张强锋 博士

研究员、副教授、博士生导师


1996-2000 中国科学技术大学 学士
2000-2006 中国科学技术大学  博士
2006-2011 哥伦比亚大学  博士
2011-2012 哥伦比亚大学  博士后
2012-2015 斯坦福大学医学院  博士后
2015-至今  清华大学生命科学学院  研究员
2015-2018 清华大学生命科学学院  助理教授
2018-至今  清华大学生命科学学院  副教授

●  研究兴趣、领域:


我们实验室是一个结构生物学、基因组学、机器学习和大数据分析等多学科交叉实验室。我们主要的研究兴趣是发展高通量实验新技术,结合计算,并应用于新兴的结构系统生物学研究。其中包括使用高通量深度测序的手段来探测RNA二级结构和计算建模,RNA功能模体(motif)等有效预测或发现方法,蛋白-蛋白、RNA-RNA、以及蛋白-RNA相互作用网络,以及结合结构和网络发展进行深入的复杂疾病(如癌症)和RNA病毒传染性疾病机制研究,并发展可能的诊断、预后及治疗手段。

●  代表性论文:


[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.

 

●  联系方式:


电子邮件:qczhang@tsinghua.edu.cn

电话:010-6279-6439(办公室),010-6279-5823(实验室)

主页:  http://zhanglab.net