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

Our laboratory is dedicated to interdisciplinary research at the intersection of artificial intelligence and life sciences. By integrating artificial intelligence and big data analysis, we focus on the development of technologies and the investigation of scientific questions in structural biology, genomics, RNA biology, and other related fields. Our research interests include, but are not limited to, RNA structure determination techniques and algorithms, single-cell genomic sequencing technologies and algorithms, and protein structure modeling based on cryo-electron microscopy.

We are particularly interested in the development of artificial intelligence algorithms, specifically exploring the current capabilities of AI methods in addressing biological questions, the unique aspects of AI approaches in biomedical data analysis that differentiate them from other AI domains, and even the potential of artificial intelligence in introducing new research paradigms for life science research.

Selected publications

1. Wenze Huang*, Tuanlin Xiong*, Yuting Zhao*, Jian Heng, Ge Han, Pengfei Wang, Zhihua Zhao, Ming Shi, Juan Li, Jiazhen Wang, Yixia Wu, Feng Liu, Jianzhong Jeff Xi^#, Yangming Wang^#, Qiangfeng Cliff Zhang^# (2024) Computational prediction and experimental validation identify functionally conserved lncRNAs from zebrafish to human, Nature Genetics.  (In press).

2. Lei Xiong*, Kang Tian*, Yuzhe Li, Weixi Ning, Xin Gao, Qiangfeng Cliff Zhang^#. (2022) Online single-cell data integration through projecting heterogeneous datasets into a common cell-embedding space. Nature Communications. 13(1):6118.

3. Shaojun Zhang*, Wenze Huang*, Lili Ren*, Xiaohui Ju*, Mingli Gong*, Jian Rao*, Lei Sun, Pan Li, Qiang Ding^#, Jianwei Wang^#, Qiangfeng Cliff Zhang^#. (2021) 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.

4. 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.

5. 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

6. 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.

7. Lei Sun*, Kui Xu*, Wenze Huang*, Yucheng T.Yang*, Pan Li, Lei Tang, Tuanlin Xiong, Qiangfeng Cliff Zhang^#. (2021) Predicting dynamic cellular protein-RNA interactions by deep learning using in vivo RNA structures. Cell Research. 31(5):495-516.

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 method for single-cell ATAC-seq analysis via latent feature extraction. Nature Communications, 10(1):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