实验室主页：http://zhoulab.whu.edu.cn/

学习经历

1999-09－2003-06 武汉大学 本科 生物学基地班

2003-09－2004-09 武汉大学 硕士 生化与分子生物学

2004-10－2005-07 法国巴黎十一大学 硕士 生物信息与生物统计学

2005-09－2008-12 武汉大学 博士 生化与分子生物学

2005-09－2008-12 法国巴黎十一大学 博士 计算机 (与武汉大学联合培养）

主要工作经历及任职情况

2009-07－2015-05 美国加州大学圣地亚哥分校 博士后

2015-05－至今 金沙8888js官方 教授

2015-08－至今 武汉大学高等研究院 兼职研究员

2019-04－至今 病毒学国家重点实验室 教授

主要研究领域及兴趣

近年来发展起来的不同高通量测序技术（如ChIP-seq、RNA-seq和GRO-seq等），带来了不同层次的定量生物学信息，扩大和加深了研究者对于细胞内基因调控的理解，包括对RNA结合蛋白在基因转录和可变剪接中作用的认识。随着测序成本持续下降，高通量测序技术将常规地用于基础和转化医学研究，这将产生海量的生物学数据，同时也带来了挑战。本实验室已经建立“Wet-and-Dry混合”的平台，专注于生物信息学及RNA系统生物学的研究。主要的工作包含：1）开发高通量测序数据分析和可视化工具，促进大数据转换成生物学发现；2）RNA核滞留的功能元件及分子机制；3）RNA结合蛋白对非编码RNA结构与功能的调控；4）miRNA的生成加工与细胞核亚结构的关系；5）RNA转录终止调控机制及其异常在相关疾病中的作用。目前在结合病毒感染以及肿瘤系统，进一步揭示RNA生成与加工的新机制和关键调控功能，为相关疾病的诊治提供理论基础和分子靶点。同时与其他国内外实验室合作，从生物信息学角度解决多种生物学问题。

教学

2016年秋季－至今 本科生 基因组学（主讲）

2016年秋季－至今 研究生 功能基因组学（主讲）

2017年春季－2019 研究生 计算生物学（主讲）

2017年秋季－至今 研究生 生物信息学（参讲）

代表性论文（#共同第一作者，*通讯作者）

1. Shaopeng Li#, Linmao Li#, Weiliang Fan, Suping Ma, Cheng Zhang, Jang Chol Kim, Kun Wang, Eugenia Russinova, Yuxian Zhu*, andYu Zhou*. LeafNet: A Tool for Segmenting and Quantifying Stomata and Pavement Cells.The Plant Cell, 2022, DOI:https://doi.org/10.1093/plcell/koac021.

2. Peng Tang#, Yang Yang#, Guangnan Li, Li Huang, Miaomiao Wen, Wen Ruan, Xiaolong Guo, Chen Zhang, Xinxin Zuo, Daji Luo, Yongzhen Xu, Xiang-Dong Fu*, andYu Zhou*. Alternative Polyadenylation by Sequential Activation of Distal and Proximal PolyA Sites.Nature Structural & Molecular Biology, 2022, 29:21-31.

3. Zhidong Tang#, Weiliang Fan#, Qiming Li#, Dehe Wang, Miaomiao Wen, Junhao Wang, Xingqiao Li, andYu Zhou*. MVIP: multi-omics portal of viral infection.Nucleic Acids Research, 2022, 50(D1):D817-D827.

4. Yangyang Li#, Zonggui Chen#, Hairong Liu#, Qiming Li, Xing Lin, Shuhui Ji, Rui Li, Shaopeng Li, Weiliang Fan, Haiping Zhao, Zuoyan Zhu, Wei Hu*,Yu Zhou*, and Daji Luo*. ASER: Animal Sex Reversal Database.Genomics, Proteomics & Bioinformatics, 2021, DOI:10.1016/j.gpb.2021.10.001.

5. Dehe Wang#, Ao Jiang#, Jiangpeng Feng#, Guangnan Li#, Dong Guo#, Muhammad Sajid, Kai Wu, Qiuhan Zhang, Yann Ponty, Sebastian Will, Feiyan Liu, Xinghai Yu, Shaopeng Li, Qianyun Liu, Xing-Lou Yang, Ming Guo, Xingqiao Li, Mingzhou Chen, Zheng-Li Shi, Ke Lan*, Yu Chen*, andYu Zhou*. The SARS-CoV-2 subgenome landscape and its novel regulatory features.Molecular Cell, 2021, 81(10):2135–2147.

6. Jiaqi Xia#, Peng Bai#, Weiliang Fan, Qiming Li, Yongzheng Li, Dehe Wang, Lei Yin*, andYu Zhou*. NEPdb: A Database of T-Cell Experimentally-Validated Neoantigens and Pan-Cancer Predicted Neoepitopes for Cancer Immunotherapy.Front Immunol, 2021, 12:644637.

7. Xinxin Zuo#, Jie Zhou#, Yinming Li#, Kai Wu, Zonggui Chen, Zhiwei Luo, Xiaorong Zhang, Yi Liang, Miguel A. Esteban,Yu Zhou*, and Xiang-Dong Fu*. TDP-43 aggregation induced by oxidative stress causes global mitochondrial imbalance in ALS.Nature Structural & Molecular Biology, 2021, 28:132–142.

8.Yong Xiong#, Yuan Liu#, Liu Cao#, Dehe Wang#, Ming Guo, Ao Jiang, Dong Guo, Wenjia Hu, Jiayi Yang, Zhidong Tang, Honglong Wu, Yongquan Lin, Meiyuan Zhang, Qi Zhang, Mang Shi, Yingle Liu,Yu Zhou*, Ke Lan* & Yu Chen*. Transcriptomic characteristics of bronchoalveolar lavage fluid and peripheral blood mononuclear cells in COVID-19 patients.Emerging Microbes & Infections2020, 9, 761–770.

9. Dehe Wang#, Weiliang Fan#, Xiaolong Guo#, Kai Wu, Siyu Zhou, Zonggui Chen, Danyang Li, Kun Wang*, Yuxian Zhu*, andYu Zhou*. MaGenDB: a functional genomics hub for Malvaceae plants.Nucleic Acids Research, 2020, 48: D1076-D1084.

10. Peng Dai#, Xin Wang#, Lan-Tao Gou#, Zhi-Tong Li#, Ze Wen#, Zong-Gui Chen#, Min-Min Hua, Ai Zhong, Lingbo Wang, Haiyang Su, Huida Wan, Kun Qian, Lujian Liao, Jinsong Li, Bin Tian, Dangsheng Li, Xiang-Dong Fu, Hui-Juan Shi*,Yu Zhou*, and Mo-Fang Liu*. A Translation-Activating Function of MIWI/piRNA during Mouse Spermiogenesis.Cell, 2019, 179:1566-1581.

11. Kun Wang#, Dehe Wang#, Xiaomin Zheng, Ai Qin, Jie Zhou, Boyu Guo, Yanjun Chen, Xingpeng Wen, Wen Ye,Yu Zhou*, and Yuxian Zhu*. Multi-strategic RNA-seq analysis reveals a high-resolution transcriptional landscape in cotton.Nature Communications, 2019, 10:4714.

12. Jianshu Wang#, Jiyun Chen#, Guifen Wu#, Hongling Zhang#, Xian Du#, Suli Chen, Li Zhang, Ke Wang, Jing Fan, Shuaixin Gao, Xudong Wu, Shouxiang Zhang, Bin Kuai, Peng Zhao, Binkai Chi, Lantian Wang, Guohui Li, Catherine C.L. Wong,Yu Zhou*, Jinsong Li*, Caihong Yun*, and Hong Cheng*. NRDE2 negatively regulates exosome functions by inhibiting MTR4 recruitment and exosome interaction.Genes & Development, 2019, 33:1-14.

13. Kai Zhang#, Xiaorong Zhang#, Zhiqiang Cai#, Jie Zhou#, Ran Cao, Ya Zhao, Zonggui Chen, Dehe Wang, Wen Ruan, Qian Zhao, Guangqiao Liu, Yuanchao Xue, Yan Qin, Bing Zhou, Ligang Wu, Timothy Nilsen,Yu Zhou*, and Xiang-Dong Fu*. A novel class of microRNA-recognition elements that function only within open reading frames.Nature Structural & Molecular Biology, 2018, 25(11):1019-1027.

14. Jiaqi Gu#, Ming Wang#, Yang Yang#, Ding Qiu, Yiqun Zhang, Jinbiao Ma*, Yu Zhou*, Gregory J. Hannon*, and Yang Yu*. GoldCLIP: Gel-omitted Ligation-dependent CLIP. Genomics, Proteomics & Bioinformatics , 2018, 16(2):136-143.

15. Li Jiang#, Changwei Shao#, Qi-Jia Wu#, Geng Chen, Jie Zhou, Bo Yang, Hairi Li, Lan-Tao Gou, Yi Zhang, Yangming Wang, Gene W Yeo,Yu Zhou*, and Xiang-Dong Fu*. NEAT1 scaffolds RNA-binding proteins and the Microprocessor to globally enhance pri-miRNA processing.Nature Structural & Molecular Biology, 2017, 24:816-824.

16. Huiwu Ouyang, Kai Zhang, Kristi Fox-Walsh, Yang Yang, Chen Zhang, Jie Huang, Hairi Li,Yu Zhou*, and Xiang-Dong Fu*. The RNA binding protein EWS is broadly involved in the regulation of pri-miRNA processing in mammalian cells.Nucleic Acids Research,2017, 45(21):12481-12495.

17. Chaoliang Wei#, Rui Xiao#, Liang Chen#, Hanwei Cui#,Yu Zhou#, Yuanchao Xue, Jing Hu, Bing Zhou, Taiki Tsutsui, Jinsong Qiu, Hairi Li, Liling Tang, and Xiang-Dong Fu*. RBFox2 Binds Nascent RNA to Globally Regulate Polycomb Complex 2 Targeting in Mammalian Genomes.Molecular Cell, 2016, 62(6):875-889.

18. Lanfeng Wang#,Yu Zhou#, Liang Xu#, Rui Xiao#, Xingyu Lu, Liang Chen, Jenny Chong, Hairi Li, Chuan He, Xiang-Dong Fu & Dong Wang*. Molecular Basis for 5-Carboxycytosine Recognition by RNA Polymerase II Elongation Complex.Nature(2015) 523, 621–625.

19.Yu Zhou, Hai-Ri Li, Jie Huang, Ge Jin, and Xiang-Dong Fu*. Multiplex analysis of polyA-linked sequences (MAPS): an RNA-seq strategy to profile poly(A+) RNA.Methods Mol Biol(2014) 1125:169-178.

20. Shatakshi Pandit#,Yu Zhou#, Lily Shiue#, Gabriela Coutinho-Mansfield, Hairi Li, Jinsong Qiu, Jie Huang, Gene W. Yeo, Manuel Ares, Jr.* and Xiang-Dong Fu*. Genome-wide analysis reveals SR protein cooperation and competition in regulated splicing. Molecular Cell(2013) 50(2), 223-235.

21.Yu Zhou#, Yann Ponty#, Stephane Vialette, Jerome Waldispuhl, Yi Zhang, and Alain Denise*. Flexible RNA design under structure and sequence constraints using formal languages. InACM BCB - ACM Conference on Bioinformatics, Computational Biology and Biomedical Informatics. Bethesda, Washigton DC, United States, (2013).

22. Yuanchao Xue#,Yu Zhou#, Tongbin Wu, Tuo Zhu, Xiong Ji, Young-Soo Kwon, Chao Zhang, Gene Yeo, Douglas L. Black, Hui Sun, Xiang-Dong Fu*, and Yi Zhang*. Genome-wide analysis of PTB-RNA interactions reveals a strategy used by the general splicing repressor to modulate exon inclusion or skipping.Molecular Cell(2009) 36(6), 996-1006.

23. Yu Zhou#, Chen Lu#, Qi-Jia Wu#, Yu Wang, Zhi-Tao Sun, Jia-Cong Deng, and Yi Zhang*. GISSD: Group I Intron Sequence and Structure Database.Nucleic Acids Research(2008) 36, D31-D37.