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  1. Wang Z, Ding GH, Geistlinger L, Hong L, Liu L, Zeng R*, Tateno Y*, Li YX*. Evolution of protein phosphorylation for distinct functional modules in vertebrate genomes. Mol Biol Evol. 2010 Oct 18.[PDF]

  2. Deng WJ, Nie S, Dai J, Wu JR, Zeng R*. Proteome, phosphoproteome, and hydroxyproteome of liver mitochondria in diabetic rats at early pathogenic stages. Mol Cell Proteomics. 2010, 9(1): 100-16.[PDF]

  3. Pei H, Yao Y, Yang Y, Liao K*, Wu JR*. Krüppel-like factor KLF9 regulates PPARgamma transactivation at the middle stage of adipogenesis. Cell Death Differ. 2010 Aug 20.[PDF]

  4. Han S, Pan HL, Zhang JH, Tan L, Ma DW, Yuan JY*, Wu JR*. Identification of a small molecule activator of novel PKCs for promoting glucose-dependent insulin secretion. Cell Res. 2010 Sep 28.[PDF]

  5. Cao XJ, Dai J, Xu H, Nie S, Chang X, Hu BY, Sheng QH, Wang LS, Ning ZB, Li YX, Guo XK, Zhao GP*, Zeng R*. High-coverage proteome analysis reveals the first insight of protein modification systems in the pathogenic spirochete Leptospira interrogans. Cell Res. 2010, 20(2): 197-210.[PDF]

  6. Li H, He Y, Ding GH, Wang C, Xie L*, Li YX*. dbDEPC: a Database of Differentially Expressed Proteins in Human Cancer. Nucleic Acids Res. 2010, 38: D658-64.[PDF]

  7. Nie S, Dai J, Ning ZB, Cao XJ, Sheng QH, Zeng R*. Comprehensive profiling of phosphopeptides based on anion exchange followed by flow-through enrichment with titanium dioxide (AFET). J Proteome Res. 2010, 9(9): 4585-94.[PDF]

  8. Niu S, Huang T, Feng ky, Cai YD*, Li YX*. Prediction of tyrosine-sulfation with mRMR feature selection and analysis. J Proteome Res. 2010, 9, 6490-6497.[PDF]

  9. Liu ZP, Wu LY, Yong Wang, Zhang XS, Chen L*. Prediction of protein-RNA binding sites by a random forest method with combined features. BIOINFORMATICS.2010, 26(13): 1616-22.[PDF]

  10. Huang T,Wang P, Ye ZQ, Xu H, He ZS,  Feng KY, Hu LL, Cui WR,  Wang K, Dong X,  Xie L, Kong XY*, Cai YD*, Li YX*. Prediction of Deleterious Non-Synonymous SNPs Based on Protein Interaction Network and Hybrid Properties. PLoS One 2010 , 5(7): e11900.[PDF]

  11. Huang T, Shi XH, Wang P, He ZS, Feng KY, Hu LL, Kong XY*, Li YX*,  Cai YD*, Chou KC*. Analysis and prediction of the metabolic stability of proteins based on their sequential features, subcellular locations and interaction networks. PLoS One. 2010 , 5(6): e10972.[PDF]

  12. Chang X, Liu S, Yu YT, Li YX*, Li YY*. Identifying modules of coexpressed transcript units and their organization of Saccharopolyspora erythraea from time series gene expression profiles. PLoS One. 2010 , 5(8): e12126.[PDF]

  13. Liu ZP, Wang Y, Zhang XS*, Chen L*. Identifying dysfunctional crosstalk of pathways in various regions of Alzheimer’s disease brains. BMC Syst Biol. BMC Syst Biol. 2010, 4 : S11.[PDF]

  14. Yu Y, Ping J, Chen H, Jiao LX, Zheng SY, Han ZG*, Hao P*, Huang J*. A comparative analysis of liver transcriptome suggests divergent liver function among human, mouse and rat. Genomics. 2010 , 96(5): 281-9.[PDF]

  15. Chang X, Wang Z, Hao P, Li YY*, Li YX*. Exploring mitochondrial evolution and metabolism organization principles by comparative analysis of metabolic networks. Genomics. 2010 , 95(6): 339-44.[PDF]

  16. Liu YS, Li C, Xing Z, Yuan XY, Wu Y, Xu MJ, Tu K, Li QR, Wu CC, Zhao MJ*, Zeng R*. Proteomic mining in the dysplastic liver of WHV/c-myc mice--insights and indicators for early hepatocarcinogenesis. FEBS J. 2010, 277(19): 4039-53.[PDF]

  17. Zhang KM, Guo W, YangY , Wu JR*. JAK2/STAT3 pathway is involved in the early stage of adipogenesis through regulating C/EBPb transcription. Journal of Cellular Biochemistry. 2010 Nov 15.[PDF]

  18. Li QR, Fan KX, Li RX, Dai J, Wu CC, Zhao SL, Wu JR, Shieh CH, Zeng R*. A comprehensive and non-prefractionation on the protein level approach for the human urinary proteome: touching phosphorylation in urine. Rapid Commun Mass Spectrom. .2010, 24(6): 823-32.[PDF]

  19. Wang Z Dong X,Ding GH*, Li YX*. Comparing the retention mechanisms of tandem duplicates and retrogenes in human and mouse genomes. Genet Sel Evol .2010, Mar 16:1-3.[PDF]

  20. Zhang J, Yang Y, Wu J*. Palmitate impairs cytokinesis associated with RhoA inhibition. Cell Research .2010, Mar 16:1-3.

  21. 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.

  22. 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].

  23. 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.

  24. 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.

  25. 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.

  26. 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.

  27. 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.

  28. 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.

  29. 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.

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

  31. 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.

  32. 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

  33. 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.

  34. 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.

  35. 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.

  36. 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.

  37. 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.

  38. 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.

  39. 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]

  40. 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

  41. 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.

  42. 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.

  43. 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.

  44. 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.

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

  46. 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.

  47. 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.

  48. 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.

  49. Ding G, Sun Y, Li H, Wang Z, Fan H, Wang C, Yang D, Li Y*. EPGD: a comprehensive web resource for integrating and displaying eukaryotic paralog/paralogon information. Nucleic Acids Res. 2008, 36 (Database issue): D255-62.

  50. 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.

  51. Cui J, Li P, Li G, Xu F, Zhao C, Li Y*, Yang Z, Wang G, Yu Q, Li Y*, Shi T*. AtPID: Arabidopsis thaliana protein interactome database—an integrative platform for plant systems biology. Nucleic Acids Res. 2008,36(Database issue): D999-1008.

  52. Kang B, Li YY, Chang X, Liu L, Li YX*. Modeling the Effects of Cell Cycle M-phase Transcriptional Inhibition on Circadian Oscillation. PLoS Comput Biol. 2008, 4(3): e1000019.

  53. Ning ZB, Li QR, Dai J, Li RX, Shieh CH, Zeng R*. Fractionation of Complex Protein Mixture by Virtual Three-Dimensional Liquid Chromatography Based on Combined pH and Salt Steps. J Proteome Res. 2008, 7(10): 4525-37.

  54. Jia P, Qian Z, Feng K, Lu W, Li Y*, Cai Y*. Prediction of membrane protein types in a hybrid space, J Proteome Res. 2008, 7(3): 1131–1137.

  55. Zheng G, Tu K, Yang Q, Xiong Y, Wei C, Xie L, Zhu Y, Li Y*. ITFP: an integrated platform of mammalian transcription factors. Bioinformatics. 2008, 24(20): 2416-7.

  56. Zheng S, Sheng J, Wang C, Wang X, Yu Y, Li Y, Michie A, Dai J, Zhong Y, Hao P*, Liu L*, Li Y*. MPSQ: A web tool for protein state searching. Bioinformatics. 2008, 24(20): 2412-3.

  57. Ding G, Yu Z, Zhao J, Wang Z, Li Y, Xing X, Wang C, Liu L, Li Y*. Tree of Life Based on Genome Context Networks. PLoS ONE. 2008, 3(10): e3357.

  58. Sun H, Skogerb G, Wang Z, Liu W*, Li Y*. Structural Relationships between Highly Conserved Elements and Genes in Vertebrate Genomes. PLoS ONE. 2008, 3(11): e3727.

  59. Dong C, Chu X, Wang Y, Wang Y, Jin L, Shi T, Huang W*, Li Y*. Exploration of Gene-Gene Interaction Effects Using Entropy-Based Methods. Eur J Hum Genet. 2008, 16(2): 229-35

  60. Yu F, Li Y, Liu L*, Li Y*. Comparative genomics of human-like Schistosoma japonicum genes indicates a putative mechanism for host-parasite relationship. Genomics. 2008, 91(2): 152-7.

  61. Zheng G, Qian Z, Yang Q, Wei C, Xie L, Zhu Y*, Li Y*. The combination approach of SVM and ECOC for powerful identification and classification of transcription factor. BMC. Bioinformatics. 2008, 9: 282

  62. Pan A, Ye X, Franco OH, Li H, Yu Z, Zou S, Zhang Z, Jiao S, Lin X*. Insulin resistance and depressive symptoms in middle-aged and elderly Chinese: Findings from the Nutrition and Health of Aging Population in China Study. J Affect Disord. 2008, 109(1-2): 75-82

  63. Huang T, Tu K, Shyr Y, Wei CC, Xie L*, Li YX*. The prediction of interferon treatment effects based on time series microarray gene expression profiles. J Transl Med. 2008, 6(1): 44.

  64. Zhou H, Dai J, Sheng QH, Li RX, Shieh CH, Guttman A, Zeng R*.A fully automated 2-D LC-MS method utilizing online continuous pH and RP gradients for global proteome analysis.Electrophoresis.2007,28:4311-4319.[PDF]

  65. Changzheng Dong,Ziliang Qian, Peilin Jia, Ying Wang, Wei Huang,* and Yixue Li*.Gene-Centric Characteristics of Genome-Wide Association Studies.PLoS ONE. 2007; 2(12): e1262.[PDF]

  66. Xiang Y, Zhu Z, Han G, Ye X, Xu B, Peng Z, Ma Y, Yu Y, Lin H, Chen AP, Chen CD*. JARID1B is a histone H3 lysine 4 demethylase up-regulated in prostate cancer. PNAS. 2007 Nov 28 (Epub ahead of print).[PDF]

  67. Tang LY, Deng N, Wang LS, Dai J, Wang ZL, Jiang XS, Li SJ, Li L, Sheng QH, Wu DQ, Li L, Zeng R*. Quantitative Phosphoproteome Profiling of Wnt3a-mediated Signaling Network. Mol Cell Proteomics. (2007)6,1952-67.[PDF]

  68. Guohui Ding, Yan Sun, Hong Li, Zhen Wang, Haiwei Fan, Chuan Wang, Dan Yang and Yixue Li*. EPGD: a comprehensive web resource for integrating and displaying eukaryotic paralog/paralogon information. Nucleic Acids Res. 2007, published online on November 5.[PDF]

  69. Li S, Liu B, Cai Y*, Li Y*.Prediction Protein N-glycosylation by Combining Functional Doman and Secretion Information.J. Biomolecular Structure & Dynamics.2007,25:49-54

  70. Changzheng Dong,Xun Chu,Ying Wang,Yi Wang,Li Jin,Tieliu Shi,Wei Huang*,Yixue Li*. Exploration of Gene-Gene Interaction Effects Using Entropy-Based Methods. European Journal of Human Genetics. 2007, online publication, 31 October. [PDF]

  71. Jian Cui, Peng Li, Guang Li, Feng Xu, Chen Zhao, Yuhua Li*, Yixue Li,* and Tieliu Shi*. AtPID: Arabidopsis thaliana protein interactome database—an integrative platform for plant systems biology. Nucleic Acids Researc. 2007, published online on October 25.[PDF]

  72. L Xiong, F Kou, Y Yang, and JR Wu*. A novel role for IGF-1R in p53-mediated apoptosisthrough translational modulation of the p53-Mdm2 feedback loop. J Cell Biol 2007, 178:995-1007 .[PDF]

  73. Jing Zhao, Guo-Hui Ding, Lin Tao, Hong Yu, Zhong-Hao Yu, Jian-Hua Luo, Zhi-Wei Cao* and Yi-Xue Li*. Modular co-evolution of metabolic networks. BMC Bioinformatics. 2007, 8:311.[PDF]

  74. FD Yu, B Kang, YY Li, YX Li*. Functional analysis of schistosomes EF-hand domain-containing tegument proteins. Chinese Science Bulletin. 2007, 52(15): 2100-2107.

  75. Wei W, McCusker JH, Hyman RW, Jones T, Ning Y, Cao Z, Gu Z, Bruno D, Miranda M, Nguyen M, Wilhelmy J, Komp C, Tamse R, Wang X, Jia P, Luedi P, Oefner PJ, David L, Dietrich FS, Li Y, Davis RW, Steinmetz LM *. Genome sequencing and comparative analysis of Saccharomyces cerevisiae strain YJM789. PNAS. 2007, 104(31):12825-30. [PDF]

  76. Ziliang Qian, Lingyi Lu, XiaoJun Liu, Yu-Dong Cai*, and Yixue Li*. An Approach to Predict Transcription Factor DNA Binding Site Specificity Based upon Gene and Transcription Factor Functional Categorization. Bioinformatics Advance Access. published online on July 10, 2007.[PDF]

  77. Boshu Liu,Sujun Li, 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. 2007,358( 1): 136-139.. [PDF]

  78. Hui Yu, Feng Wang, Kang Tu, Lu Xie, Yuan-Yuan Li* and Yi-Xue Li*. Transcript-level annotation of Affymetrix probesets improves the interpretation of gene expression data. BMC Bioinformatics. 2007, 8:194.[PDF]

  79. 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. 2007,357(2):66-370.[PDF]

  80. Dai J, Jin WH, Sheng QH, Shieh CH, Wu JR, Zeng R*. Protein phosphorylation and expression profiling by Yin-yang multidimensional liquid chromatography (Yin-yang MDLC) mass spectrometry. J Proteome Res. 2007,6(1): 250-62. [PDF]

  81. JB Zhu, Y Yang and JR Wu*. Bcl-2 cleavages at two adjacent sites by different caspases promote cisplatin-induced apoptosis .Cell Research. 2007, 17:441-448. [PDF]

  82. J Zhao, L Tao, H Yu, JH Luo, ZW Cao*, YX Li*. Bow-tie topological features of metabolic networks and the functional significance. Chinese Science Bulletin. 2007, 52( 8): 1036-1045.

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

  84. Fu N, Drinnenberg I, Kelso J, Wu JR, Paabo S, Zeng R*, Khaitovich P*. Comparison of protein and mRNA expression evolution in humans and chimpanzees. PLoS ONE. 2007 ,2: e216. [PDF]

  85. HX Liu, GR Huang, HM Zhang, S Jiang, JR Wu*, ZJ Yao . A Structure-Activity Guided Strategy for Fluorescent Labeling of Annonaceous Acetogenin Mimetics and their Application in Cell Biology. Chembiochem. 2007, 8:172-177. [PDF]

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

  87. huo Fang, Jiong Yang, Yixue Li, Qingming Luo and Lei Liu* . Knowledge guided analysis of microarray data. J Biomed Inform. 2006, 39( 4) : 401-411.[PDF]

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

  89. Yuan-Yuan Li, Lei Qin, Zong-Ming Guo, Lei Liu, Hao Xu, Pei Hao, Jiong Su, Yixiang Shi, Wei-Zhong He*, and Yi-Xue Li* . In silico discovery of human natural antisense transcripts. BMC Bioinformatics. 2006, 7:18.[PDF]

  90. Niu G, Huang L, Wang Q, Jiang L, Huang M, Shen P, Fei J*. A novel strategy to identify the regulatory DNA-organized cooperations among transcription factors. FEBS Lett. 2006,580(2):415-24.[PDF]

  91. Sujun Li, Boshu Liu, Rong Zeng*, Yudong Cai *, Yixue Li*. Predicting O-glycosylation sites in mammalian proteins by using SVMs .Comput Biol Chem. 2006, 30(3): 203-208.[PDF]

  92. Jinguo Ding, Jiahao Shi, Dafu Cui, Linfeng Xu, Shuhui Duan, Lihe Guo, Jian FEI* .Development of Peptidic Dopamine Transporter Inhibitors via Aromatic Modification Mediated Conformational Restriction. Journal of Medicinal Chemistry.2006,49(14):4048-51. [PDF]

  93. Luo Ruoyu, Liao Sha, Zeng Shaoqun, Li Yixue and Luo Qingming* . FluxExplorer: a general platform for modeling and analyses of metabolic networks based on stoichiometry. Chinese Science Bulletin. 2006, 51( 6): 689 – 696.[PDF]

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

  95. Xu LF, Chu WJ, Qing XY, Li S, Wang XS, Qing GW, Fei J, Guo LH*. Protopine inhibits serotonin transporter and noradrenaline transporter and has the antidepressant-like effect in mice models. Neuropharmacology. 2006 50(8):934-40.[PDF]

  96. Zhuo FANG, Lei LIU, Jiong YANG, Qing-Ming LUO*, Yi-Xue LI*. Comparisons of Graph-structure Clustering Methods for Gene Expression Data. Acta Biochimica et Biophysica Sinica . 2006, 38(6): 379–384.. [PDF]

  97. Xiaojing Yu,Chuan Wang, Yixue Li*, 2006, Classification of protein quaternary structure by functional domain composition. BMC Bioinformatics. 2006, 7:187. [PDF]

  98. Ruoyu Luo, Sha Liao, Guanyang Tao, Yuanyuan Li, Yixue Li*, Qingming Luo*. Dynamic analysis of optimality in myocardial energy metabolism under normal and ischemic conditions. Molecular Systems Biology. 2006, 2:2006.0031. [PDF]

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

  100. Zhuo Wang, Xin-Guang Zhu, Yazhu Chen, Yuanyuan Li, Yixue Li*, Lei Liu*. Exploring photosynthesis evolution by comparative analysis of metabolic networks between chloroplasts and photosynthetic bacteria. BMC Genomics. 2006, 7:100.[PDF]

  101. Wu Wei, Guohui Ding, Xiaojing Wang, Jingchun Sun, Kang Tu, Pei Hao, Chuan Wang, Yi Zhong, Zhiwei Cao*, Tieliu Shi*, Yixue Li*. Comparative analysis of whole-genome sequences of Streptococcus suis. Chinese Science Bulletin. 2006, 51:1199 –1209. [PDF]

  102. You-Qing Cai, Guo-Qiang Cai, Guo-Xiang Liu, Qing Cai, Jia-Hao Shi, Jun Shi, Sun-Kai Ma, Xia Sun, Zhe-Jin Sheng, Zhen-Tong Mei, Dafu Cui, Lihe Guo, Zhugang Wang and Jian Fei* . Mice With Genetically Altered GABA Transporter Subtype I (GAT1) Expression Show Altered Behavioral Responses to Ethanol. Journal of Neuroscience Research. 2006, 84(2):255-67.[PDF]

  103. Wu Wei, ZhiWei Cao, Yu-Li Zhu, XiaoJing Wang, GuoHui Ding, Hao Xu, PeiLin Jia, Di Qu*, Antoine Danchin*,and YiXue Li*. Conserved genes in a path from commensalism to pathogenicity:comparative phylogenetic profiles of Staphylococcus epidermidis RP62A and ATCC12228. BMC Genomics. 2006, 7:112.[PDF]

  104. PL Jia, TL Shi*, YD Cai*.and YX Li*. Demonstration of two novel methods for predicting functional siRNA efficiency. BMC Bioinformatics. 2006, 7:271.[PDF]

  105. Lili Wang, Zhong Yang, Yuanyuan Li, Fudong Yu, Paul J. Brindley, Donald P. McManus, Dongzhi Wei, Zeguang Han, Zheng Feng, Yixue Li,*, Wei Hu*. Reconstruction and in silico analysis of MAPK signalling pathways in the human blood fluke, Schistosoma japonicum. FEBS Letters. 2006, 580:3677-3686.[PDF]

  106. Sun J-Ch, Xu J-L, Cao J-P, Liu Q, Guo X-K, Shi T-L*, Li Y-X*. Prediction and systematic study of protein-protein interaction networks of Leptospira interrogans. Chinese Science Bulletin. 2006, 51(11):1296-1305. [PDF]

  107. Jing Zhao, Hong Yu, Jianhua Luo, Z.W Cao, Yi-Xue Li*. Complex networks theory for analyzing metabolic networks. Chinese Science Bulletin . 2006 , 51 (13 ): 1529-1537.[PDF]

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

  109. LI Rong, CAO Shunliang, LI Yuanyuan, TAN Hao, ZHU Yangyong, ZHONG Yang, LI Yixue*. A Measure of Semantic Similarity between Gene Ontology Terms Based on Semantic Pathway Covering.P rogress in Natural Science. 2006, 16, (7): 721-726. 2007-7-31

  110. Hao Pei,Chen Min,Zhang Guoqing, He Weizhong, Li, Yixue*. Bioinformatics Research on the SARS Coronavirus (SARS_CoV) in China. Curr. Pharm. Design. 2006, 12, Nr. 35.

  111. Huang YB, Li J, Gao X, Sun JR, Lu Y, Feng T, Fei J, Cui DF, Xia QC, Ren J, Zhang YS. Human proinsulin C-peptide from a precursor overexpressed in Pichia pastoris. Acta Biochim Biophys Sin (Shanghai). 2006, 38(8): 586-92. [PDF]

  112. Guohui Ding, Jiuhong Kang, Qi Liu, Tieliu Shi, Gang Pei, and Yixue Li*. Insights into the coupling of duplication events and macroevolution from an age distribution of animal transmembrane gene families. Plos Computational Biology.2006, 2( 8):e102. [PDF]

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

  114. Ziliang Qian, Yudong Cai, Yixue Li*. Automatic Transcription Factor Classifier based on Functional Domain Composition. BBRC. 2006 , 347(1):141-4. [PDF]

  115. QH Sheng, LS Wang, J Dai, XS Jiang, RX Li, DJ Ma, YX Li, R Zeng, JR Wu*. Comparison of a proteomic approach with a microarray-based approach to detect exons in the mouse genome. Nat Genet. 2006, 38:1223-1224. [PDF]

  116. Bao S, Fei J*, Shen J, Gong SJ, Fang H, Husband AJ. Reserpine-induced model of stress suppresses mucosal immunity. Immunol Cell Biol. 2006 ,84(6):537-42

 

   
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