张强锋 博士

研究员,青年千人

 

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.        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.

 

● 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