清华合成与系统生物学中心
Tsinghua Center for Synthetic and Systems Biology
luz
鲁 志 (Zhi John Lu)
PI,博士生导师
教育部“新世纪人才计划”获得者






联系方式
清华大学生命科学学院,北京,100084,中国
Tel.: +86-10-62789217
E-mail:
zhilu@tsinghua.edu.cn
实验室主页: http://bioinfo.life.tsinghua.edu.cn

教育背景及工作履历
2011−至今  清华大学 生命科学学院  PI,博导
2008−2011  美国 耶鲁大学(Yale University)生物信息学 博士后
2008       美国 罗切斯特大学(University of Rochester) 生物物理学 博士
2003       中国 科学技术大学 生命科学学院   学士

 
主要研究领域与方向
实验室主要从事生物信息学和系统生物学研究, 从事以生物学、统计学、计算机科学等多学科的交叉学科研究。我们主要以Dynamic Programming, Machine Learning等计算统计方法,结合最新一代的大规模测序技术,预测和研究人类基因组、模式生物基因组和植物基因组里的新型非编码基因(ncRNA), 和编码基因之间的网络调控,以及其他表观遗传问题。除了基础研究工作(如植物基因组)外,实验室也侧重和cancer等遗传疾病相关的研究。同时, 我们特别加强自主开发RNA二级结构预测和新ncRNA预测归类的算法,相关网络服务及桌面软件。

主要论文

ong Hu, Chao Di, Mingxuan Kai, Yu-Cheng T. Yang, Yang Li, Yunjiang Qiu, Xihao Hu, Kevin Y. Yip, Michael Q. Zhang and Zhi John Lu (2015) A common set of distinct features that characterize noncoding RNAs across multiple species. Nucleic Acids Research 43(1): 104-114.

u-Cheng T. Yang*, Chao Di*, Boqin Hu*, Meifeng Zhou, Yifang Liu, Nanxi Song, Yang Li, Jumpei Umetsu and Zhi John Lu (2015) CLIPdb: a CLIP-seq database for protein-RNA interactions. BMC Genomics In press. (*contributed equally)

hao Di*, Jiapei Yuan*, Yue Wu, Jingrui Li, Huixin Lin, Long Hu, Ting Zhang, Yijun Qi, Mark B. Gerstein, Yan Guo and Zhi John Lu (2014) Characterization of Stress-responsive lncRNAs in Arabidopsis thaliana by Integrating Expression, Epigenetic and Structural Features. The Plant Journal 80:848–861

u ZJ*, Yip KY*, Wang G, Shou C, Hillier LW, et al. (2011) Predicting and characterizing non-coding RNA in C. elegans by integrating conservation, secondary structure and high-throughput sequencing and array data. Genome Research 21: 276-2857 (*contributed equally) [modENCODE special issue – Cover Story]

erstein MB *#, Lu ZJ*, Van Nostrand EL*, Cheng C*, Arshinoff BI*, et al. (2010) Integrative analysis of the Caenorhabditis elegans genome by the modENCODE project. Science 330(6012): 1775-1787 (*co-first authors, #corresponding authors) [Cover Story]

Gerstein MB, Joel Rozowsky, Koon-Kiu Yan, Lu Z, Thomas Gingeras and Robert Waterston (2014) Comparative Analysis of the Transcriptome across Distant Species. Nature 512(7515):445-448.

Yang YC, Umetsu J, Lu ZJ (2014) Global signatures of protein binding on structured RNAs in Saccharomyces cerevisiae. Science China Life Sciences (Tsinghua Special Issue) 57:1, 22-35

Hu X, Wong TKF, Lu ZJ, Chan TF, Lau TCK, Yiu SM and Yip KY. (2014) Computational Identification of Protein Binding Sites on RNAs using High-Throughput RNA Structure-Probing Data. Bioinformatics vol. 30, no. 8, pp. 1049-1055.

Freeberg MA, Han T, Moresco JJ, Kong A, Yang YC2, Lu ZJ2, Yates JR, Kim JK. (2013) Pervasive and dynamic protein binding sites of the mRNA transcriptome in Saccharomyces cerevisiae. Genome Biology 14 (2), R13. (2Lu Lab, School of Life Sciences, Tsinghua University)

Kudron M, Niu W, Lu ZJ, Wang GL, Gerstein MB, Snyder M, Reinke V. (2013) Tissue-specific direct targets of Caenorhabditis elegans Rb/E2F dictate distinct somatic and germline programs. Genome Biology. 14 (1), R5.

ENCODE Project Consortium#. (2012) An Integrated Encyclopedia of DNA Elements in the Human Genome. Nature 489, 57–74. (#Lu Z is part of ENCODE Consortium) [Cover Story]

Tan X, Hu L2, Luquette LJ, Gao G, Liu YF2, Qu HJ, Xi RB, Lu ZJ2, Park PJ & Elledge SJ. (2012) Systematic Identification of Synergistic Drug Pairs Targeting HIV. Nature Biotech. 30:1125-1130 (2Lu Lab, School of Life Sciences, Tsinghua University)

Tan X, Lu ZJ 2, Gao G, Xu QK, Hu L2, Fellmann C, Li MZ, Qu HJ, Lowe SW, Hannon GJ & Elledge SJ. (2012) Tiling genomes of pathogenic viruses identifies potent antiviral shRNAs and reveals a role for secondary structure in shRNA efficacy. Proc. Natl. Acad. Sci. U. S. A., 109(3): 869-74 (2Lu Lab, School of Life Sciences, Tsinghua University)

He CF, Li YX, Zhang GX, Gu ZG, Yang R, Li J, Lu ZJ, Zhou ZH, Zhang CY, Wang J. (2012) MiRmat: Mature microRNA Sequence Prediction. PLoS ONE 7(12):e51673.

Niu W, Lu ZJ, Zhong M, Sarov M, Murray JI, et al. (2011) Diverse transcription factor binding features revealed by genome-wide ChIP-seq in C. elegans. Genome Research 21: 245-254.

Mu XJ, Lu ZJ, Kong Y, Lam HYK, Gerstein MB (2011) Analysis of genomic variation in non-coding elements using population-scale sequencing data from the 1000 Genomes Project. Nucleic Acids Research, 39 (16): 7058-7076.

Li Y, Du X, Lu ZJ, Wu D, Zhao Y, et al. (2011) Regulatory Feedback Loop of Two phz Gene Clusters through 5′-Untranslated Regions in Pseudomonas sp. M18. PLoS ONE 6(4): e19413

ENCODE Project Consortium# (2011) A user's guide to the encyclopedia of DNA elements (ENCODE). PLoS Biology 9: e1001046. (#Lu Z is part of ENCODE Consortium)

Cheng C, Yan KK, Hwang W, Qian J, Bhardwaj N, Rozowsky J, Lu ZJ, Niu W, Alves P, Kato M, Gerstein MB. (2011) Construction and analysis of an integrated regulatory network derived from high-throughput sequencing data. PLoS Comput Biol 7: e1002190

Zhong M, Niu W, Lu ZJ, Sarov M, Murray JI, et al. (2010) Genome-wide identification of binding sites defines distinct functions for Caenorhabditis elegans PHA-4/FOXA in development and environmental response. PLoS Genetics 6(2): e1000848.

Lu ZJ, Gloor JW, Mathews DH (2009) Improved RNA secondary structure prediction by maximizing expected pair accuracy. RNA 15: 1805-1813.

Lu ZJ, Mathews DH (2008) OligoWalk: an online siRNA design tool utilizing hybridization thermodynamics. Nucleic Acids Research 36:W104-W108.

Lu ZJ and Mathews DH (2008) Efficient siRNA selection using hybridization thermodynamics. Nucleic Acids Research 36:640-647.

Lu ZJ, Mathews DH. (2008) Fundamental differences in the equilibrium considerations for siRNA and antisense oligodeoxynucleotide design. Nucleic Acids Research 36:3738-3745.

Lu ZJ, Turner DH, Mathews DH (2006) A set of nearest neighbor parameters for predicting the enthalpy change of RNA secondary structure formation. Nucleic Acids Research 34:4912-4924.


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