A comparative atlas of single-cell chromatin accessibility in the human brain

Cited by (173)

Items 101–173 of 173

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    Yang Xie, Lei Chang, Guojie Zhong, Jonathan A. Rink, Tatiana Baez-Becerra, Ethan J. Armand, Wubin Ding, Kai Li, Éric Bonne, Anita Lie et al. · 2026 · bioRxiv (Cold Spring Harbor Laboratory)
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36. Single-nucleus multiple-organ chromatin accessibility mapping in the rat
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41. Protocol for conducting a single-cell sequencing assay for transposase-accessible chromatin analysis
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42. Identification of enhancer chromatin signatures involved in dopaminergic induction through multi-omics analysis
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    Tetsuya Yamada, Mari Sepp, Ioannis Sarropoulos, Henrick Kaessmann · 2025 · bioRxiv
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    Luis M. Solis, William L Melendez, Shantanu H Fuke, Sayantan Paul, Anthony B. Garza, Rolando García, Marc S. Halfon, Hani Z. Girgis · 2025 · NAR Genomics and Bioinformatics
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    Chrysania Lim, Javen Tan Yih Ruay, Tim Stuart · 2025 · bioRxiv (Cold Spring Harbor Laboratory)
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    Dubnov, Serafima, Laski, Lihen, Zchut, Ido, Avidan, Ofek, Bennett, Estelle R., Greenberg, David S., Turjeman, Adi, Nitzan, Mor, Paldor, Iddo, Soreq, Hermona · 2026
52. Cell type–specific gene regulatory atlas prioritizes drug targets and repurposable medicines in Alzheimer's disease
    Yunxiao Ren, Ming Hu, Li Yang, Andrew A. Pieper, Jeffrey L. Cummings, Feixiong Cheng · 2026 · Genome Research
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    Zhaoning Wang, Songpeng Zu, Ethan J. Armand, Timothy H. Loe, Jonathan A. Rink, Wanying Wu, Yang Xie, Lei Chang, Chenxu Zhu, Nicholas D. Johnson et al. · 2026 · bioRxiv (Cold Spring Harbor Laboratory)
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    Zian Wang, Xiaoyang Chen, Xuejian Cui, Zijing Gao, Zhen Li, Keyi Li, Rui Jiang · 2026 · bioRxiv (Cold Spring Harbor Laboratory)
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    Qiongyu Sheng, Yang Zhou, Fengping Zhu, Li Xu, Shuilin Jin · 2026 · Nature Communications
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    Brianne B. Rogers, Ashlyn G. Anderson, Iván Rodríguez-Nunez, Samuel C. Bartley, S. Quinn Johnston, Jared W. Taylor, Sarah Kristen Meadows, Kimberly M. Newberry, R Myers, J. Nicholas Cochran · 2026 · iScience
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    Wei He, Weizhen Hou, Chengyong Jiang, Xiuxiu Zhang, Yaoyi Wang, Yi Zhou, Kevin T. Gobeske, Shaojie Ma, Jiachen Fan, Haiyang Wang et al. · 2026 · Genome biology
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