Qiangfeng Cliff ZHANG Ph.D.
Associate Professor
1996-2000 University of Science and Technology of China, B.S. in Computer Science and Technology
2000-2006 University of Science and Technology of China, Ph.D. in Computer Science
2006-2011 Columbia University, Ph.D. in Biochemistry and Molecular Biophysics
2011-2012 Columbia University, Center of Computational Biology and Bioinformatics, Postdoctoral scholar
2012-2015 Columbia University, School of Medicine, Postdoctoral scholar
2015-2018 Tsinghua University, School of Life Sciences, Assistant Professor
2018-present Tsinghua University, School of Life Sciences, Associate Professor
Research interest
Working in the interface of structural biology, genomics, machine learning and big data analysis, our lab’s main research interest is to develop novel enabling techniques that combines high throughput experimentation and machine learning AI methods for the study of structural systems biology. It includes but not limited to RNA structure sequencing technologies and algorithms, single cell chromatin structure sequencing technologies and algorithms, protein structural modeling, and interaction networks of macromolecules. We are also interested in bridging macromolecule structures and networks for the better diagnosis, prognosis and developing viable treatments for complex human diseases.
Selected publications
1. Meiling Piao, Pan Li, Xiaomin Zeng, Xi-Wen Wang, Lan Kang, Jinsong Zhang, Yifan Wei, Shaojun Zhang, Lei Tang, Jianghui Zhu, Chun Kit Kwok, Xiaoyu Hu#, Qiangfeng Cliff Zhang# (2022) An ultra low-input method for global RNA structure probing uncovers Regnase-1-mediated regulation in macrophages, Fundamental Research 2 (1), 2-13
2. Shaojun Zhang*, Wenze Huang*, Lili Ren*, Xiaohui Ju*, Mingli Gong*, Jian Rao*, Lei Sun, Pan Li, Qiang Ding#, Jianwei Wang#, Qiangfeng Cliff Zhang# (2022) Comparison of viral RNA-host protein interactomes across pathogenic RNA viruses informs rapid antiviral drug discovery for SARS-CoV-2, Cell Research 32 (1), 9-23
3. Jing Gong*, Kui Xu*, Ziyuan Ma, Zhi John Lu, Qiangfeng Cliff Zhang# (2021) A deep learning method for recovering missing signals in transcriptome-wide RNA structure profiles from probing experiments, Nature Machine Intelligence 3 (11), 995-1006
4. Qing-Jun Luo*, Jinsong Zhang*, Pan Li*, Qing Wang, Yue Zhang, Biswajoy Roy-Chaudhuri, Jianpeng Xu, Mark A. Kay#, Qiangfeng Cliff Zhang# (2021) RNA structure probing reveals the structural basis of Dicer binding and cleavage, Nature Communications 12 (1), 1-12
5. Lei Sun*, Pan Li*, Xiaohui Ju*, Jian Rao*, Wenze Huang*, Lili Ren, Shaojun Zhang, Tuanlin Xiong, Kui Xu, Xiaolin Zhou, Mingli Gong, Eric Miska, Qiang Ding#, Jianwei Wang#, Qiangfeng Cliff Zhang#. (2021) In vivo structural characterization of the SARS-CoV-2 RNA genome identifies host proteins vulnerable to repurposed drugs, Cell 184(7):1865-1883. e20
6. Lei Sun*, Kui Xu*, Wenze Huang*, Yucheng Yang*, Lei Tang, Tuanlin Xiong, Qiangfeng Cliff Zhang#. (2021) Predicting dynamic cellular protein-RNA interactions using deep learning and in vivo RNA structure, Cell Research 31(5):495-516
7. Boyang Shi*, Jinsong Zhang*, Jian Heng*, Jing Gong*, Ting Zhang, Pan Li, Bao-Fa Sun, Ying Yang, Ning Zhang, Yong-Liang Zhao, Hai-Lin Wang, Feng Liu#, Qiangfeng Cliff Zhang#, Yun-Gui Yang#. (2020) RNA structural dynamics regulates early embryogenesis through controlling transcriptome fate and function, Genome Biology 21(1):1-27.
8. Xiaocheng Weng*, Jing Gong*, Yi Chen, Tong Wu, Fang Wang, Shixi Yang, Yushu Yuan, Guanzheng Luo, Kai Chen, Lulu Hu, Honghui Ma, Pingluan Wang, Qiangfeng Cliff Zhang#, Xiang Zhou#, Chuan He#. (2020) Keth-seq for transcriptome-wide RNA structure mapping. Nature Chemical Biology 16(5):489-492
9. Lei Xiong*, Kui Xu, Kang Tian, Yanqiu Shao, Lei Tang, Ge Gao, Michael Zhang, Tao Jiang, Qiangfeng Cliff Zhang#. (2019) SCALE: Single-cell ATAC-seq analysis via latent feature extraction. Nature Communications 10:4576
10. Lei Sun*, Furqan M Fazal*, Pan Li*, James P Broughton, Byron Lee, Lei Tang, Wenze Huang, Eric T Kool, Howard Y Chang#, Qiangfeng Cliff Zhang#. (2019) RNA structure maps across mammalian cellular compartments. Nature structural & molecular biology 26(4):322-330
11. Kui Xu*, Zhe Wang, Jianping Shi, Hongsheng Li, Qiangfeng Cliff Zhang#. (2019) A2-Net: Molecular Structure Estimation from Cryo-EM Density Volumes. In the Proceedings of the Thirty-Fourth AAAI Conference on Artificial Intelligence (AAAI 2019):1230-1237. Jan. 27-Feb.1, Hawaii, USA
12. Pan Li*, Yifan Wei*, Miao Mei*, Lei Tang*, Lei Sun, Wenze Huang, Jianyu Zhou, Chunlin Zou, Shaojun Zhang, Cheng-feng Qin, Tao Jiang, Jianfeng Dai, Xu Tan#, Qiangfeng Cliff Zhang#. (2018) Integrative Analysis of Zika Virus Genome RNA Structure Reveals Critical Determinants of Viral Infectivity. Cell Host & Microbe 24(6):875-886
Contact information
Email: qczhang@tsinghua.edu.cn
Phone: 010-6279-6439 (Office), 010-6279-5823 (Lab)
Homepage: http://zhanglab.net
