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1. Xue Y#, Ren J#, Gao XJ, Jin CJ, Wen LP, Yao XB. GPS 2.0, a tool to predict kinase-specific phosphorylation sites in hierarchy. Molecular & Cellular Proteomics. 2008;7(9):1598-1608. ( IF: 8.834, cited by 222) 2. Ren J, Wen LP, Gao XJ, Jin CJ, Xue Y, Yao XB. CSS-Palm 2.0: an updated software for palmitoylation sites prediction. Protein Eng Des Sel. 2008;21(11):639-644. (IF: 3.023, cited by 165) 3. Ren J, Wen LP, Gao XJ, Jin CJ, Xue Y, Yao XB. DOG 1.0: illustrator of protein domain structures. Cell Research. 2009;19(2):271-273. (IF: 12.413, cited by 105) 4. Ren J, Gao XJ, Jin CJ, Zhu M, Wang XW, Shaw A, Wen LP, Yao XB, Xue Y. Systematic study of protein sumoylation: Development of a site-specific predictor of SUMOsp 2.0. Proteomics. 2009;9(12):3409-3412. (IF: 4.815, cited by 105) 5. Zhao Q, Xie YB, Zheng YY, Jiang S, Liu WZ, Mu WP, Liu ZX, Zhao Y, Xue Y* and Ren J*. GPS-SUMO: a tool for the prediction of sumoylation sites and SUMO-interaction motifs. Nucleic Acids Research. 2014;42: W325-30. (IF: 9.112, cited by 4) 6. Liu WZ, Xie YB, Ma JY, Luo XT, Nie P, Zuo ZX, Lahrmann U, Zhao Q, Zheng YY, Zhao Y, Xue Y* and Ren J*. IBS: an illustrator for the presentation and visualization of biological sequences. Bioinformatics. 2015; doi: 10.1093/bioinformatics/btv362. (IF: 4.981, In press) 7. Xue Y, Liu ZX, Gao XJ, Jin CJ, Wen LP, Yao XB, Ren J*. GPS-SNO: Computational Prediction of Protein S-Nitrosylation Sites with a Modified GPS Algorithm. Plos One. 2010;5(6): e11290. (IF: 4.411, cited by 53) 8. Xue Y, Liu ZX, Cao J, Ma Q, Gao X, Wang QQ, Jin CJ, Zhou YH, Wen LP, Ren J*. GPS 2.1: enhanced prediction of kinase-specific phosphorylation sites with an algorithm of motif length selection. Protein Eng Des Sel. 2011;24(3):255-260. (IF: 3.023, cited by 39) 9. Ren J, Jiang CH, Gao XJ, Liu ZX, Yuan ZN, Jin CJ, Wen LP, Zhang ZL, Xue Y, Yao XB. PhosSNP for Systematic Analysis of Genetic Polymorphisms That Influence Protein Phosphorylation. Molecular & Cellular Proteomics. 2010;9(4):623-634. (IF: 8.354, cited by 24) 10. Ren J, Liu ZX, Gao XJ, Jin CJ, Ye ML, Zou HF, Wen LP, Zhang ZL, Xue Y, Yao XB. MiCroKit 3.0: an integrated database of midbody, centrosome and kinetochore. Nucleic Acids Research. 2010;38:D155-D160. (IF: 9.112, cited by 11) 11. Liu ZX, Cao J, Gao XJ, Zhou YH, Wen LP, Yang X, Yao XB, Ren J*, Xue Y*. CPLA 1.0: an integrated database of protein lysine acetylation. Nucleic Acids Research. 2011;39:D1029-1034. (IF: 9.112, cited by 17) 12. Song CX, Ye ML, Jiang XN, Han GH, Songyang Z, Tan YX, Wang HY, Ren J*, Xue Y* & Zou HF*. Systematic analysis of protein phosphorylation networks from phosphoproteomic data. Molecular & Cellular Proteomics. 2012;11(10):1070-1083. (IF: 7.398, cited by 23) 13. Liu ZX#, Ren J#, Cao J#, He J, Yang Q, Ma Q, Gao XJ, Yao XB, Jin CJ, Xue Y. Systematic analysis of the Plk-mediated phosphoregulation in eukaryotes. Briefings in Bioinformatics. 2013;14 (3):344-360 (IF: 9.617) 14. Xue Y, Gao XJ, Cao J, Liu ZX, Jin CJ, Wen LP, Yao XB, Ren J*. A Summary of Computational Resources for Protein Phosphorylation. Current Protein & Peptide Science. 2010;11(6):485-496. (IF: 3.83, cited by 22) 15. Zheng YY, Guo JJ, Li X, Xie YB, Hou MM, Fu XY, Dai SK, Diao RC, Miao YY* and Ren J*. An integrated overview of spatiotemporal organization and regulation in mitosis in terms of the proteins in the functional supercomplexes. Frontiers in Microbiology. 2014; 5: 573 (IF: 3.989) 16. Liu ZX, Gao X, Ma Q, Cao J, Ren J*, Xue Y*. GPS-CCD: A novel computational program for prediction of calpain cleavage sites. Plos One.2011;6(4):e19001. (IF: 4.411, cited by 11) 17. Liu ZX, Cao J, Ma Q, Gao XJ, Ren J*, Xue Y*. GPS-YNO2: computational prediction of tyrosine nitration sites in proteins. Mol Biosyst. 2011; 7(4):1197-1204. (IF: 3.825, cited by 19) 18. Liu ZX, Ma Q, Cao J, Gao XJ, Ren J*, Xue Y*. GPS-PUP: computational prediction of pupylation sites in prokaryotic proteins. Mol Biosyst. 2011;7(10):2737-2740. (IF: 3.825, cited by 7) 19. Ren J, Gao XJ, Liu ZX, Cao J, Ma Q, Xue Y. Computational Analysis of Phosphoproteomics: Progresses and Perspectives. Current Protein & Peptide Science. 2011;7(12):591-601.(IF: 3.83) 20. Xue Y, Liu ZX, Cao J, Ren J.(2011) Systems and Computational Biology - Molecular and Cellular Experimental Systems. InTech. ISBN 978-953-307-280-7(Book Chapter)
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