Dr.Li's research interests include bioinformatics, systems biology and computational biology. Recently, his research focuses on: biological applications of next generation sequencing technology; comparative genomics and function evolution of biological modules; gene regulatory network; small molecule mediated biological pathways; protein-protein interaction network.

Yi-Xue Li was born in Xinjiang, China. Currently, he is the director in Shanghai Center for Bioinformation Technology，vice director and a full research professor of Key Laboratory of Systems Biology at Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences. Dr. Li received his BSc. and Msc. degrees in theoretical physics from Xinjiang University, China, in 1982 and 1987, respectively, and his Ph.D. degree in theoretical physics from the University of Heidelberg, Germany, in 1996. After Dr. Li got his Ph.D. degree he worked as a bioinformatics research staff in European Molecular Biology Laboratory (EMBL) from 1997-2000, and came back to Shanghai, China in the middle of 2000.

Dr. Li has published more than 100 journal papers published in various international scientific journals, such as Science, Nature Genetics, Nature Biotechnology, PNAS, Bioinformatics, NAR, Plos Computational Biology, Plos One, Molecular Systems Biology, Molecular Cellular Proteomics, Oncogene, BMC Bioinformatics, Genome Biology, etc., and his research results have been cited by more than 1500 researchers worldwide in books, theses, journal and conference papers. He has served as a reviewer/panelist for many national research foundations/agencies such as the Chinese National Science Foundation, the National High-Tech Program(863) and National Key Basic Research Program(973). Dr. Li has served as an editorial board member for 5 scientific journals. He has organized several international conferences and workshops and has also served as a program committee member for several major national and international conferences like GIW, HUPO and National Bioinformatics Conference etc.

Main Publications of the last five year:

1.      Tu, Kang; Yu, Hui; Hua, Youjia; Li, Yuanyuan; Liu, Lei, Xie, Lu, Yixue Li*, 2009, Combinatorial network of primary and secondary microRNA-driven regulatory mechanisms, accepted by Nucleic Acids Research.

2.      Jing Sun, Di Wu, Tianlei Xu, Xiaojing Wang, Xiaolian Xu, Lin Tao, Y. X. Li* and Z. W. Cao*，SEPPA: a computational server for spatial epitope prediction of protein antigens，Nucleic Acids Research. 2009，W612–W616.

3.      Hong Li, Guohui Ding, Lu Xie^* and Yixue Li^*, PAnnBuilder: an R package for assembling proteomic annotation data, Bioinformatics , 2009, 25(8):1094-1095.

4.      Hong Li, Xiaobing Xing, Guohui Ding, Lu Xie*, Rong Zeng*, Yixue Li*, SysPTM - a systematic resource for proteomic research of  post-translational modifications, Molecular and Cellular Proteomics. 2009, 8(8):1839-49

5.       Zhen Wang, Guohui Ding, Zhonghao Yu, Lei Liu*, Yixue Li *, CHSMiner: a  GUI tool to identify chromosomal homologous segments. Algorithms Mol. Biol., 2009, 4(1):2.

6.      Songling Li, Hong Li, Minfa Li, Lu Xie*, Yixue Li*. 2009，Improved prediction of lysine acetylation by support vector machines. Accepted by Protein and Peptide Letters.

7.       Pei Hao, Siyuan Zheng, Jie Ping, Kang Tu, Christian Gieger, Rui Wang-Sattler, Yang Zhong*, Yixue Li*，Human gene expression sensitivity according to large scale meta-analysis，BMC Bioinformatics. 2009, 10(Suppl 1):S56.

8.       Hong Sun, Geir Skogerbo, Xiaohui Zheng, Wei Liu* and Yixue Li*, Genomic regions with distinct genomic distance conservation in vertebrate genomes, BMC Genomics, 2009, 10:133.

9.    Hong Xi, …, Yixue Li*, SysPIMP: the web-based systematical platform for identifying human disease-related mutated sequences from mass spectrometry, Nucleic Acids Research. 2009 37:D913-D920.

10.Sujun Li, Hong Li, Yixue Li*, Rong Zeng, Sys-BodyFluid: a Systematical Database for Human Body Fluid Proteome Research, Nucleic Acids Research. 2009 Jan;37:D907-12.

11.Guohui Ding, …, Yixue Li*, H.J. Thiesen*, SysZNF: the C2H2 Zinc Finger Gene database, Nucleic Acids Research. 2009 37:D267-D273

12.Zhen Wang, Guohui Ding, Zhonghao Yu, Lei Liu*, Yixue Li*, Modeling the age distribution of gene duplications in vertebrate genome using mixture density. Genomics. 2009;93(2):146-51.

13.Ruo-Yu Luo, Hai-Bin Wei, Lin Ye, Kankan Wang, Lei Liu,Yuan-Yuan Li, Yi-Xue Li* and Yang Zhong*,Photosynthetic metabolism of C3 plants shows highly cooperative regulation to maintain function under changing environmental conditions: a systems biological analysis of robustness, PNAS.2009, vol. 106 no. 3 847-852.

14.Hong Sun,…, Wei, Liu*, Yixue Li*, Structural Relationships between Highly Conserved Elements and Genes in Vertebrate Genomes, Plos One. 2008, Vol. 3, No. 11, e3727.

15.Guohui Ding, …, Yixue Li*, Tree of Life Based on Genome Context Networks, Plos One. 2008, Vol.3, No.10,e3357.

16.Yun Li, Pei Hao, Siyuan Zgeng, Kang Tu, Lei Liu*, Yixue Li*, 2008, Gene Expression Module based Chemical Function Similarity Search, Nucleic Acids Research，2008, Vol. 36, No. 20 e137.

17.Guangyong Zheng, Kang Tu, …, Yixue Li*,ITFP: an integrated platform of mammalian transcription factors, Bioinformatics. 2008 24(20):2416-2417.

18.W Li, L Xie, X He, J Li, K Tu, L Wei, J Wu, Y Guo, Wenxi Li, Lu Xie, Xianghuo He, Jinjun Li, Kang Tu,…,Yixue Li*, Jianren Gu*, 2008, Diagnostic and prognostic implications of microRNAs in human hepatocellular carcinoma, Int. J. Cancer, 123, 1616–1622.

19.Siyuan Zheng, …, Pei Hao*, Lei Liu*, Yixue Li*, 2008, MPSQ: A web tool for protein state searching, Bioinformatics. 2008 24(20):2412-2413.

20.Tao Huang, Kang Tu, Yu Shyr, Chao-Chun Wei, Lu Xie* and Yi-Xue Li*, The prediction of interferon treatment effects based on time series microarray gene expression profiles, Journal of Translational Medicine, 2008 Aug 9;6(1):44.

21.Guangyong Zheng, Ziliang Qian, Qing Yang, Chaochun Wei,Lu Xie, Yangyong Zhu* and Yixue Li*, 2008, The combination approach of SVM and ECOC for powerful identification and classification of transcription factor, BMC Bioinformatics, 9:282.

22.Hua YJ, Tu K., Tang ZY, Li YX*, Xiao HS*, 2008, Comparison of normalization methods with microRNA microarray. Genomics, doi:10.1016/j.ygeno.2008.04.002.

23.Qingwei Xu, Yixiang Shi, Qiang Lu, Guoqing Zhang, Qingming Luo* and Yixue Li*，2008，GORouter: an RDF model for providing semantic query and inference services for Gene Ontology and its associations，BMC Bioinformatics, 9(Suppl 1):S6.

24.C Bin, Kang, Lie Liu*, Yixue Li*, 2008, Modeling Effects of Cell Cycle M-phase Transcriptional Inhibition on Circadian Oscillator, Plos computational Biology, V. 4, Issue 3.

25.Peilin Jia, Ziliang Qian, Kaiyan Feng, Wencong Lu, Yixue Li*, Yudong Cai*, 2008, Prediction of membrane protein types in a hybrid space, J Proteome Research, 7 (3), 1131–1137.

26.Changzhen Dong, …, Yixue Li*, Gene-centric Characteristics of Genome-wide Association Studies, Plos One, 2007; 2(12): e1262.

27.Jing Li, Zijing Liu, Yuchun Pan, Qi Liu, Xing Fu, Nigel G.F. Cooper, Yixue Li*, Mengsheng Qiu* and Tieliu Shi*, Regulatory Module Network of bHLH Transcription Factors in Mouse Brain, Genome Biology 2007, 8:R244.

28.Guohui Ding, Yan Sun, Hong Li, Zhen Wang, Haiwei Fan, Chuan Wang, Dan Yang and Yixue Li*, 2007, EPGD: a comprehensive web resource for integrating and displaying eukaryotic paralog/paralogon information. Nucleic Acids Research, v.36(Database issue): D255–D262.

29.Jian Cui, Peng Li, Guang Li, Feng Xu, Chen Zhao, Yuhua Li, Zhongnan Yang, Guang Wang, Qingbo Yu, Yixue Li* and Tieliu Shi*, AtPID: Arabidopsis thaliana protein interactome database—an integrative platform for plant systems biology, 2007, Nucleic Acids Research, 36: D999-D1008.

30.Peilin Jia, Ziliang Qian，Zhen Bin Zeng, Yudong Cai*, and Yixue Li*, Prediction of subcellular protein localization based on functional domain composition, Biochemical and Biophysical Research Communications，Volume 357, Issue 2, 1 June 2007, Pages 366-370.

31.Ziliang Qian, Lingyi Lu, XiaoJun Liu, Yu-Dong Cai*, and Yixue Li*，2007, An Approach to Predict Transcription Factor DNA Binding Site Specificity Based upon Gene and Transcription Factor Functional Categorization, Bioinformatics, 23(18):2449-2454.

32.Boshu Liub,Sujun Lib, Yinglin Wang, Lin Lu, Yixue Li* and Yudong Cai*，Predicting the protein SUMO modification sites based on Properties Sequential Forward Selection (PSFS)，Biochemical and Biophysical Research Communications，2007， Volume 358, Issue 1, 22 June 2007, Pages 136-139.

33.L Lu, Z Qian, YD Cai*, Y Li*，Software note: ECS: An automatic enzyme classifier based on functional domain composition，2007，Computational Biology and Chemistry, Volume 31， 226-232.

34.Jing Zhao, Guo-Hui Ding, Lin Tao, Hong Yu, Zhong-Hao Yu, Jian-Hua Luo, Zhi-Wei Cao* and Yi-Xue Li*，2007，Modular co-evolution of metabolic networks，BMC Bioinformatics, 8:311, doi:10.1186/1471-2105-8-311.

35.Hui Yu, Feng Wang, Kang Tu, Lu Xie, Yuan-Yuan Li* and Yi-Xue Li*， 2007，Transcript-level annotation of Affymetrix probesets improves the interpretation of gene expression data，BMC Bioinformatics, 8:194, doi:10.1186/1471-2105-8-194.

36.Changzheng Dong，Xun Chu，Ying Wang，Yi Wang，Li Jin，Tieliu Shi，Wei Huang*，Yixue Li*，2007, Exploration of Gene-Gene Interaction Effects Using Entropy-Based Methods， European Journal of Human Genetics, 16(2):229-35.

37.Wu Wei, …, Yixue Li, Lars Steinmetz*, 2007, "Genome sequencing and comparative analysis of Saccharomyces, PNAS, vol. 104,  no. 31, 12825-12830.

38.Sujun Li, …, Yixue Li*, 2007, Prediction Protein N-glycosylation by Combining Functional Doman and Secretion Information, J. Biomolecular Structure & Dynamics, Vol. 25, 49-54.

39.Quanhu Sheng, …, Yixue Li, Rong Zeng*, Jiarui Wu*, 2006, Comparison of Proteomic Approach to Microarray-based Approach for Detecting Exons of Mouse Genome. Nature Genetics, 38, 1223 – 1224.

40.Guohui Ding, Jiuhong Kang, Qi Liu, Tieliu Shi, Gang Pei, and Yixue Li*, 2006, Insights into the coupling of duplication events and macroevolution from an age distribution of animal transmembrane gene families, Plos Computational Biology, Vol. 2, issue 8, e102.

41.Jing Zhao, Hong Yu, Jian-Hua Luo, Zhi-Wei Cao,Yi-Xue Li*，2006,  Hierarchical modularity of nested bow-ties in metabolic networks，BMC Bioinformatics, 7:386.

42.Ziliang Qian, Yudong Cai, Yixue Li*, 2006, Automatic Transcription Factor Classifier based on Functional Domain Composition, Biochemical and Biophysical Research Communications， 18;347(1):141-4.

43.PL Jia, TL Shi*, YD Cai*.and YX Li*, 2006, Demonstration of two novel methods for predicting functional siRNA efficiency, BMC Bioinformatics, 7:271, doi: 10.1186/ 471-2105-7-271.

44.Pei Hao, …, Yixue Li*, 2006, “Bioinformatics Research on the SARS Coronavirus in China”, Curr. Pharm. Design. Vol. 12, Nr. 35.

45.Ziliang Qian，Yanbin Yin，Yong Zhang, Lingyi Lu,Yixue Li and Ying Jiang*，2006, Genomic characterization of ribitol teichoic acid synthesis in Staphylococcus aureus: genes, genomic organization and gene duplication, BMC Genomics, 7: 74.

46.Wu Wei, Ziwei Cao, …,Yixue Li*，2006, The path from commensalism to pathogenicity: comparative phylogenetic profiles of Staphylococcus epidermidis RP62A and ATCC12228, BMC Genomics, 7:112，doi:10.1186/1471-2164-7-112.

47.Xiaojing Yu, …, Yixue Li*, 2006, Classification of protein quaternary structure by functional domain composition, BMC Bioinformatics, 7:187.

48.Yuanyuan Li, …, Yixue Li*, 2006, "In silico discovery of human natural antisense transcripts", BMC Bioinformatics. 13;7:18.

49.Sujun Li, …, Yixue Li*, 2006, Predicting O-glycosylation sites in mammalian proteins by using SVMs, Comput Biol Chem. 30(3): 203-208.

50.Kang Tu, …, Yixue Li*, 2006, Combining Gene Expression Profiles and Protein-Protein Interaction data to infer Gene Functions Bioinformatics: microarray analysis & PPI network analysis, Journal of Biotechnology, 124,475-485.

51.Yu X, Cao J, Cai Y, Shi T, Yixue Li*. 2006, Predicting rRNA-, RNA-, and DNA-binding proteins from primary structure with support vector machines. J Theor. Biol.  21;240(2):175-84.

52.Zhuo Wang, Xin-Guang Zhu, …, Yuanyuan Li, Yixue Li*, Lei Liu*, 2006, Exploring photosynthesis evolution by comparative analysis of metabolic networks between chloroplasts and photosynthetic bacteria, BMC Genomics., 7:100, doi: 10.1186/1471-2164-7-100.

53.Ruoyu Luo, Sha Liao, Guanyang Tao, Yuanyuan Li, Yixue Li*, Qingming Luo*. 2006, Dynamic analysis of optimality in myocardial metabolic network under normal and ischemic conditions, Molecular Systems Biology, 2:2006.0031.

54.Yuan-Yuan Li, Hui Yu, Zong-Ming Guo, Ting-Qing Guo, Kang Tu, Wei Lin, Yi-Xue Li*, 2006, Systematic analysis of head-to-head gene organization: evolutionary conservation and potential biological relevance, Plos Computational Biology, Vol. 2, issue 7, e74.

55.Guo-qing Zhang, Zhi-wei Cao, Qing-ming Luoa, Yu-Dong Cai, Yixue Li*，2006, Operon prediction based on SVM，Comput Biol Chem, 30, 233-240.

56.Lili Wang, Zhong Yang, …, Yixue Li*, Wei Hu*, 2006, Reconstruction and in silico analysis of MAPK signalling pathways in the human blood fluke, Schistosoma japonicum, FEBS Letters 580, 3677-3686.

57.Zhuo Fang, Jiong Yang, Yixue Li, 2006, Qingming Luo and Lei Liu*, Knowledge guided analysis of microarray data, J Biomed Inform, Volume 39, Issue 4, p:401-411.

58.Jing Li, Qi Liu, Mengsheng Qiu, Yuchun Pan,Yixue Li and Tieliu Shi, 2006, Identification and analysis of the mouse basic/Helix-Loop-Helix transcription factor family, Biochemical and Biophysical Research Communications, Volume 350, Issue 3, 24 November 2006, Pages 648-656.

59.Lu Q, Hao P, Curcin V, He W, Li YY, Luo QM, Guo YK, Li YX. 2005, KDE Bioscience: Platform for bioinformatics analysis workflows. J Biomed Inform, Volume 39, Issue 4, August 2006, Pages 440-450.

60.Pei Hao, …, Yixue Li*，Guoping Zhao*, 2005, Cross-host evolution of SARS coronavirus in palm civet and human, PNAS. 102(7)，2430–2435.

61.Jingchun Sun, …, Yixue Li*, 2005, Refined phylogenetic profiles method for predicting protein-protein interactions, Bioinformatics, 15;21(16):3409-15.

62.Pei Hao, …, Yixue Li* & Yang Zhong*, 2005,“MPSS: an integrated database system for surveying a set of proteins”，Bioinformatics. Vol. 21 no. 9, 2142–2143.

63.Lu W, Wu XD, …,  Li YX, …, Pei G, Wu JR, Sun B, et al., 2005, Synthetic peptides derived from SARS coronavirus S protein with diagnostic and therapeutic potential. FEBS Lett. 11;579(10):2130-6.

64.Pei Hao, ……, Yixue Li, ……, Guoping Zhao, et.al., 2004, ‘Molecular evolution of the SARS-coronavirus during the course of the SARS epidemic in China’, Science, 12 March, 303: 1666-1669.

65.Henning Hermjakob，……, Yixue Li, ……, Chris Hogue & Rolf Apweiler, 2004, The HUPO PSI's Molecular Interaction format—a community standard for the representation of protein interaction data, Nature Biotechnology,22，pp177–183.

66.Lijian Hui,……,Yixue Li*，et al., 2004, “Identification of Alternatively Spliced mRNA Variants Related to Cancers by Genome-wide ESTs Alignment.”, Oncogene， 1-11.

67.Cheng Luo, ……, Yixue Li, Xu She, and Hualiang Jiang, 2004, Nucleocapsid protein of SARS coronavirus tightly binds to human cyclophilin A, Biochem Biophys Res Commun. Aug 27;321(3):557-65.

68.Deng X, Qiu L, Yixue L*, 2004, Scoring hidden Markov models to discriminate beta-barrel membrane proteins. Comput Biol Chem,  Jul;28(3):189-94.

* Corresponding author.