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Prof. Yi-Xue Li

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Prof. Yi-Xue Li Prof. Yi-Xue Li Professor & Leader of proposed Shanghai Institutes for Bio-Medicine Director Shanghai Center for Bioinformation Technology Vice Director Key Laboratory of Systems Biology Shanghai Institutes for Biological Sciences Topic： Protein phosphorylation plays an essential role in the evolution of vertebrates Abstract： Recent publications have revealed that the evolution of phosphosites are influenced by local protein structures and whether the phosphosites have characterized functions or not. With knowledge of the wide functional range of phosphorylation, we attempted to clarify whether the evolutionary conservation of phosphosites is different among distinct functional modules. We grouped the phosphosites in the human genome into modules according to the functional categories of KEGG, and we investigated their evolutionary conservation in several vertebrate genomes from mouse to zebrafish. We found that phosphosites in the basic functional modules (BFMs) such as metabolic and genetic processes, display a lower evolutionary conservation than those in the vertebrate-specific functional modules (VFMs) such as signaling processes and more complex organic systems. The phosphosites in the VFMs are also significantly more conserved than their flanking regions, but those in the BFMs are not. The above results hold for both serine/threonine and tyrosine residues, although the fraction of phosphorylated tyrosine is raised in the VFMs. Moreover, the difference in evolutionary conservation of the phosphosites cannot be explained by their difference in local protein structures, and there are also more phosphosites with known functions in the VFMs. Based on these results, we concluded that protein phosphorylation may play more dominant roles for the VFMs than the BFMs. As phosphorylation is a quite rapid biological reaction, the VFMs that quickly respond to outer stimuli and inner signals might more heavily depend on this regulatory mechanism. Our results imply that phosphorylation may have an essential role in the evolution of vertebrates. Resume: Yi-Xue Li was born in Xinjiang, China. Currently, he is vice Director and a full research professor of Key Laboratory of Systems Biology at Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences， Director in Shanghai Center for Bioinformation Technology， Dean of Department of Bioinformatics and Biostatistics, Shanghai Jiaotong University. 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 Heidelberg University, 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 Biology and Evolution, 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). Selected publications: 1. Zhen Wang, Guohui Ding, Ludwig Geistlinger, Li Hong, Lei Liu, Rong Zeng*, Yoshio Tateno*, Yixue Li*，2010，Evolution of protein phosphorylation for distinct functional modules in vertebrate genomes，on Oct. 18 online published by Molecular Biology and Evolution. 2. Shen Niu, Tao Huang, Kaiyan Feng, Yudong Cai*, Yixue Li*，Prediction of tyrosine‐sulfation with mRMR feature selection and analysis，on Oct.16 onloine published by Journal of Proteome Research. 3. Huang T，…, Yudong Cai, Yixue Li*: Prediction of Deleterious Non‐Synonymous SNPs Based on Protein Interaction Network and Hybrid Properties. PLoS ONE 2010, 5(7):e11900. 4. Hong Li, Guohui Ding, Lu Xie, Yixue Li*, 2010, dbDEPC: a Database of Differentially Expressed Proteins in Human Cancer. Nucleic Acids Research.;38(Database issue):D658‐64. 5. Huang T, …, Yixue Li*, Yudong Cai*, 2010, Analysis and prediction of the metabolic stability of proteins based on their sequential features, subcellular locations and interaction networks. PLoS ONE, 5(6):e10972. 6. Zhao J, Geng C, Tao L, Zhang D, Jiang Y, Tang K, Zhu R, Yu H, Zhang W, He F, Li Y*, Cao Z*. 2010，Reconstruction and Analysis of Human Liver‐Specific Metabolic Network Based on CNHLPP Data. JOURNAL OF PROTEOME RESEARCH, 9( 4):1648‐1658. 7. Yi Yang, Zili Zhang, Yixue Li*, Xinguang Zhu*, Qi Liu*. 2010, Identifying cooperative transcriptional factors by combing ChIP‐chip data and knock‐out data. Accepted by Cell Research. 8. Peter Lorenz, Sabine Dietmann, Thomas Wilhelm, Dirk Koczan, Sandra Autran, Sophie Gad, Gaiping Wen, Guohui Ding, Yixue Li, Marie‐Françoise Rousseau‐Merck and Hans‐Juergen Thiesen，The ancient mammalian KRAB zinc finger gene cluster on human chromosome 8q24.3 illustrates principles of C2H2 zinc finger evolution associated with unique expression profiles in human tissues，BMC Genomics 2010, 11:206doi:10.1186/1471‐2164‐11‐206. 9. Zhen Wang,Xiao Dong, Guohui Ding,and Yixue Li*, Comparing the retention mechanisms of tandem duplicates and retrogenes in human and mouse genomes, Genet Sel Evol. 2010; 42(1): 24. 10. Tao Huang, Weiren Cui, Zhi‐Song S. He, Lele Hu, Fang Liu, Tieqiao Wen, Yixue Li*, Yudong Cai*, 2009, Functional association between influenza A (H1N1) virus and human. Biochemical and biophysical research ommunications. Volume 390, Issue 4, Pages 1111‐1113. 11. Tao Huang , WeiRen Cui, LeLe Hu, KaiYan Feng, Yi‐Xue Li*, Yu‐Dong Cai, 2009, Prediction of Pharmacological and Xenobiotic Responses to Drugs Based on Time Course Gene Expression Profiles. Plos One, 2009, 4(12):e8126. 12. Hui Yu, Fu‐Dong Yu, Guo‐Qing Zhang, Xiang Shen, Yun‐Qin Chen, Yuan‐Yuan Li,* and Yi‐Xue Li*, DBH2H: vertebrate head‐to‐head gene pairs annotated at genomic and post‐genomic levels. Database , 2009, doi:10.1093/database/bap006. 13. Yao Yu，Kang Tu, Siyuan Zheng, Yun Li, Guohui Ding, Jie Ping, Pei Hao and Yixue Li*，GEOGLE: context mining tool for the correlation between gene expression and the phenotypic distinction. BMC Bioinformatics 2009, 10:264 doi:10.1186/1471‐2105‐10‐264. 14. Tu, Kang; Yu, Hui; Hua, Youjia; Li, Yuanyuan; Liu, Lei, Xie, Lu, Yixue Li*, Combinatorial network of primary and secondary microRNA‐driven regulatory mechanisms, Nucleic Acids Research. 2009，37(18):5969‐80. 15. 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. 16. Hong Li, Guohui Ding, Lu Xie* and Yixue Li*, PAnnBuilder: an R package for assembling proteomic annotation data, Bioinformatics , 2009, 25(8):1094‐1095. 17. Hong Li, Xiaobing Xing, Guohui Din proteomic g, Lu Xie*, Rong Zeng*, Yixue Li*, SysPTM ‐ a systematic resource for research of post‐translational modifications, Molecular and Cellular Proteomics. 2009, 8(8):1839‐49. 18. 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. 19. 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. 20. 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. 21. 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. 22. 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. 23. 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. 24. Guohui Ding, ⋯, Yixue Li*, H.J. Thiesen*, SysZNF: the C2H2 Zinc Finger Gene database, Nucleic Acids Research. 2009 37:D267-D273. 25. 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. 26. 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. 27. 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. 28. Guohui Ding, ⋯, Yixue Li*, Tree of Life Based on Genome Context Networks, Plos One. 2008, Vol.3, No.10,e3357. 29. 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,
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