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李轩博士介绍(PI)

 

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课题组长: 李轩,博士,研究员。1988年毕业于北京大学生物系,1996年获美国圣路易斯大学生物化学博士学位。1996年至2000年在美国杜克大学进行博士后研究工作,从事免疫发育和免疫反应的调控基因研究。主要研究成果发表在J Exp MedPNAS, J Immunol, NARCell ResearchPloS OneGenomics 等杂志上。曾先后任职于美国Curagen、葛兰素史克、米氏健康信息系统公司。2007以来任上海生物信息技术研究中心研究员。作为负责人承担十一五国家863重大科研项目。共发表学术论文30余篇。



【课题组研究方向】
1)植物、微生物和昆虫的功能基因组分析和进化比较研究;
2)基因组、表达组、蛋白质组和代谢组等组学数据整合及Meta分析的算法研究;
3)生物系统的基因调控网络及小分子扰动的建模分析;
4)高通量测序技术的应用算法
研究和支持分析平台构建, 特别是二代高通量测序在表达组、基因组和基因多态性研究的分析方法和平台。

【主要论文】

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.

【学术专著章节】
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.