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  1. Li S, Li H, Li M, Shyr Y, Xie L*, Li Y*. Improved prediction of Iysine acetylation by support vector machines. Protein and Peptide Letters. 2009, 16(8): 977-983.

  2. Zhao XM*, Chen L, Aihara K. A discriminative approach to identifying domain-domain interactions from protein-protein interactions. Proteins. 2009 Oct 26. [Epub ahead of print].

  3. Wang Z, Zhu XG*, Chang X, Chen YZ, Liu L*. Though with constraints imposed by endosymbiosis, preferential attachment is still a plausible mechanism responsible for evolution of chloroplast metabolic network. J Evol Biol. 2009, 22(1): 71-79.

  4. Huang T, Cui W, Hu L, Feng K, Li YX*, Cai YD*. Prediction of pharmacological and xenobiotic responses to drugs based on time course gene expression profiles. PLoS One. 2009, 4(12): e8126.

  5. Wang J, Zhang S, Wang Y, Chen L*, Zhang XS*. Disease-aging network reveals significant roles of aging genes in connecting genetic diseases. PLoS Computational Biology. 20095(9): e1000521.

  6. Sun J, Wu D, Xu T, Wang X, XU X, Tao L, Li YX*, Cao ZW*. SEPPA: a computational server for spatial epitope prediction of protein antigens. Nucleic Acids Research. 2009, 37: W612-W616.

  7. 武雪梅, 肖华胜. miRNA与肿瘤细胞耐药的关系. 中国科C辑: 生命科学. 2009, 39(3): 813-820.

  8. 武雪梅, 肖华胜. 人类基因组结构便已检测研究进展. 中国科C辑: 生命科学. 2009, 39(3): 237-244.

  9. Zhang JH, Yang Y, Wu J*. B23 interacts with PES1 and is involved in nucleoar localization of PES1. Acta Biochim Biophys Sin. 2009, 41(12): 991-997.

  10. Xue L, Yuan Q, Yang Y, Wu J*. Enzymatic Prepartion of an artificial mircoRNA library. Biochem Biophys Res Commun. 2009, 390(3): 791-796.

  11. 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): 149-151.

  12. Rongxia Li, Rong Zeng*. Dynamic proteomics for investigating the response of individual cancer cells under drug action. Expert Rev Proteomics. 2009, 6(1): 19-21

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

  14. Wei Guo, Kun-Ming Zhang, Kang Tu, Yi-Xue Li, Li Zhu, Hua-Sheng Xiao, Ying Yang, Jia-Rui Wu*. Adipogenesis licensing and execution are dispararely linked to cell proliferation. Cell Research. 2009, 19(2): 216-223.

  15. Qing-run Li, Zhi-bin Ning, Jia-shu Tang, Song Nie and Rong Zeng*. Effect of Peptide-to-TiO2 beads Ratio on Phosphopeptide Enrichment Selectivity. J Proteome Res. In press.

  16. Hong Li, Ying He, Guohui Ding, Chuan Wang, Lu Xie* and Yixue Li*. dbDEPC: a Database of Differentially Expressed Proteins in Human Cancer. Nucleic Acids Research. Epub 2009 Nov 9.

  17. Kang Tu, Hui Yu, You-Jia Hua, Yuan-Yuan Li, Lei Liu*, Lu Xie* and Yi-Xue Li*. Combinatorial network of primary and secondary microRNA-driven regulatory mechanisms. Nucleic Acids Research. 2009,37(18):5969-5980.

  18. Su-Jun Li, Mao Peng, Hong Li, Bo-Shu Liu, Chuan Wang, Jia-Rui Wu, Yi-Xue Li* and Rong Zeng*. Sys-Body Fluid: a systematical database for human body fluid proteome research. Nucleic Acids Research. 2009,37: D907-D912.

  19. Wen-Jun Deng, Song Nie, Jie Dai, Jia-Rui Wu and Rong Zeng*. Proteome, phosphoproteome and hydroxyproteome of liver mitochondria in diabetic rats at early pathogenic stages. Mol Cell Proteomics. 2009, Aug 23. [Epub ahead of print]

  20. Yi-Bo Wu, Jie Dai, Xing-Lin Yang, Su-Jun Li, Shi-Lin Zhao, Quan-Hu Sheng, Jia-Shu Tang, Guang-Yong Zheng, Yi-Xue Li, Jia-Rui Wu and Rong Zeng*. Concurrent quantification of proteome and phosphoproteome to reveal system-wide association of protein phosphorylation and gene expression. Mol Cell Proteomics. 2009, 8(12): 2089-26

  21. You-Jia Hua, Zhong-Yi Tang, Kang Tu, Li Zhu1, Yi-Xue Li, Lu Xie* and Hua-Sheng Xiao*. Identification and target prediction of miRNAs specifically expressed in rat neural tissue. BMC Genomics. 2009, 10: 214 doi:10.1186/1471-2164-10-214.

  22. Hong Li, Xiaobin Xing, Guohui Ding, Qingrun Li, Chuan Wang, Lu Xie, Rong Zeng*, Yixue Li*,SysPTM: A Systematic Resource for Proteomic Research on Post-translational Modifications, MCP Papers. 2009, 8(8): 1839-49.

  23. Guohui Ding, Peter Lorenz, Michael Kreutzer, Yixue Li*, and Hans-Juergen Thiesen*, SysZNF: the C2H2 Zinc Finger Gene database, Nucleic Acids Research. 2009 37:D267-D273.

  24. 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.

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

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

  27. 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.

  28. Hong Xi, Jongsun Park, Guohui Ding, Yong-Hwan Lee and 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.

   
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