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Principal Investigator (Lu Xie, Ph.D.)

 

xieluLu XIE, Ph.D., M.D., Professor
Vice Director
Shanghai Center for Bioinformation Technology,
Shanghai Academy of Science and Technology
1278 Keyuan Rd. Fl. 2, Shanghai 201203, P.R.China
Tel: +86-21-20283705. Email: xielu@scbit.org

Introduction to the Principal Investigator of Translational Medicine
Research Group

Lu XIE, Ph.D., M.D., Professor, PI of Translational Medicine Research Group. Vice Director of Shanghai Center for Bioinformation Technology. She got her M.D. and Ph.D. in Xiangya Medical College of Central South University in 2000. She was a Postdoctoral Research Fellow in Medical Center of Vanderbilt University in USA during 2000.8-2005.7. She joined Shanghai Center for Bioinformation Technology in 2005.8 and established the Translational Medicine Research Group. She became a full professor in 2010.4. Lu XIE had six years of Clinical Medicine training, but her major career was in Cancer Research. Her research directions have transited through years from Tumor Immunology, Tumor Pathophysiology, to Cancer Bioinformatics, and Proteomics Bioinformatics. She therefore owns a mixed academic background of Medicine, Experimental Oncology and Bioinformatics. She once won the Second Level Science and Technology Advancement Award of Hunan Province (2001), once won the first Level Medical and Health Science Technology Advancement Award of Hunan Province (1996), once won Scholar-in-Training Award of American Association for Cancer Research (AACR, 2004), and twice won Postdoctoral Research Funds from Vanderbilt University (2001-2003). She has undertaken more than 10 national and local research projects, including National Key Basic Research Plan (“973”Plan), National High Science and Technology Development Plan (“863”Plan), Key Projects with Infectious Diseases (issued by Ministry of Science and Technology of China), National Natural Science Foundation Project, etc. Her group has developed more than 10 bioinformatics software and tools. She has published more than 80 scientific papers. She was awarded Shanghai Pujiang Talents in 2006, Shanghai Women’s Innovation Prize in 2010. She won Nomination Award for Shanghai Distinguished Women (2011-2012). She is a committee member for Proteomics Committee of Chinese Biochemistry and Molecular Biology Society. She is a Board Member for Shanghai Bioinformatics Society.

Main research directions of Translational Medicine Group:
1. Cancer Bioinformatics: Including Cancer Genomics; Regulatory Network; Biomarker discovery; Clinical Prediction Modeling.
2. Proteomics Bioinformatics: Including Post-translational Modification Database Construction and Functional Studies; Protein Functional Annotation and Signal Transduction; Proteogenomics.

Scientific Research Projects Undertaken by Translational Medicine Research Group:
1. “The Addition and Revision to Protein Coding Genes in Genome Based on High-accuracy Tandem Mass Spectrometry Data”(2010CB912702). National Key Basic Research Plan(“973”Plan),2009.12-2014.12. PI: Lu XIE.
2. “The Reconstruction of Phosphorylation-mediated Intracellular Signaling Transduction Network”。National Natural Science Foundation (31070752). 2011.1-2013.12. PI: Lu XIE.
3. Key Projects with Infectious Diseases (AIDs and Virus Hepatitis etc.) issued by the Ministry of Science and Technology under the Twelfth Five-Year Plan(2012ZX10002012-014:the Construction of Regulatory Network in Liver Cancer Metastasis). 2011.6-2014.12. Lu XIE: Co-PI.
4. Key Projects with Infectious Diseases (AIDs and Virus Hepatitis etc) issued by the Ministry of Science and Technology under the Eleventh Five-Year Plan(2008ZX10002-021:The Studies of New Strategies on Liver Cancer Metastasis and Recurrence Related Molecular Biomarker, Prediction and  Intervention). 2008.10-2011.5. Lu XIE: Co-PI.
5. “Development of Collaborative Software for High-throughput Quantitative Proteomics Data Analysis Workflow” (2009AA02Z304). National High Science and Technology Development Plan(“863”Plan). 2008.12-2011.12. PI: Lu XIE.
6. “The Bioinformatics Study on the Difference in Transcription and Translation Level in Malignant Tumors”( 06PJ14073). Shanghai Pujiang Talents Program. 2006.9- 2008.9. PI: Lu XIE.
7. “Bioinformatics Integrative Network Analysis of mRNA and microRNA Biomarkers in Tumors” (08ZR1415800). Shanghai Natural Science Foundation. 2008.10-2010.9. PI: Lu XIE.
8. “Finding Disease Causal Factors from Transcriptome Data”. A Joint Postdoctoral Research Project Between Merck Co. and Shanghai Center for Bioinformation Technology. 2008.9-2010.12. Lu XIE: Co-PI.
9. “Major Brain Diseases Related Functional Proteomics Study” (04DZ14005). Shanghai Key Basic Research Project. 2004.8-2007.12. Lu XIE: Co-PI.

Notice: Translational Medicine Research Group is recruiting an Assistant Professor in Proteomics Bioinformatics, for details please refer to our Job Opportunity webpage. For those who are interested, please contact Dr. Lu XIE at: E-mail: xielu@scbit.org, Tel: 021-20283705.

Representative Publications in recent three years (for full publication list please refer to: https://forum-iamscbit.rhcloud.com/viewtopic.php?f=19&t=42):
1. Han Sun, Xiaobin Xing, Jing Li, Fengli Zhou, Yunqin Chen, Ying He, Wei Li, Guangwu Wei, Xiao Chang, Jia Jia, Yixue Li, Lu Xie*. Identification of Gene Fusions from Human Lung Cancer Mass Spectrometry Data. BMC Genomics. 2013, 14(Suppl 8):S5) doi:10.1186/1471-2164-14-S8-S5.
2. 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. Phosphoproteomics Study on the Activated PKCδ-Induced Cell Death. Journal of Proteome Research. 2013 Oct 4;12(10):4280-301.
3. Weilan Yuan, Tao Huang, Jian Yu, Lingyao Zeng, Baofeng Lian, Qinwen He, Yixue Li, Xiaoyan Zhang, Fengli Zhou, Lu Xie*. Comparative analysis of viral protein interaction networks in Hepatitis B Virus and Hepatitis C Virus infected HCC. Biochimica et Biophysica Acta (BBA) - Proteins and Proteomics. Available online 14 June 2013  http://dx.doi.org/10.1016/j.bbapap.2013.06.002
4. 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. miR-612 Suppresses the Invasive-Metastatic Cascade in Hepatocellular Carcinom.Journal of Experimental Medicine. 2013, 210(4):789-803. doi: 10.1084/jem.20120153.
5. 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. Novel biomarkers for pre-diabetes identified by metabolomics. Molecular Systems Biology. 2012, (8): doi:10.1038/msb.2012.43.
6. 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*. SyStemCell: a database populated with multiple levels of experimental data from stem cell differentiation research. PLoS ONE. 2012 7(7): e35230. doi:10.1371/journal.pone.0035230.
7. Lingyao Zeng, Jian Yu, Tao Huang, Huliang Jia, Qiongzhu Dong, Fei He, Weilan Yuan, Lunxiu Qin, Yixue Li, Lu Xie*. Differential combinatorial regulatory network analysis related to venous metastasis of hepatocellular carcinoma. BMC Genomics. 2012, 13(Suppl 8):S14.  http://www.biomedcentral.com/1471-2164/13/S8/S14.
8. Ying He, Zhonghao Yu, Jing Li, Rui Wang-Sattler, Lu Xie*, Yixue Li. Cell Type Specificity of Signaling: View from Membrane Receptors Distribution and Their Downstream Transduction Networks. Protein & Cell. 2012, DOI: 10.1007/s13238-012-2049-y.
9. Ying He, Zhonghao Yu, Ina Giegling, Lu Xie, Annette M. Hartmann, Cornelia Prehn, Jerzy Adamski, Rene Kahn, Yixue Li, Thomas Illig, Rui Wang-Sattler, Dan Rujescu. Schizophrenia shows a unique metabolomics signature in plasma. Translational Psychiatry. 2012 Aug 14;2:e149. doi: 10.1038/tp.2012.76.
10. Tao Huang, Chuan Wang, Guoqing Zhang, Lu Xie*, Yixue Li. SySAP: a system-level predictor of deleterious single amino acid polymorphisms. Protein & Cell. Accepted November 14, 2011.  DOI 10.1007/s13238-011-1130-2. (2013 IF=3.22)
11. 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*. dbDEPC 2.0: updated database of differentially expressed proteins in human cancers. Nucleic Acids Research. 2011, 1-8. doi:10.1093/nar/gkr936. Advance Access published November 16, 2011.
12. Xiaobin Xing, Qingrun Li, Han Sun, Xing Fu, Fei Zhan, Xiu Huang, Jing Li, Chunlei Chen, Yu Shyr, Rong Zeng, Yixue Li, Lu Xie*. The discovery of novel protein-coding features in mouse genome based on mass spectrometry data. Genomics. Volume 98, Issue 5, November 2011, Pages 343-351. Online 4-AUG-2011 DOI: 10.1016/j.ygeno.2011.07.005.
13. Tao Huang, Jian Zhang, Lu Xie, Xiao Dong, Lei Zhang, Yu-Dong Cai, Yi-Xue Li. Dynamic Cross-Tissue Co-Expression Network of Aging. OMICS: A Journal of Integrative Biology. Volume: 15 Issue 10: October 6, 2011 Online Ahead of Print: July 13, 2011.
14. Tao Huang, Lei Liu, Qi Liu, Guohui Ding, Eugene Tan, Zhidong Tu, Yixue Li, Hongyue Dai, Lu Xie*. The role of hepatitis C virus in the dynamic protein interaction networks of hepatocellular cirrhosis and carcinoma. International Journal of Computational Biology and Drug Design 2011, 4(1): 5-18.

Introduction of Representative Software:

12dbDEPC

The database of Differentially Expressed Proteins in Human Cancer (dbDEPC)  has more than 4000 protein entries, curated from 331 experiments across 20 types of human cancers. This resource allows researchers to search whether their interested proteins have been reported changing in certain cancers, to compare their own proteomic discovery with previous studies, to picture selected protein expression heatmap across multiple cancers and to relate protein expression changes with aberrance in other genetic level. 
http://lifecenter.sgst.cn/dbdepc/index.do
 

23PAnnBuilder
PAnnBuilder is an R package to automatically assemble protein annotation information from public resources to provide uniform annotation data for large-scale proteomic studies. Sixteen public databases have been parsed and fifty-four annotation packages have been constructed based on R environment or SQLite database. These ready-to-use packages cover most frequently needed protein annotation for three model species including human, mouse and rat. Several extended applications such as annotation based on protein sequence similarity are also provided.
 
http://www.biosino.org/PAnnBuilder/

23MGSEA
MGSEA is a tool which combines meta-analysis and Gene Set Enrichment Analysis to extract consistent expression pattern change from multiple microarray datasets at pathway level.
http://lifecenter.sgst.cn/mgsea/

2
SysPTM
SysPTM provides a systematic and sophisticated platform for proteomic PTM research, equipped not only with a knowledge base of manually curated multi-type modification data, but also with four fully developed, in-depth data mining tools.
http://www.biosino.org/SysPTM/


23Fudan Score
Fudan Score is a new outcome prediction system for Chinese HCC patients undergoing resective surgery treatment. It is a user-friendly web server that provide prediction of prognosis as well as post-operative adjuvant treatment recommendation.
http://lifecenter.sgst.cn/outcomeph/

2SyStemCell
The SyStemCell is a comprehensive database deposited with multiple levels of original qualitative and quantitative experiment information on stem cell researches, including DNA CpG Hydroxy/methylation, histone modification, transciptional factor regulation, transcript products, microRNA information, protein products, and phosphorylation proteins.  It aims to provide a basic platform for users to cross reference multiple-level experimental data of stem cells.
http://lifecenter.sgst.cn/SyStemCell/


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