学习经历

2003-09至2009-06  武汉大学, 生化与分子生物学, 博士

2005-09至2009-03  巴黎十一大学（联合培养）, 计算机, 博士

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

1999-09至2003-06  武汉大学, 生物学基地班, 学士

主要工作经历与任职情况

2017-01至今, 武汉大学, 生命科学学院, 教授

2015-05至2016-12, 武汉大学, 生命科学学院, 研究员

2009-07至2015-05, 美国加州大学圣地亚哥分校，博士后

主要社会兼职

担任多个杂志审稿人；受邀为Frontiers Editorial Board在RNA和RNA Bioinformatics领域的Reviewer Editor；受聘中国生化与分子生物学RNA专业分会委员等学术任职。

研究内容

RNA是真核生物中基因表达的关键分子，包括携带编码蛋白质信息的信使RNA（mRNA）和大量的非编码RNA（ncRNA）。RNA的调控是遗传信息传递的关键环节，是遗传信息高效、精准传递的基本保证。RNA的异常会导致神经退行性疾病和癌症等多种人类重大疾病，严重威胁人类生命健康。RNA病毒近年来备受关注，而病毒RNA的生成与调控对病毒复制、逃逸宿主免疫等过程至关重要。不同的高通量组学技术带来了多个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表达调控的理解。目前高通量测序技术已常规地用于基础和转化医学研究，产生了海量的生物学数据，同时也带来了挑战。解析RNA生成与加工等代谢调控机制及相关生理和病理功能具有非常重要的生物学意义和广泛的应用前景。目前，本实验室科研领域集中于生物信息与RNA生物学领域，包括开发RNA研究新技术、生物信息分析新方法，进行RNA调控机制和RNA异常与疾病（包括病毒感染与神经退行性疾病等）相关研究。

主持课题项目

1. RNA生成与加工，国家优秀青年科学基金 ，2020年1月至2022年12月

2. 细胞压力诱导转录通读的机制和功能，国家面上项目，2019年1月至2022年12月

3. RNA核滞留的功能元件及分子机制，国家面上项目，2017年1月至2020年12月

4. NF110与DDX5对长非编码RNA结构与功能的调控，国家重大研究计划培育项目，2017年1月至2020年12月

代表性论文（本人名字加粗，通讯作者名字上用“*”标示，第一作者加“#”）

1. Dehe Wang#, Xiao Hu#, Hanzhe Ye, Yue Wang, Qian Yang, Xiaodong Liang, Zilin Wang, Yifan Zhou, Miaomiao Wen, Xueyan Yuan, Xiaomin Zheng, Wen Ye, Boyu Guo, Mayila Yusuyin, Eugenia Russinova, Yu Zhou*, Kun Wang*. Cell-specific clock-controlled gene expression program regulates rhythmic fiber cell growth in cotton, Genome Biology, 2023, 24:49.

2. Guangnan Li#, Zhidong Tang#, Weiliang Fan#, Xi Wang#, Li Huang, Yu Jia, Manli Wang, Zhihong Hu, Yu Zhou*. Atlas of interactions between SARS-CoV-2 macromolecules and host proteins, Cell Insight, 2023, 2(1): 100068.

3. Peng Tang#, Yu Zhou*. Alternative polyadenylation regulation: insights from sequential polyadenylation, Transcription, 2022, 13: 89-95.

4. 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*, Yu Zhou*. Alternative polyadenylation by sequential activation of distal and proximal PolyA sites, Nature Structural & Molecular Biology, 2022, 29(1): 21-31.

5. Shaopeng Li#, Linmao Li#, Weiliang Fan, Suping Ma, Cheng Zhang, Jang Chol Kim, Kun Wang, Eugenia Russinova, Yuxian Zhu*, Yu Zhou*. LeafNet: a tool for segmenting and quantifying stomata and pavement cells, The Plant Cell, 2022, 34: 1171-1188.

6. Bingbing Xu#, Yanda Zhu#, Changchang Cao#, Hao Chen#, Qiongli Jin#, Guangnan Li#, Junfeng Ma#, Siwy Ling Yang#, Jieyu Zhao#, Jianghui Zhu#, Yiliang Ding*, Xianyang Fang*, Yongfeng Jin*, Chun Kit Kwok*, Aiming Ren*, Yue Wan*, Zhiye Wang*, Yuanchao Xue*, Huakun Zhang*, Qiangfeng Cliff Zhang*, Yu Zhou*. Recent advances in RNA structurome, Science China Life Sciences, 2022, 65: 1285-1324.

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

8. Geng Chen#, Yang Yang#, Qi-Jia Wu#, Liu Cao#, Wen Ruan, Changwei Shao, Li Jiang, Peng Tang, Suping Ma, Ao Jiang, Zhen Wang, Kai Wu, Qiangfeng Cliff Zhang, Xiang-Dong Fu, Yu Zhou*. ILF3 represses repeat-derived microRNAs targeting RIG-I mediated type I interferon response, Journal of Molecular Biology, 2022, 434(7).

9. Kai Wu, Dehe Wang, Junhao Wang, Yu Zhou*. Translation landscape of SARS-CoV-2 noncanonical subgenomic RNAs, Virologica Sinica, 2022, 37: 813-822.

10. 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*, Yu Zhou*. The SARS-CoV-2 subgenome landscape and its novel regulatory features. Molecular Cell, 2021, 81(10):2135–2147.

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

12. 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*, Daji Luo*. ASER: Animal Sex Reversal Database, Genomics, Proteomics & Bioinformatics, 2021, 19(6):873-881.

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

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

15. 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 & Infections 2020, 9, 761–770.

16. 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*, Mo-Fang Liu*. A Translation-Activating Function of MIWI/piRNA during Mouse Spermiogenesis. Cell, 2019, 179:1566-1581.

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

18. 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*, Hong Cheng*. NRDE2 negatively regulates exosome functions by inhibiting MTR4 recruitment and exosome interaction. Genes & Development, 2019, 33:1-14.

19. 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*, 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.

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

21. 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*, 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.

22. Huiwu Ouyang#, Kai Zhang, Kristi Fox-Walsh, Yang Yang, Chen Zhang, Jie Huang, Hairi Li, Yu Zhou*, 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.

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

24. 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.

25. Yu Zhou#, Hai-Ri Li, Jie Huang, Ge Jin, 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.

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

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

28. 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*, 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.

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