream targets via a tandem T-site repeat. by Raquel Castellanos, Qing Xie, Deyou Zheng, Ales Cvekl, Bernice E Morrow

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Spatiotemporal Gene Coexpression and Regulation in Mouse Cardiomyocytes of Early Cardiac Morphogenesis by Yang Liu, Pengfei Lu, Yidong Wang, Bernice E. Morrow, Bin Zhou, Deyou Zheng

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Allele-biased expression in differentiating human neurons: implications for neuropsychiatric disorders. by Mingyan Lin, Anastasia Hrabovsky, Erika Pedrosa, Tao Wang, Deyou Zheng, Herbert M Lachman

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Transcriptome analysis of microglia in a mouse model of Rett syndrome: differential expression of genes associated with microglia/macrophage activation and cellular stress by Dejian Zhao, Ryan Mokhtari, Erika Pedrosa, Rayna Birnbaum, Deyou Zheng, Herbert M. Lachman

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Dynamic changes in whole genome DNA methylation, chromatin and gene expression during mouse lens differentiation by William Chang, Yilin Zhao, Danielle Rayêe, Qing Xie, Masako Suzuki, Deyou Zheng, Ales Cvekl

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Polycomb repressive complex 2 in adult hair follicle stem cells is dispensable for hair regeneration. by Pooja Flora, Meng-Yen Li, Phillip M Galbo, Maider Astorkia, Deyou Zheng, Elena Ezhkova

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

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Differential deployment of REST and CoREST promotes glial subtype specification and oligodendrocyte lineage maturation. by Joseph J Abrajano, Irfan A Qureshi, Solen Gokhan, Deyou Zheng, Aviv Bergman, Mark F Mehler

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REST and CoREST modulate neuronal subtype specification, maturation and maintenance. by Joseph J Abrajano, Irfan A Qureshi, Solen Gokhan, Deyou Zheng, Aviv Bergman, Mark F Mehler

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RNA-Seq of human neurons derived from iPS cells reveals candidate long non-coding RNAs involved in neurogenesis and neuropsychiatric disorders. by Mingyan Lin, Erika Pedrosa, Abhishek Shah, Anastasia Hrabovsky, Shahina Maqbool, Deyou Zheng, Herbert M Lachman

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Polycomb Repressive Complex 1 Controls Maintenance of Fungiform Papillae by Repressing Sonic Hedgehog Expression by Carmit Bar, Idan Cohen, Dejian Zhao, Venu Pothula, Anna Litskevitch, Haruhiko Koseki, Deyou Zheng, Elena Ezhkova

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ETS family transcriptional regulators drive chromatin dynamics and malignancy in squamous cell carcinomas by Hanseul Yang, Daniel Schramek, Rene C Adam, Brice E Keyes, Ping Wang, Deyou Zheng, Elaine Fuchs

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