Full time faculty

Adjunct professor

Chair professor


Qiangfeng Zhang

Qiangfeng Cliff Zhang, Ph.D.

Principal Investigator

Young 1000-Talent Plan



University of Science and Technology of China Special Class for Gifted           Young B.S.


University of Science and Technology of China Computer Science and Technology Ph.D.


Columbia University Biochemistry and Molecular Biophysics Ph.D.


Columbia University Center of Computational Biology and Bioinformatics Postdoc


Stanford University School of Medicine Department of Dermatology, Department of Genetics Postdoc

 Research Interests

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 use computation and high throughput experimentation for the study of structural systems biology. It includes but not limited to RNA secondary structure experimental probing and computational modeling, RNA functional motif discovery, protein-protein interaction and protein-RNA interaction network reconstruction. We are also interested in bridging structures and networks for the better diagnosis, prognosis and developing viable treatments for complex human diseases.

Selected Recent Publications  

1.         Quinn JJ*, Zhang QC*, Georgiev P, Ilik IA, Akhtar A, Chang HY.  (2016)Rapid evolutionary turnover underlies conserved lncRNA–genome interactions. Genes & Development, 30 (2), 191-207. (*equal contribution)

2.         Flynn RA*, Zhang QC*, Spitale RC, Lee B, Mumbach MR, and Chang HY.  (2016)Transcriptome-wide interrogation of RNA secondary structure in living cells with icSHAPE. Nature Protocols, 11 (2), 273-290 (*equal contribution)

3.         Spitale R*, Flynn RA*, Zhang QC*, Pete Crisalli, Byron Lee, Jong-Wha Jung, Hannes Y. Kuchelmeister, Pedro J. Batista, Eduardo A. Torre, Eric T. Kool, and Chang HY. (2015) Structural imprints in vivo decode mechanisms of RNA regulation. Nature. 519 (7544): 486-90. (*equal contribution)

4.         Chu C, Zhang QC, Texira S, Bharadwaj M, Calabrese M, Magnuson T, Heard H and Chang HY. (2015) Developmentally regulated and modular assembly of Xist RNA binding proteins coordinate chromatin silencing. Cell. 161 (2): 404-16.

5.         Wan Y*, Qu K*, Zhang QC, Manor O, Ouyang Z, Zhang J, Snyder MP, Segal E and Chang HY. (2014) Landscape and variation of RNA secondary structure across the human transcriptome. Nature, 505 (7485), 706-9.

6.         Kasowski M*, Kyriazopoulou-Panagiotopoulou S*, Grubert F*, Zaugg JB*, Kundaje A*, Liu Y, Boyle AP, Zhang QC, Zakharia F, Spacek DV, Li J, Xie D, Steinmetz LM, Hogenesch JB, Kellis M, Batzoglou S, Snyder M. Extensive Variation in Chromatin States Across Human Individuals and Populations. (2013) Science 342 (6159), 750-752.

7.         Zhang QC, Petrey D, Garzon J, Deng L, and Honig B. (2013) PrePPI: A structure-informed database of protein-protein interactions. Nucleic Acids Research, 41:D828-33.

8.         Zhang QC*, Petrey D*, Deng L, Qiang L, Shi Y, Chan AT, Bisikirska B, Lefebvre C, Accili D, Hunter T, Maniatis T, Califano A, and Honig B. (2012) Structure-based prediction of protein-protein interactions on a genome-wide scale. Nature, 490 (7421): 556-560 (*equal contribution)

9.         Zhang QC*, Deng L*, Guan J, Honig B and Petrey D. PredUs: a web server for predicting protein interfaces using structural neighbors. (2011) Nucleic Acids Research, 39: W283-87 (*equal contribution)

10.     Zhang QC, Petrey D, Norel R, and Honig B, (2010) Protein interface conservation across structural space. Proceedings of the National Academy of Sciences, 107(24): 10896-109

         11.      J Gong, D Shao, K Xu, Z Lu, ZJ Lu, YT Yang, QC Zhang, RISE: a database of RNA interactome from sequencing experiments (2018) Nucleic Acids Research 46 (D1), D194-D201.


Email: zhang.lab@biomed.tsinghua.edu.cn

Phone: 010-6279-6439 (Office), 010-6279-5823 (Lab)

Homepage: http://zhanglab.net 

Tsinghua University,Beijing,China,100084
Tel:+86-10-62788604  Fax:+86-10-62788604  Email:admin-life@biomed.tsinghua.edu.cn