主要学术成绩

　　从1997年以来一直使用神经网络、统计物理等方法从事与DNA序列相关的软件开发研究，特别发展了时间序列的统计相关算法。独自研发的大规模、高通量、自动化的DNA序列测序分析专家系统被EMBL命名为LI－Tracker，分别运用于德、法、挪威等国的研究所和LION Bioscience等生物技术公司。在基因水平上研究总结出SARS病毒传播和变异规律，发现18条免疫多肽序列并用于SARS病毒检测和治疗研究，为研制抗SARS 病毒的药物和疫苗做出了重要贡献。领衔承担了列为科教兴市重大产业化项目的“一网两库”工程，经过两年多的建设，该系统已经拥有各类科技资源信息量6TB,访问量达到190万余人，累计对外服务22.2万人次，并广泛辐射到长三角地区，有效推动了本市及长三角地区科技创新和知识服务业的发展

　　2000年回国后，先后主持和承担了国家“九五”863计划生物技术领域《生物信息学数据库开发和建设》重大项目。作为首席科学家主持了中科院《生物信息学重大基础理论与应用》重大研究项目；国家973《重大疾病相关蛋白质组学生物信息学》课题；中科院上海生科院《生物信息技术平台建设》项目等。

　　近5年共发表论文近60余篇，包括Science, Nature Genetics，Nature Biotechnology, Oncogene, PNAS, Bioinformatics等，论文总影响因子200点以上，被引用400多次。共申请发明专利8项，获得软件著作权15项。

　　近年发表主要论文

　　1．Liu T, Zhang Q, Wang L, Yu L, Leng W, Yang J, Chen L, Peng J, Ma L, Dong J, Xu X, Xue Y, Zhu Y, Zhang W, Yang L, Li W, Sun L, Wan Z, Ding G, Yu F, Tu K, Qian Z, Li R, Shen Y, Li Y, Jin Q. The use of global transcriptional analysis to reveal the biological and cellular events involved in distinct development phases of Trichophyton rubrum conidial germination. BMC Genomics. 2007 Apr 11;8(1):100（2005 SCI IF 4.092）

　　2．Shen J, Zhang J, Luo X, Zhu W, Yu K, Chen K, Li Y, Jiang H. Predicting protein-protein interactions based only on sequences information. Proc Natl Acad Sci U S A. 2007 Mar 13;104(11):4337-41. Epub 2007 Mar 5. （2005 SCI IF 10.231）

　　3．Hao P, Chen M, Zhang G, He W, Li Y. Bioinformatics research on the SARS coronavirus (SARS_CoV) in China. Curr Pharm Des. 2006;12(35):4565-72. Review. （2005 SCI IF 4.829）

　　7．Wang L, Ma L, Leng W, Liu T, Yu L, Yang J, Yang L, Zhang W, Zhang Q, Dong J, Xue Y, Zhu Y, Xu X, Wan Z, Ding G, Yu F, Tu K, Li Y, Li R, Shen Y, Jin Q. Analysis of the dermatophyte Trichophyton rubrum expressed sequence tags. BMC Genomics. 2006 Oct 11;7:255. （2005 SCI IF 4.092）

　　4． Sheng QH, Wang LS, Dai J, Jiang XS, Li RX, Ma DJ, Li YX, Zeng R, Wu JR. Comparison of a proteomic approach with a microarray-based approach to detect exons in the mouse genome. Nat Genet. 2006 Nov;38(11):1223-4. （2005 SCI IF 25.797）

　　5．Ding G, Kang J, Liu Q, Shi T, Pei G, Li Y. Insights into the coupling of duplication events and macroevolution from an age profile of animal transmembrane gene families. PLoS Comput Biol. 2006 Aug 11;2(8):e102. Epub 2006 Jun 26.

　　6．Han L, Cui J, Lin H, Ji Z, Cao Z, Li Y, Chen Y. Recent progresses in the application of machine learning approach for predicting protein functional class independent of sequence similarity. Proteomics. 2006 Jul;6(14):4023-37. （2005 SCI IF 6.088）

　　7．Jia P, Shi T, Cai Y, Li Y. Demonstration of two novel methods for predicting functional siRNA efficiency. BMC Bioinformatics. 2006 May 29;7:271.（2005 SCI IF 4.958）

　　8．Wei W, Cao Z, Zhu YL, Wang X, Ding G, Xu H, Jia P, Qu D, Danchin A, Li Y. Conserved genes in a path from commensalism to pathogenicity: comparative phylogenetic profiles of Staphylococcus epidermidis RP62A and ATCC12228. BMC Genomics. 2006 May 10;7:112. （2005 SCI IF 4.092）

　　9．Wang Z, Zhu XG, Chen Y, Li Y, Hou J, Li Y, Liu L. Exploring photosynthesis evolution by comparative analysis of metabolic networks between chloroplasts and photosynthetic bacteria. BMC Genomics. 2006 Apr 30;7:100. （2005 SCI IF 4.092）

　　10．Qian Z, Yin Y, Zhang Y, Lu L, Li Y, Jiang Y. Genomic characterization of ribitol teichoic acid synthesis in Staphylococcus aureus: genes, genomic organization and gene duplication. BMC Genomics. 2006 Apr 5;7:74. （2005 SCI IF 4.092）

　　11．Yu X, Wang C, Li Y. Classification of protein quaternary structure by functional domain composition. BMC Bioinformatics. 2006 Apr 4;7:187.（2005 SCI IF 4.958）

　　12．Zhao J, Yu H, Luo JH, Cao ZW, Li YX. Hierarchical modularity of nested bow-ties in metabolic networks. BMC Bioinformatics. 2006 Aug 18;7:386. （2005 SCI IF 4.958）

　　13．Li YY, Yu H, Guo ZM, Guo TQ, Tu K, Li YX. Systematic analysis of head-to-head gene organization: evolutionary conservation and potential biological relevance. PLoS Comput Biol. 2006 Jul 7;2(7):e74. Epub 2006 May 15.

　　14．Luo RY, Liao S, Tao GY, Li YY, Zeng S, Li YX, Luo Q. Dynamic analysis of optimality in myocardial energy metabolism under normal and ischemic conditions. Mol Syst Biol. 2006;2:2006.0031. Epub 2006 Jun 6.

　　15．Li YY, Qin L, Guo ZM, Liu L, Xu H, Hao P, Su J, Shi Y, He WZ, Li YX. In silico discovery of human natural antisense transcripts. BMC Bioinformatics. 2006 Jan 13;7:18. （2005 SCI IF 4.958）

　　16．Sun J, Xu J, Liu Z, Liu Q, Zhao A, Shi T, Li Y. Refined phylogenetic profiles method for predicting protein-protein interactions. Bioinformatics. 2005 Aug 15;21(16):3409-15. Epub 2005 Jun 9. （2005 SCI IF 6.019）

　　17．Hui L, Zhang X, Wu X, Lin Z, Wang Q, Li Y, Hu G. Identification of alternatively spliced mRNA variants related to cancers by genome-wide ESTs alignment. Oncogene. 2004 Apr 15;23(17):3013-23. （2005 SCI IF 6.872）

　　18．Hermjakob H, Montecchi-Palazzi L, Bader G, Wojcik J, Salwinski L, Ceol A, Moore S, Orchard S, Sarkans U, von Mering C, Roechert B, Poux S, Jung E, Mersch H, Kersey P, Lappe M, Li Y, Zeng R, Rana D, Nikolski M, Husi H, Brun C, Shanker K, Grant SG, Sander C, Bork P, Zhu W, Pandey A, Brazma A, Jacq B, Vidal M, Sherman D, Legrain P, Cesareni G, Xenarios I, Eisenberg D, Steipe B, Hogue C, Apweiler R. The HUPO PSIs molecular interaction format--a community standard for the representation of protein interaction data. Nat Biotechnol. 2004 Feb;22(2):177-83. （2005 SCI IF 22.355）

　　19．Shi TL, Li YX, Cai YD, Chou KC. Computational methods for protein-protein interaction and their application. Curr Protein Pept Sci. 2005 Oct;6(5):443-9. （2005 SCI IF 4.148）

　　20．Hao P, He WZ, Huang Y, Ma LX, Xu Y, Xi H, Wang C, Liu BS, Wang JM, Li YX, Zhong Y. MPSS: an integrated database system for surveying a set of proteins. Bioinformatics. 2005 May 1;21(9):2142-3. Epub 2005 Feb 4. （2005 SCI IF 6.019）

　　21．Song HD, Tu CC, Zhang GW, Wang SY, Zheng K, Lei LC, Chen QX, Gao YW, Zhou HQ, Xiang H, Zheng HJ, Chern SW, Cheng F, Pan CM, Xuan H, Chen SJ, Luo HM, Zhou DH, Liu YF, He JF, Qin PZ, Li LH, Ren YQ, Liang WJ, Yu YD, Anderson L, Wang M, Xu RH, Wu XW, Zheng HY, Chen JD, Liang G, Gao Y, Liao M, Fang L, Jiang LY, Li H, Chen F, Di B, He LJ, Lin JY, Tong S, Kong X, Du L, Hao P, Tang H, Bernini A, Yu XJ, Spiga O, Guo ZM, Pan HY, He WZ, Manuguerra JC, Fontanet A, Danchin A, Niccolai N, Li YX, Wu CI, Zhao GP. Cross-host evolution of severe acute respiratory syndrome coronavirus in palm civet and human. Proc Natl Acad Sci U S A. 2005 Feb 15;102(7):2430-5. Epub 2005 Feb 4. （2005 SCI IF 10.231）

　　22．Jiang XS, Zhou H, Zhang L, Sheng QH, Li SJ, Li L, Hao P, Li YX, Xia QC, Wu JR, Zeng R.A high-throughput approach for subcellular proteome: identification of rat liver proteins using subcellular fractionation coupled with two-dimensional liquid chromatography tandem mass spectrometry and bioinformatic analysis. Mol Cell Proteomics. 2004 May;3(5):441-55. Epub 2004 Jan 22. （2005 SCI IF 9.876）