周 宇：武漢大學生命科學學院研究員。學科專業：生物信息與功能基因組學研究方向：生物信息學、功能基因組學、RNA組學。
學習經歷
1999-09－2003-06 武漢大學 本科 生物學基地班
2003-09－2004-09 武漢大學 碩士 生化與分子生物學
2004-10－2005-07 法國巴黎十一大學 碩士 生物信息與生物統計學
2005-09－2008-12 武漢大學 博士 生化與分子生物學
2005-09－2008-12 法國巴黎十一大學 博士 計算機 (與武漢大學聯合培養）
主要工作經歷及任職情況
2009-07－2015-05 美國加州大學聖地亞哥分校 博士後
2015-05－至今 武漢大學 研究員
2015-08－至今 武漢大學高等研究院 兼職研究員
1999-09－2003-06 武漢大學 本科 生物學基地班
2003-09－2004-09 武漢大學 碩士 生化與分子生物學
2004-10－2005-07 法國巴黎十一大學 碩士 生物信息與生物統計學
2005-09－2008-12 武漢大學 博士 生化與分子生物學
2005-09－2008-12 法國巴黎十一大學 博士 計算機 (與武漢大學聯合培養）
主要工作經歷及任職情況
2009-07－2015-05 美國加州大學聖地亞哥分校 博士後
2015-05－至今 武漢大學 研究員
2015-08－至今 武漢大學高等研究院 兼職研究員
主要研究領域及興趣
近年來發展起來的不同高通量測序技術（如ChIP-seq、RNA-seq和GRO-seq等），帶來了不同層次的定量生物學信息，擴大和加深了研究者對於細胞內基因調控的理解，包括對RNA結合蛋白在基因轉錄和可變剪接中作用的認識。隨著測序成本持續下降，高通量測序技術將常規地用於基礎和轉化醫學研究，這將產生海量的生物學數據，同時也帶來了挑戰。本實驗室將建立“乾濕混合”的平台，並將專注於生物信息學及RNA系統生物學的研究。主要的工作包含：（1）開發高通量測序數據的可視化和分析工具以及異質型數據的整合平台，幫助生物學研究人員提高數據處理加工速度和能力，促進高通量測序數據轉換成生物學發現；2）鑑定RNA轉錄終止和通讀的調控機制及其在相關疾病中的作用；3）基於RASL-seq檢測平台建立特定疾病的基因表達及可變剪接的特徵圖譜；4）miRNA的生成加工及功能；5）非編碼RNA的結構與功能。同時與其他國內外實驗室合作，從生物信息學角度解決多種生物學問題。
近年來發展起來的不同高通量測序技術（如ChIP-seq、RNA-seq和GRO-seq等），帶來了不同層次的定量生物學信息，擴大和加深了研究者對於細胞內基因調控的理解，包括對RNA結合蛋白在基因轉錄和可變剪接中作用的認識。隨著測序成本持續下降，高通量測序技術將常規地用於基礎和轉化醫學研究，這將產生海量的生物學數據，同時也帶來了挑戰。本實驗室將建立“乾濕混合”的平台，並將專注於生物信息學及RNA系統生物學的研究。主要的工作包含：（1）開發高通量測序數據的可視化和分析工具以及異質型數據的整合平台，幫助生物學研究人員提高數據處理加工速度和能力，促進高通量測序數據轉換成生物學發現；2）鑑定RNA轉錄終止和通讀的調控機制及其在相關疾病中的作用；3）基於RASL-seq檢測平台建立特定疾病的基因表達及可變剪接的特徵圖譜；4）miRNA的生成加工及功能；5）非編碼RNA的結構與功能。同時與其他國內外實驗室合作，從生物信息學角度解決多種生物學問題。
代表性論文：
1. 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.
2. 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.
3. 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.
4. 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.
5. 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) 1125:169-78.
6. Yu Zhou#, Yann Ponty#, Stephane Vialette, Jerome Waldispuhl, Yi Zhang, and Alain Denise*. Flexible RNA design under structure and sequence constraints using formal languages. Proceedings of ACM Conference on Bioinformatics, Computational Biology and Biomedical Informatics (2013).
7. Chaoliang Wei, Jinsong Qiu, Yu Zhou, Yuanchao Xue, Jing Hu, Kunfu Ouyang, Indroneal Banerjee, Caimei Zhang, Biyi Chen, Hairi Li, Ju Chen, Long-Sheng Song, Xiang-Dong Fu*. Repression of the Central Splicing Regulator RBFox2 Is Functionally Linked to Pressure Overload-Induced Heart Failure. Cell Reports (2015) 10: 1521-1533.
8. Nova Fong#, Hyunmin Kim#, Yu Zhou, Xiong Ji, Jinsong Qiu, Tassa Saldi, Katrina Diener, Ken Jones, Xiang-Dong Fu, and David L. Bentley*. Pre-mRNA Splicing is Facilitated by an Optimal RNA Polymerase II Elongation Rate. Genes & Dev. (2014) 28: 2663-2676.
9. Changwei Shao#, Bo Yang#, Tongbin Wu#, Jie Huang, Peng Tang, Yu Zhou, Jie Zhou, Jinsong Qiu, Li Jiang, Hairi Li, Geng Chen, Hui Sun, Yi Zhang, Alain Denise, Dong-Er Zhang, and Xiang-Dong Fu*. Mechanisms for U2AF to define 3' splice sites and regulate alternative splicing in the human genome. Nat. Struct. Mol. Biol. (2014) 21, 997-1005.
10. Pingping Wang, Zhihong Zhou, Anchang Hu, Claudio Ponte de Albuquerque, Yu Zhou, Lixin Hong, Emma Sierecki, Masahiko Ajiro, Michael Kruhlak, Curtis Harris, Kunliang Guan, Zhi-Ming Zheng, Alexandra C. Newton, Peiqing Sun, Huilin Zhou, and Xiang-Dong Fu*. Both Decreased and Increased SRPK1 Levels Promote Cancer by Interfering with PHLPP-Mediated Dephosphorylation of Akt. Molecular Cell (2014) 54(3):378-391.
11. Xiaorong Zhang, Xinxin Zuo, Bo Yang, Zongran Li, Yuanchao Xue, Yu Zhou, Jie Huang, Xiaolu Zhao, Jie Zhou, Yun Yan, Huiqiong Zhang, Peipei Guo, Hui Sun, Lin Guo, Yi Zhang,and Xiang-Dong Fu*. MicroRNA Directly Enhances Mitochondrial Translation during Muscle Differentiation. Cell (2014) 158, 607-619.
12. Areum Han, Peter Stoilov, Anthony J. Linares, Yu Zhou, Xiang-Dong Fu, Douglas L. Black*. De novo prediction of PTBP1 binding and splicing targets reveals unexpected features of its RNA recognition and function. PLoS Computational Biology (2014) 10(1), e1003442.
13. Yuanchao Xue, Kunfu Ouyang, Jie Huang, Yu Zhou, Hong Ouyang, Hairi Li, Gang Wang, Qijia Wu, Chaoliang Wei, Yanzhen Bi, Li Jiang, Zhiqiang Cai, Hui Sun, Kang Zhang, Yi Zhang, Ju Chen, Xiang-Dong Fu*. Direct Conversion of Fibroblasts to Neurons by Reprogramming PTB-Regulated MicroRNA Circuits. Cell (2013) 152(1-2), 82-96.
14. Xiong Ji, Yu Zhou, Shatakshi Pandit, Jie Huang, Hairi Li, Charles Y. Lin, Rui Xiao, Christopher B. Burge, Xiang-Dong Fu*. SR proteins collaborate with 7SK and promoter-associated nascent RNA to release paused polymerase. Cell (2013) 153(4), 855-868.
15. Hairi Li, Hongyan Zhou, Dong Wang, Jinsong Qiu, Yu Zhou, Xiangqiang Li, Michael G. Rosenfeld, Sheng Ding*, and Xiang-Dong Fu*. Versatile pathway-centric approach based on high-throughput sequencing to anticancer drug discovery. Proc Natl Acad Sci U S A (2012) 109(12), 4609-4614.
1. 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.
2. 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.
3. 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.
4. 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.
5. 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) 1125:169-78.
6. Yu Zhou#, Yann Ponty#, Stephane Vialette, Jerome Waldispuhl, Yi Zhang, and Alain Denise*. Flexible RNA design under structure and sequence constraints using formal languages. Proceedings of ACM Conference on Bioinformatics, Computational Biology and Biomedical Informatics (2013).
7. Chaoliang Wei, Jinsong Qiu, Yu Zhou, Yuanchao Xue, Jing Hu, Kunfu Ouyang, Indroneal Banerjee, Caimei Zhang, Biyi Chen, Hairi Li, Ju Chen, Long-Sheng Song, Xiang-Dong Fu*. Repression of the Central Splicing Regulator RBFox2 Is Functionally Linked to Pressure Overload-Induced Heart Failure. Cell Reports (2015) 10: 1521-1533.
8. Nova Fong#, Hyunmin Kim#, Yu Zhou, Xiong Ji, Jinsong Qiu, Tassa Saldi, Katrina Diener, Ken Jones, Xiang-Dong Fu, and David L. Bentley*. Pre-mRNA Splicing is Facilitated by an Optimal RNA Polymerase II Elongation Rate. Genes & Dev. (2014) 28: 2663-2676.
9. Changwei Shao#, Bo Yang#, Tongbin Wu#, Jie Huang, Peng Tang, Yu Zhou, Jie Zhou, Jinsong Qiu, Li Jiang, Hairi Li, Geng Chen, Hui Sun, Yi Zhang, Alain Denise, Dong-Er Zhang, and Xiang-Dong Fu*. Mechanisms for U2AF to define 3' splice sites and regulate alternative splicing in the human genome. Nat. Struct. Mol. Biol. (2014) 21, 997-1005.
10. Pingping Wang, Zhihong Zhou, Anchang Hu, Claudio Ponte de Albuquerque, Yu Zhou, Lixin Hong, Emma Sierecki, Masahiko Ajiro, Michael Kruhlak, Curtis Harris, Kunliang Guan, Zhi-Ming Zheng, Alexandra C. Newton, Peiqing Sun, Huilin Zhou, and Xiang-Dong Fu*. Both Decreased and Increased SRPK1 Levels Promote Cancer by Interfering with PHLPP-Mediated Dephosphorylation of Akt. Molecular Cell (2014) 54(3):378-391.
11. Xiaorong Zhang, Xinxin Zuo, Bo Yang, Zongran Li, Yuanchao Xue, Yu Zhou, Jie Huang, Xiaolu Zhao, Jie Zhou, Yun Yan, Huiqiong Zhang, Peipei Guo, Hui Sun, Lin Guo, Yi Zhang,and Xiang-Dong Fu*. MicroRNA Directly Enhances Mitochondrial Translation during Muscle Differentiation. Cell (2014) 158, 607-619.
12. Areum Han, Peter Stoilov, Anthony J. Linares, Yu Zhou, Xiang-Dong Fu, Douglas L. Black*. De novo prediction of PTBP1 binding and splicing targets reveals unexpected features of its RNA recognition and function. PLoS Computational Biology (2014) 10(1), e1003442.
13. Yuanchao Xue, Kunfu Ouyang, Jie Huang, Yu Zhou, Hong Ouyang, Hairi Li, Gang Wang, Qijia Wu, Chaoliang Wei, Yanzhen Bi, Li Jiang, Zhiqiang Cai, Hui Sun, Kang Zhang, Yi Zhang, Ju Chen, Xiang-Dong Fu*. Direct Conversion of Fibroblasts to Neurons by Reprogramming PTB-Regulated MicroRNA Circuits. Cell (2013) 152(1-2), 82-96.
14. Xiong Ji, Yu Zhou, Shatakshi Pandit, Jie Huang, Hairi Li, Charles Y. Lin, Rui Xiao, Christopher B. Burge, Xiang-Dong Fu*. SR proteins collaborate with 7SK and promoter-associated nascent RNA to release paused polymerase. Cell (2013) 153(4), 855-868.
15. Hairi Li, Hongyan Zhou, Dong Wang, Jinsong Qiu, Yu Zhou, Xiangqiang Li, Michael G. Rosenfeld, Sheng Ding*, and Xiang-Dong Fu*. Versatile pathway-centric approach based on high-throughput sequencing to anticancer drug discovery. Proc Natl Acad Sci U S A (2012) 109(12), 4609-4614.
