张强锋 博士

研究员

 

1996-2000

中国科学技术大学

少年班

学士

2000-2006

中国科学技术大学

计算机科学与技术

博士

2006-2011

哥伦比亚大学

生物化学和分子生物物理

博士

2011-2012

哥伦比亚大学

计算生物和生物信息中心

博士后

2012-2015

斯坦福大学医学院

皮肤系和遗传系

博士后

 

● 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计算和高通量实验相结合的方法,并应用于新兴的结构系统生物学研究,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一步疾病诊断、预后以及发展可能的治疗手段。

● 代表性论文:

[1].  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.

[2]   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.

[3].  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)

[4]   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.

[5].  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.

[6].  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.

[7].  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.

[8].  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.

[9].  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.

[10]. 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.

[11]. 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.

[12]. 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.

[13]. 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.

[14]. 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:zhang.lab@biomed.tsinghua.edu.cn

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

主页:  http://zhanglab.net