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谢鹭博士介绍(PI)

 

xielu谢鹭
博士,研究员,博导
副主任,党支部副书记
上海生物信息技术研究中心/上海科学院
上海市科苑路1278号2楼,邮编201203
电话/传真:021-20283705
邮箱:
luxiex2017@outlook.com
网页:http://www.scbit.org


谢鹭,博士,研究员,博导。上海生物信息技术研究中心副主任,党支部副书记。

教育训练:
1985.9-2000.7:中南大学湘雅医学院,六年制临床医学本科(1985-1991),肿瘤免疫学硕士(1991-1994),实习研究员(1994-1996),肿瘤病理生理学博士(1996-2000)。于2000年获中南大学医学博士学位。
2000.8-2005.7:美国范德堡大学(Vanderbilt University)医学院,博士后。采用基因芯片技术、蛋白质质谱技术、生物信息学数据挖掘进行肿瘤分子机制研究。

工作经历:
2005.8-目前(2016.3):上海生物信息技术研究中心。创建应用医学研究组(2005-)。为副研究员(2005-2009),研究员(2010-)。任主任助理(2008-2011),党支部副书记(2012-),副主任(2013-)。兼任生物信息研发服务事业部主管(2014-)。

承担项目:
曾主持或作为参与单位负责人主持973子课题一项,863课题三项(一项在研),科技重大专项三项(十一五、十二五、十三五在研),国家自然科学基金两项(一项在研),中国人类蛋白质国际合作项目两项(在研),以及多项上海市地方课题。

发表论文:
截至2016年3月国内外已发表学术论文超过100篇,其中国际杂志SCI论文的总影响因子接近300分,引用次数超过2000次。文章全文可从ResearchGate网站查阅,账号:Lu Xie.链接:https://www.researchgate.net/profile/Lu_Xie4

科技奖励:
曾获上海市自然科学一等奖(2014:蛋白质功能特征的生物信息学系统研究),上海市五一巾帼创新奖(2010:个人),上海市浦江人才(2006),美国癌症协会(AACR)年会年轻学者奖(2004),湖南省科技进步二等奖(2001:鼻咽癌抗独特型抗体的制备及主动免疫研究),湖南省医药卫生科学技术进步一等奖(1996)。

荣誉称号:
曾获2010-2014年度上海市先进工作者(劳模);2011-2012年度上海市三八红旗手标兵提名奖。

学术任职:
上海市生物信息学会理事,中国生物化学与分子生物学会蛋白质组学专业委员会委员,中国医药生物技术协会生物信息技术分会委员会委员,上海市浦东新区科技发展基金专家。南京医科大学兼职博导,复旦大学、上海理工大学、上海海洋大学、上海师范大学兼职硕导。

生物信息研发服务部工作方向:

研究领域:蛋白质功能研究涉及定位、定量、翻译后修饰到相互作用,现集中于蛋白质功能网络的多组学水平数据注释及整合分析;转化医学研究主要从事各遗传信息水平分子标记物筛选、临床预后疗效等预测模型建立,现拓展到药物重定位以及网络药物研究。总的宗旨是利用生物信息学手段分析多组学数据以及临床数据,为临床应用转化提供理论基础和软件工具。
提供服务:基因组、转录组、表观遗传组测序数据分析;临床预后或疗效预测建模;信号通路或功能网络分析;定制数据库;定制多组学数据整合分析。
软件工具:拥有十多项软件著作权,提供蛋白质翻译后修饰、肿瘤差异蛋白质、磷酸化蛋白质及信号通路数据库及分析平台,提供肝癌预后分子数据库及在线建模工具。主要如下:
dbPHCC:肝癌预后分子数据库及在线预后建模,http://lifecenter.sgst.cn/dbphcc/
PhoSigNet:磷酸化介导的人信号通路网络构建和分析,http://lifecenter.sgst.cn/PhoSigNet/
SysPTM 2.0:综合蛋白质翻译后修饰数据库和分析工具,http://lifecenter.sgst.cn/SysPTM/
dbDEPC 2.0:人肿瘤差异表达蛋白质数据库,http://lifecenter.sgst.cn/dbDEPC/index.do
SyStemCell:干细胞多组学数据库及整合分析工具,http://lifecenter.sgst.cn/SyStemCell/

团队照片:

group


本研究组招收博士后,欢迎有相关研究背景和兴趣的博士毕业生加入。

代表性论文:
【2016】
dbPHCC: a database of prognostic biomarkers for hepatocellular carcinoma that provides online prognostic modeling.
Jian Ouyang, Ying Sun, Wei Li, Wen Zhang, Dandan Wang, Xiangqiong Liu, Yong Lin, Baofeng Lian, Lu Xie.
Biochimica et Biophysica Acta, 2016, http://dx.doi.org/10.1016/j.bbagen.2016.02.017

【2015】
Construction and deciphering of human phosphorylation mediated signaling transduction network.
Menghuan Zhang, Hong Li, Ying He, Jing Li, Li Xia, Lishun Wang, Peng Cui, Bo Sun, Jing Li, Yixue Li, Lu Xie.
Journal of Proteome Research. 2015, DOI: http://dx.doi.org/10.1021/acs.jproteome.5b00249

Revealing Missing Human Protein Isoforms Based on Ab Initio Prediction, RNA-seq and Proteomics.
Zhiqiang Hu, Hamish S. Scott, Guangrong Qin, Guangyong Zheng, Xixia Chu, Lu Xie, David L. Adelson, Bergithe E. Oftedal, Parvathy Venugopal, Milena Babic, Christopher N. Hahn, Bing Zhang, Xiaojing Wang, Nan Li & Chaochun Wei.
Scientific Reports. 2015, 5:10940 | DOI: 10.1038/srep10940.

Identification of HPV integration and gene mutation in HeLa cell line by integrated analysis of RNA-Seq and MS/MS data.
Han Sun, Chen Chen, Baofeng Lian, Menghuan Zhang, Xiaojing Wang, Bing Zhang, Yixue Li, Pengyuan Yangand Lu Xie.
J Proteome Research. 2015, DOI: http://dx.doi.org/10.1021/pr500944c.

Identifying Prognostic Features by Bottom-up Approach and Correlating to Drug Repositioning.
Wei Li, Jian Yu, Baofeng Lian, Han Sun, Jing Li, Menghuan Zhang, Ling Li, Yixue Li, Qian Liu, Lu Xie.
Plos ONE. 2015, DOI: 10.1371/journal.pone.0118672

【2014】
Integration of mass spectrometry and RNA-Seq data to confirm human ab initio predicted genes and lncRNAs.
Han Sun, Chen Chen, Meng Shi, Dandan Wang, Mingwei Liu, Daixi Li, Pengyuan Yang, Yixue Li, Lu Xie.
Proteomics. 2014, 14, 2760–2768

Integrative Analysis of Transcriptional Regulatory Network and Copy Number Variation in Intrahepatic Cholangiocarcinoma.
Ling Li, Baofeng Lian, Chao Li, Wei Li, Jing Li, Yuannv Zhang, Xianghuo He, Yixue Li, Lu Xie. PloS ONE. 2014, doi: 10.1371/journal.pone.0098653

SysPTM 2.0: an updated systematic resource for post-translational modification.
Jing Li, Jia Jia, Hong Li, Jian Yu, Han Sun, Ying He, Daqing Lv, Xiaojuan Yang, Michael O. Glocker, Liangxiao Ma, Jiabei Yang, Ling Li, Wei Li, Guoqing Zhang, Qian Liu, Yixue Li, Lu Xie.
Database(Oxford).2014, doi: 10.1093/database/bau025

PU.1 is essential for MLL leukemia partially via crosstalk with the MEISHOX pathway.
J Zhou, J Wu, B Li, D Liu, J Yu, X Yan, S Zheng, J Wang, L Zhang, L Zhang, F He, Q Li, A Chen, Y Zhang, X Zhao, Y Guan, X Zhao, J Yan, J Ni, M A Nobrega, B Löwenberg, R Delwel, P J M Valk, A Kumar, L Xie, D G Tenen, G Huang and Q-f Wang.
Leukemia. 2014, doi: 10.1038/leu.2013.384

Comparative analysis of viral protein interaction networks in Hepatitis B Virus and Hepatitis C Virus infected HCC.
Weilan Yuan, Tao Huang, Jian Yu, Lingyao Zeng, Baofeng Lian, Qinwen He, Yixue Li, Xiaoyan Zhang, Fengli Zhou, Lu Xie.
Biochimica et Biophysica Acta (BBA) – Proteins and Proteomics. 2014, 1844 (1): 271

【2013】
Identification of Gene Fusions from Human Lung Cancer Mass Spectrometry Data.
Han Sun, Xiaobin Xing, Jing Li, Fengli Zhou, Yunqin Chen, Ying He, Wei Li, Guangwu Wei, Xiao Chang, Jia Jia, Yixue Li, Lu Xie.
BMC Genomics. 2013, doi:10.1186/1471-2164-14-S8-S5.

Phosphoproteomics Study on the Activated PKCδ-Induced Cell Death.
Li Xia, Tong-Dan Wang, Shao-Ming Shen, Meng Zhao, Han Sun, Ying He, Lu Xie, Zhao-Xia Wu, San-Feng Han, Li-Shun Wang, Guo-Qiang Chen.
Journal of Proteome Research. 2013, 12(10):4280-301

miR-612 Suppresses the Invasive-Metastatic Cascade in Hepatocellular Carcinom.
Zhong-Hua Tao, Jin-Liang Wan, Ling-Yao Zeng, Lu Xie, Hui-Chuan Sun, Lun-Xiu Qin, Lu Wang, Jian Zhou, Zheng-Gang Ren, Yi-Xue Li, Jia Fan, Wei-Zhong Wu.
Journal of Experimental Medicine. 2013, 210(4):789-803. doi: 10.1084/jem.20120153.

【2012】
Novel biomarkers for pre-diabetes identified by metabolomics.
Rui Wang-Sattler, Zhonghao Yu, Christian Herder, Ana C. Messias, Anna Floegel, Ying He, Katharina Heim, Monica Campillos, Christina Holzapfe, Barbara Thorand, Harald Grallert, Tao Xu, Erik Bader, Cornelia Huth, Kirstin Mittelstrass, Angela Döring, Christa Meisinger, Christian Gieger, Cornelia Prehn, Werner Roemisch-Marg, Maren Carstensen, Lu Xie, Hisami Yamanaka-Okumura, Guihong Xing, Uta Ceglarek, Joachim Thiery, Guido Giani, Heiko Lickert, Xu Lin, Yixue Li, Heiner Boeing, Hans-Georg Joost, Martin Hrabé de Angelis, Wolfgang Rathmann, Karsten Suhre, Holger Prokisch, Annette Peters, Thomas Meitinger, Michael Roden, H.-Erich Wichmann, Tobias Pischon, Jerzy Adamski, Thomas Illig.
Molecular Systems Biology. 2012, (8): doi:10.1038/msb.2012.43

SyStemCell: a database populated with multiple levels of experimental data from stem cell differentiation research.
Jian Yu, Xiaobin Xing, Lingyao Zeng, Jiehuan Sun, Wei Li, Han Sun, Ying He, Jing Li, Chuan Wang, Guoqing Zhang, Yixue Li, and Lu Xie.
PLoS ONE. 2012, doi:10.1371/journal.pone.0035230.

Differential combinatorial regulatory network analysis related to venous metastasis of hepatocellular carcinoma.
Lingyao Zeng, Jian Yu, Tao Huang, Huliang Jia, Qiongzhu Dong, Fei He, Weilan Yuan, Lunxiu Qin, Yixue Li, Lu Xie.
BMC Genomics. 2012, 13(8):1-14

Cell Type Specificity of Signaling: View from Membrane Receptors Distribution and Their Downstream Transduction Networks.
He Y, Yu Z, Ge D, Wang-Sattler R, Thiesen HJ, Xie L, Li Y.
Protein & Cell. 2012, DOI: 10.1007/s13238-012-2049-y.

dbDEPC 2.0: updated database of differentially expressed proteins in human cancers.
Ying He, Menghuan Zhang, Yuanhu Ju, Zhonghao Yu, Daqing Lv, Han Sun, Weilan Yuan, Fei He, Jianshe Zhang, Hong Li, Jing Li, Rui Wang-Sattler Yixue Li, Guoqing Zhang and Lu Xie.
Nucleic Acids Research. 2012 Jan; 40(Database issue): D964–D971. DOI:10.1093/nar/gkr936.

【2011】
SySAP: a system-level predictor of deleterious single amino acid polymorphisms.
Tao Huang, Chuan Wang, Guoqing Zhang, Lu Xie, Yixue Li.
Protein & Cell. 2011, DOI 10.1007/s13238-011-1130-2


The discovery of novel protein-coding features in mouse genome based on mass spectrometry data.
Xiaobin Xing, Qingrun Li, Han Sun, Xing Fu, Fei Zhan, Xiu Huang, Jing Li, Chunlei Chen, Yu Shyr, Rong Zeng, Yixue Li, Lu Xie.
Genomics. 2011, DOI: 10.1016/j.ygeno.2011.07.005

The role of hepatitis C virus in the dynamic protein interaction networks of hepatocellular cirrhosis and carcinoma.
Tao Huang, Lei Liu, Qi Liu, Guohui Ding, Eugene Tan, Zhidong Tu, Yixue Li, Hongyue Dai, Lu Xie.
International Journal of Computational Biology and Drug Design.2011, 4(1): 5-18.

【2010】
Using GeneReg to construct time delay gene regulatory networks.
Tao Huang, Lei Liu, Ziliang Qian, Kang Tu, Yixue Li, Lu Xie.
BMC Research Notes. 2010, 3:142.

TF-centered downstream gene set enrichment analysis: Inference of causal regulators by integrating TF-DNA interaction and protein post-translational modification information.
Qi Liu, Yejun Tan, Tao Huang, Guohui Ding, Zhidong Tu, Lei Liu, Yixue Li, Hongyue Dai, Lu Xie.
BMC Bioinformatics. 2010, doi: 10.1186/1471-2105-11-S11-S5.

Cross-platform microarray data integration combining meta-analysis and gene set enrichment analysis.
Jian Yu, Jun Wu, Miaoxin Li, Yajun Yi, Yu Shyr, Yixue Li, Lu Xie.
Interdisciplinary Research and Applications in Bioinformatics, Computational Biology, and Environmental Sciences,Chapter 2, page 12-27, published in the United States of America by Medical Information Science Reference (an imprint of IGI Global)

Acetylation of Metabolic Enzymes Coordinates Carbon Source Utilization and Metabolic Flux.
Qijun Wang, Yakun Zhang, Chen Yang, Hui Xiong, Yan Lin, Jun Yao,Hong Li, Lu Xie, Wei Zhao, Yufeng Yao, Zhi-Bin Ning, Rong Zeng, Yue Xiong, Kun-Liang Guan, Shimin Zhao, Guo-Ping Zhao.
Science. 2010,327, 1004; DOI: 10.1126/science.1179687

dbDEPC: a database of Differentially Expressed Proteins in human Cancers.
Hong Li, Ying He, Guohui Ding, Chuan Wang, Lu Xie and Yixue Li.
Nucleic Acids Research.2010 Jan;38 (Database issue): D658-64.

Elevation of receptor tyrosine kinase EphA2 mediates resistance to trastuzumab therapy.
Zhuang G, Brantley-Sieders DM, Vaught D, Yu J, Xie L, Wells S, Jackson D, Muraoka-Cook R, Arteaga C, Chen J.
Cancer Research. 2010, 70(1):299-308.

【2009】
SysPTM – a Systematic Resource for Proteomic Research of Post-translational Modifications.
Hong Li, Xiaobin Xing, Guohui Ding, Qingrun Li, Chuan Wang, Lu Xie, Rong Zeng, Yixue Li. Molecular and Cellular Proteomics.2009, 8 (8): 1839-1849.

Combinatorial network of primary and secondary microRNA-driven regulatory mechanisms.
Kang Tu, Hui Yu, Youjia Hua, Yuan-Yuan Li, Lei Liu, Lu Xie, Yixue Li.
Nucleic Acids Research.2009, 37 (18): 5969-5980.

PAnnBuilder: An R Package for Assembling Proteomic Annotation Data.
Hong Li, Guohui Ding, Lu Xie, Yixue Li.
Bioinformatics.2009, doi: 10.1093/bioinformatics/btp100.

Improved Prediction of Lysine Acetylation by Support Vector Machines.
Songling Li, Hong Li, Mingfa Li, Yu Shyr, Lu Xie, Yixue Li.
Protein and Peptide Letters, 2009, 16(8): 977-983.

Web-based Interrogation of Gene Expression Signatures Using EXALT.
Jun Wu, Qingchao Qiu, Lu Xie, Joseph Fullerton, Jian Yu, Yu Shyr, Alfred L George Jr and Yajun Yi.
BMC Bioinformatics.2009, 10:420.

【2008】
The prediction of interferon treatment effects based on time series microarray gene expression profiles.
Tao Huang , Kang Tu, Yu Shyr, Chao-Chun Wei, Lu Xie and Yi-Xue Li.
Journal of Translational Medicine.2008, 6:44.

MicroRNA Signatures in Hepatocellular Carcinoma Diagnostic and Prognostic Implications.
Wenxi Li, Lu Xie, Xianghuo He, Jinjun Li, Kang Tu, Lin Wei , Jun Wu, Yong Guo, Xi Ma, Pingping Zhang, Zhimei Pan, Xin Hu, Yingjun Zhao, Haiyang Xie, Guoping Jiang, Taoyang Chen, Jianneng Wang, Shusen Zheng, Jing Cheng, Dafang Wan, Shengli Yang, Yixue Li, Jianren Gu.
International Journal of Cancer. 2008, 123(7):1616-1622.

【2007及更早】
A Transcript-level View of Affymetrix Probesets Enhances the Interpretation and Exploitation of Gene Expression Data.
Hui Yu, Feng Wang, Kang Tu, Lu Xie, Yuan-Yuan Li, Yi-Xue Li.  
BMC Bioinformatics.2007, 8(1):194.

Genomic and proteomic Analysis of Mammary Tumors Arising in Transgenic Mice.
Lu Xie, Jonathan B. Xu, Agnes Gorska, Yu Shyr, Sara Schwartz, Nikki Cheng, Shawn Levy, Brian Bierie , Richard Caprioli, Harold Moses.
Journal of Proteome Research.2005, 4: 2088-2098.

Activation of the Erk pathway is required for TGF-ß1-induced epithelial to mesenchymal transition in vitro.
Lu Xie, Brian Law, Anna Chytil, Kimberly Brown, Mary Aakre and Harold Moses.
Neoplasia,2004, 6(5): 603-610.

Transforming growth factor beta-regulated gene expression in a mouse mammary gland epithelial cell line.
Lu Xie, Brian K Law, Mary E Aakre, Mary Edgerton, Yu Shyr, Neil A Bhowmick and Harold L Moses.
Breast Cancer Research.2003, 5: R187-R198

Basic Study and Phase I Clinical Trial of Anti-Idiotypic Antibody Mimicking Nasopharyngeal Carcinoma Cell Antigen.
Xie Lu, Li Guancheng, Li Xiaoling, Yang Jianfei, Zhu Jiangao, Zhou Guohua, Cai Xiaohong and Sun Qubing.
Chinese Journal of Cancer Research.1997, 9(2):127-132.