Qiangfeng ZHANG, Ph.D.

Principal Investigator


1996/09-2000/06

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

2000/09-2006/07

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

2006/08-2011/10

Columbia University Biochemistry and Molecular Biophysics Ph.D.

2011/11-2012/09

Columbia University Center of Computational Biology and Bioinformatics Postdoc

2012/12-2015/02

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



 

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 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 publications


[1]. Shi, B.Y.#, Zhang, J.S.#, Heng, J.#, Gong, J.#, Zhang, T., Li,P., Sun, B.F.,Yang, Y., Zhang, N., Zhao, Y.L., Wang, H.L., Liu, F.*, Zhang, Q.C.*, Yang, Y.G.*(2020) RNA structural dynamics regulates early embryogenesis through controlling transcriptome fate and function, Genome Biology (accepted)
[2]. Weng, X, Gong, J, Chen, Y, Wu, T, Wang, F, Yang, S, Yuan, Y, Luo, G, Chen, K, Hu, L, Ma, H, Wang, P, Zhang QC*, Zhou, X*, and He C* (2020)  Keth-seq for transcriptome-wide RNA structure mapping. Nature Chemical Biology (https://doi.org/10.1038/s41589-019-0459-3)
[3]. P.Li, R. Shi, Q.C. Zhang. (2019) icSHAPE-pipe: A comprehensive toolkit for icSHAPE data analysis and evaluation. Methods Mol Biol
[4]. Xiong L, Xu K, Tian K, Shao Y, Tang L, Gao G, Zhang M, Jiang T, Zhang QC.(2019)SCALE method for single-cell ATAC-seq analysis via latent feature extraction. Nat Commun, 10: 4576.

[5].  L Sun*, FM Fazal*, P Li*, JP Broughton, B Lee, L Tang, W Huang, HY Chang#, QC Zhang# (2019) RNA structure maps across mammalian cellular compartments. Nat Struct Mol Biol. 26(4):322-330.

[6]  Zhao, J.*, Qian, X.*, Yeung, P. Y.*, Zhang, Q. C.#, and Kwok, C. K. # (2019) Mapping In Vivo RNA Structures and Interactions. Trends Biochem Sci 44, 555-556
[7]  Xu, K., Wang, Z., Shi, J.P., Li, H.S. and Zhang, Q.C. (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) Jan. 27 – Feb.1, Hawaii, USA

[8]   P Li*, Y Wei*, M Mei*, L Tang*, L Sun, W Huang, J Zhou, C Zou, S Zhang, CF Qin, T Jiang, J Dai, X Tan#, QC Zhang#. (2018) Integrative Analysis of Zika Virus Genome RNA Structure Reveals Critical Determinants of Viral Infectivity. Cell host & microbe 24(6): 875-886.

[9].  X Qian*, J Zhao*, PY Yeung*, QC Zhang# , CK Kwok#. (2018) Revealing lncRNA Structures and Interactions by Sequencing-Based Approaches. Trends in biochemical sciences 44(1): 33-52. (review)

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

[11].  Lu Z*, Zhang QC* , Lee B, Flynn RA, Smith MA, Robinson JT, Davidovich C, Gooding AR, Goodrich KJ, Mattick JS, Mesirov JP, Cech, TR, Chang HY. (2016) RNA duplex map in living cells reveals higher order transcriptome structure. Cell, 165 (5), 1267-1279.

[12].  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.

[13].  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.

[14].  Spitale R*, Flynn RA*, Zhang QC* , Crisalli P, Lee B, Jung JW, Kuchelmeister HY, Batista PJ, Torre EA, Kool ET, and Chang HY. (2015) Structural imprints in vivo decode RNA regulatory mechanisms. Nature, 519: 486-90.

[15].  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), 404-416.

[16]. 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), 706-709.

[17]. 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.

[18]. 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: 556-60.

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

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

Contact information


Email: qczhang@tsinghua.edu.cn

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

Homepage: http://zhanglab.net