Qiangfeng ZhANG

Qiangfeng ZhANG


Tsinghua University

School of Life Sciences

Principal Investigator


Education and Work Experience

2000      University of Science and Technology of China Special Class for Gifted Young B.S.

 2006      University of Science and Technology of China Computer Science and Technology Ph.D.

 2012       Columbia University Biochemistry and Molecular Biophysics Ph.D.

 2011-2012  Columbia University Center of Computational Biology and Bioinformatics Postdoc

 2012-2015  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 Publication

1. Flynn RA*, Zhang QC*, Spitale RC*, Lee B, Mumbach MR, and Chang HY. (2015) icSHAPE:  Transcriptome-wide interrogation of RNA secondary structure in living cells. Nature Protocol. (In press, *Co-first authorship).

2. 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. (*Co-first authorship)

3. 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.

4. 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.

5. 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.

6. 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.

7. 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 (*Co-first authorship)

8. 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 (*Co-first authorship)

9. 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




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