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Principal Investigator ( Xuan Li, Ph. D.)

 

lixuanPrincipal Investigator:

Li Xuan, Ph.D. Professor. 
Dr Li graduated from Peking University in 1988 with a major in Biology. He received his Ph.D. from St. Louis University in 1996 with a major in Biochemistry. He was a postdoc fellow at Duke University studying the regulatory mechanism of immune development and immune response. His works were published over the years in
J Exp Med
PNAS, J Immunol, Genomics, etc. Dr Li held appointments at Curagen, GSK, and Misys Healthcare systems. He jointed Shanghai Center for Bioinformation Technology in 2007, and served as professor and Principal Investigator since then. Dr Li was selected and awarded from Shanghai and CAS scholarship programs. He has published over 30 research articles. 


Research Interests:

The major research interests of the Dr Li’s group are:
1) Functional genomics and evolution study of plants, microorganisms and insects. 2) Integration of omics data: genomics, transcriptomics, proteomics, and metabonomics, for meta-analysis. 3) Gene regulation networks of biological systems. 4) Applications of high-throughput sequencing, and analysis methods and pipeline.

Selected Publications:

Pan B, Sheng J, Sun W, Zhao Y, Hao P
*, Li X*. OrysPSSP: a comparative platform for small secreted proteins from rice and other plants. Nucleic Acids Res 2013; DOI: 10.1093/nar/gks1090.

Yu S, Zheng L, Li Y, Li C, Ma C, Yu Y, Li X,
Hao P. Causal co-expression method with module analysis to screen drugs with specific target. Gene 2013; DOI: 10.1016/j.gene.2012.11.051.

Wang Y, Yu Y, Pan B, Hao P, Li Y, Shao Z, Xu X
* and Li X*
. Optimizing hybrid assembly of next-generation sequence data from Enterococcus faecium: a microbe with highly divergent genome. BMC Systems Biology 2012; 6(Suppl 3):S21.

Yu S, Zheng L, Yu Y, Li Y, Wang Y, Ma C, Li Y, Li X* and Hao P*. A cross-species analysis method to analyze animal models’ similarity to human’s disease state. BMC Systems Biology 2012; 6(Suppl 3):S18. 

Wang YJ, Wang JF, Ping J, Yu Y, Wang Y, Lian P,
Li X, Li YX, Hao P. Computational Studies on the Substrate Interactions of Influenza A Virus PB2 Subunit. PLoS One 2012; 7(9): e44079.

Ping J, Wang Y, Yu Y, Li YX, Li X*, Hao P*. A comparative analysis of tissue gene expression data from high-throughput studies. Chinese Science Bulletin 2012; 57(22): 2920-2927.

Shao W, Zhao Q-Y, Wang XY, Xu X-Y, Tang Q, Li M, Li X* and Xu Y-Z*. Alternative splicing and trans-splicing events revealed by analysis of the Bombyx mori transcriptome. RNA 2012; 18(7):1395-407. (* Corresponding author)


Wang YJ, Wang JF, Li X, Shao ZF, Li YX, Hao P. Negatively cooperative binding properties of human Cytochrome P450 2E1 with monocyclic Substrates. Curr Drug Metab 2012; 13(7):1024-31.

Chen Y, Liu F, Yang B, Lu A, Wang S, Wang J, Ling QZ, Li X, Beerntsen BT, Ling E.
Specific amino acids affecting Drosophila melanogaster prophenoloxidase activity in vitro. Dev Comp Immunol 2012; 38(1):88-97

Wang J-F, Hao P, Li Y-X, Dai J-L, Li X. Exploration of conformational transition in the aryl-binding site of human FXa using molecular dynamics simulations. J Mol Model 2012;18(6):2717-25.

Zhao Q-Y, Wang Y, Kong Y-M, Luo D, Li X* and Hao P*. Optimizing de novo transcriptome assembly from short-read RNA-Seq data: a comparative study. BMC Bioinformatics 2011; 12(Suppl 14):S2.

Li Y, Tu K, Zheng S, Wang J, Li Y-X, Hao P, Li X*. Association of feature gene expression with structural fingerprints of chemical compounds. J Bioinform Comput Biol 2011;9(4):503-19

Zhong Y, Chang X, Cao X, Zhang Y, Zheng H-J, Zhu Y-Z, Cai C-S, Li Y-Y, Zhao G-P, Wang S-Y, Li Y-X*, Zeng R*, Li X*, Guo X-K*. Comparative Proteogenomic Analysis of the Leptospira interrogans Virulence Attenuated Strain IPAV against the Pathogenic Strain 56601. Cell Res 2011;21(8):1210-29.

Wei W, Liu F, Liu L, Li Z, Zhang X, Jiang F, Shi Q, Zhou X, Sheng W, Cai S, Li X*, Xu Y*, Nan P*. Distinct mutations in MLH1 and MSH2 genes in Hereditary Non-polyposis Colorectal Cancer (HNPCC) families from China. BMB Rep 2011;44(5):317-22.

Hao P, Zheng H, Yu Y, Ding G, Gu W, Chen S, Yu Z, Ren S, Oda M, Konno T, Wang S, Li X*, Ji Z-S* and Zhao G*. Complete sequencing and pan-genomic analysis of Lactobacillus delbrueckii subsp. bulgaricus reveal its genetic basis for industrial yogurt production. PLoS One 2011; 6(1):e15964.

Yu Y, Xu T, Yu Y, Hao P*, Li X*. Association of tissue lineage and gene expression: conservatively and differentially expressed genes define common and special functions of tissues. BMC Bioinformatics 2010; 11(Suppl 11):S1.

Xu T, Yu Y, Yu T, Yu Y, Hao P*, Li X*. Revealing parasite influence in metabolic pathways in Apicomplexa infected patients. BMC Bioinformatics 2010; 11(Suppl 11):S13.

韦雯倩, 南蓬, 陈燕,张晓艳, 李轩, 刘雷, 李作峰. Protégé的文本标注工具在药物知识表示中的应用及其比较. 复旦学报 2009; 481): 127-133.

Li Y, Hao P, Zheng S, Tu K, Fan H, Zhu R, Ding G, Dong C, Wang C, Li X, Thiesen HJ, Chen YE, Jiang H, Liu L, Li Y. Gene Expression Module based Chemical Function Similarity Search. Nucleic Acids Res 2008; 36(20):e137.

Li X, Tu L, Murphy PG, Kadono T, Steeber DA, Tedder TF. CHST1 and CHST2 sulfotransferase expression by vascular endothelial cells regulates shear-resistant leukocyte rolling via L-selectin. J Leukoc Biol 2001; 69: 565-574.

Li X and Tedder TF. CHST1 and CHST2 sulfotransferases expressed by human vascular endothelial cells: cDNA cloning, expression, and chromosomal localization. Genomics 1999; 55: 345-347.

Li X, Steeber DA, Tang MLK, Farrar MA, Perlmutter RM, and Tedder, TF. Regulation of L-Selectin-mediated Rolling through Receptor Dimerization. J Exp Med 1998; 188: 1385-1390.

Li X, Chang Y-H. Amino-terminal protein processing in Saccharomyces cerevisiae is an essential function that requires two distinct methionine aminopeptidases.
Proc Natl Acad Sci USA
1995; 92(26): 12357-12361.

Book Chapters:

李轩刘雷文静然。基因信息和个性化医疗14。中国医疗卫生信息化进展:p394-426. 上海交通大学出版社,20109月。 ISBN: 978-7-313-06580-3/R.
Tedder TF, Li X, and Steeber DA. The selectins and their ligands: adhesion molecules of the vasculature.  Adv
ances in Molecular Cell Biology 28: 65-111.  JAI Press Inc. 1999. ISBN: 0-7623-0495-2.



 




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