PUBLICATIONS

2017

  • Yueyuan Zheng, Peng Nie, Di Peng. Zhihao He, Mengni Liu, Yubin Xie, Yanyan Miao, Zhixiang Zuo, Jian Ren. m6AVar: a database of functional variants involved in m6A modification. Nucleic Acids Research. gkx895 | Published: 03 October 2017. doi:10.1093/nar/gkx895
    [ Abstract ] [ Full Text ]
  • He Peng, Zhihong Liu, Xin Yan, Jian Ren & Jun Xu. A de novo substructure generation algorithm for identifying the privileged chemical fragments of liver X receptorβ agonists. Scientific Reports. 2017; 6:11121.
    [ Abstract ] [ Full Text ]
  • Jinwen Feng, Chen Ding, Naiqi Qiu, Xiaotian Ni, Dongdong Zhan, Wanlin Liu, Xia Xia, Peng Li, Bingxin Lu, Qi Zhao, Peng Nie, Lei Song, Quan Zhou, Mi Lai, Gaigai Guo Weimin Zhu, Jian Ren, Tieliu Shi & Jun Qin. Firmiana: towards a one-stop proteomic cloud platform for data processing and analysis. Nature Biotechnology. 35, 409–412 (2017) | doi:10.1038/nbt.3825.
    [ Abstract ] [ Full Text ] [ Software ]
  • Yubin Xie, Xiaotong Luo, Zhihao He, Yueyuan Zheng, Zhixiang Zuo, Qi Zhao, Yanyan Miao and Jian Ren*. VirusMap: A visualization database for the influenza A virus. Journal of Genetics and Genomics. 2017; Vol 44, Issue 4.
    [ Abstract ] [ Full Text ] [ Software ]
  • 2016

  • Xie YB, Zheng YY, Li HY, Luo XT, He ZH, Cao S, Shi Y, Zhao Q, Xue Y, Zuo ZX, Ren J*. GPS-Lipid: a robust tool for the prediction of multiple lipid modification sites. Scientific Reports. 2016; 6:28249.
    [ Abstract ] [ Full Text ] [ Software ]
  • Xie SQ, Nie P, Wang Y, Wang H, Li H, Yang Z, Liu Y*, Ren J*, Xie Z*. RPFdb: a database for genome wide information of translated mRNA generated from ribosome profiling. Nucleic Acids Research. 2016; 44:D254-D258.
    [ Abstract ] [ Full Text ] [ Database ]
  • 2015

  • 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; 31(20):3359-61
    [ Abstract ] [ Full Text ] [ Software ] [ ESI Hot Paper ]
  • Huang ZN, Ma LL, Wang YB, Pan ZC, Ren J, Liu ZX, Xue Y. MiCroKiTS 4.0: a database of midbody, centrosome, kinetochore, telomere and spindle. Nucleic Acids Research. 2015;43: D328-D334.
    [ Abstract ] [ Full Text ] [ Database ]
  • Jiang W, Liu N, Chen XZ, Sun Y, Li B, Ren XY, Qin WF, Jiang N, Xu YF, Li YQ, Ren J, Cho WCS, Yun JP, Zeng J, Liu LZ, Li L, Guo Y, Mai HQ, Zeng MS, Kang TB, Jia WH, Shao JY, Ma J. Genome-Wide Identification of a Methylation Gene Panel as a Prognostic Biomarker in Nasopharyngeal Carcinoma. 2864-2873. Molecular Cancer Therapeutics. 2015;14(12)
    [ Abstract ] [ Full Text ]
  • Wang YB, Cheng H, Pan ZC, Ren J, Liu ZX and Xue Y. Reconfiguring phosphorylation signaling by genetic polymorphisms affects cancer susceptibility. Journal of Molecular Cell Biology. 2015;7(3):187-202.
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  • Lin MN, Xie ZY, Zhou YT, Li YM, Ren J, Peng XX, Yao MC, Yang ZZ, Liao QF. Dynamic metabonomic and microbiological response of rats to lincomycin exposure: an integrated microbiology and metabonomics analysis. Rsc Advances. 2015;5(80): 65415-65426.
    [ Abstract ] [ Full Text ]
  • Shi C, Yin J, Liu Z, Wu JX, Zhao Q, Ren J, Yao N. A systematic simulation of the effect of salicylic acid on sphingolipid metabolism. Frontiers in Plant Science. 2015;6:186.
    [ Abstract ] [ Full Text ]
  • 2014

  • 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
    [ Abstract ] [ Full Text ]
  • 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.
    [ Abstract ] [ Full Text ] [ Software ] [ ESI HCP ]
  • Liu ZX, Wang YB, Gao TS, Pan ZC, Cheng H, Yang Q, Cheng ZY, Guo AY, Ren J and Xue Y. CPLM: a database of protein lysine modifications. Nucleic Acids Research. 2014;42:D531-536.
    [ Abstract ] [ Full Text ] [ Database ]
  • Cheng H, Deng WK, Wang YB, Ren J, Liu ZX, Xue Y. dbPPT: a comprehensive database of protein phosphorylation in plants. Database. 2014;2014.
    [ Abstract ] [ Full Text ] [ Database ]
  • Wang YB, Dai ZY, Cheng H, Liu ZX, Pan ZC, Deng WK, Gao TS, Li XT, Yao YG, Ren J and Xue Y. Towards a better understanding of the novel avian-origin H7N9 influenza A virus in China. Scientific Reports. 2014; 3:2318.
    [ Abstract ] [ Full Text ]
  • Pan ZC, Liu ZX, Cheng H, Wang YB, Gao TS, Ullah S, Ren J and Xue Y. Systematic Analysis of the in Situ Crosstalk of Tyrosine Modifications Reveals No Additional Natural Selection on Multiply Modified Residues. Scientific Reports. 2014;4:7331.
    [ Abstract ] [ Full Text ]
  • Yao YG, Ma LL, Jia Q, Deng WK, Liu ZX, Zhang YW, Ren J, Xue Y, Jia HB, Yang Q. Systematic characterization of small RNAome during zebrafish early developmental stages. BMC Genomics. 2014;15:117.
    [ Abstract ] [ Full Text ]
  • 2013

  • 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
    [ Abstract ] [ Full Text ]
  • Gao TS, Liu ZX, Wang YB, Cheng H, Yang Q, Guo AY, Ren J and Xue Y. UUCD: a family-based database of ubiquitin and ubiquitin-like conjugation. Nucleic Acids Research. 2013;41:D445-51
    [ Abstract ] [ Full Text ] [ Database ]
  • 2012

  • 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.
    [ Abstract ] [ Full Text ]
  • Liu ZX, Yuan F, Ren J, Cao J, Zhou YH, Yang Q, Xue Y. GPS-ARM: Computational Analysis of the APC/C Recognition Motif by Predicting D-Boxes and KEN-Boxes. Plos One. 2012; 7(3):e34370
    [ Abstract ] [ Full Text ] [ Software ]
  • 31. Cai RK, Liu ZX, Ren J, Ma C, Gao TS, Zhou YH, Yang Q, Xue Y. GPS-MBA: computational analysis of MHC class II epitopes in type 1 diabetes. Plos One. 2012; 7(3):e33884.
    [ Abstract ] [ Full Text ] [ Software ]
  • 2011

  • 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.
    [ Abstract ] [ Full Text ]
  • 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.
    [ Abstract ] [ Full Text ] [ Software ]
  • 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.
    [ Abstract ] [ Full Text ] [ Software ]
  • 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.
    [ Abstract ] [ Full Text ] [ Software ]
  • 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.
    [ Abstract ] [ Full Text ] [ Database ]
  • Liu ZX, Gao XJ, Cao J, Ma Q, Ren J, Xue Y. Computational studies of protein phosphorylation: from site-specific prediction to systematic network analysis. Amino Acids. 2011;41:S17.
    [ Abstract ] [ Full Text ]
  • 2010

  • 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.
    [ Abstract ] [ Full Text ]
  • 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.
    [ Abstract ] [ Full Text ] [ Software ]
  • 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.
    [ Abstract ] [ Full Text ] [ Software ]
  • 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.
    [ Abstract ] [ Full Text ] [ Database ]
  • 2009

  • 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.
    [ Abstract ] [ Full Text ] [ Software ]
  • 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.
    [ Abstract ] [ Full Text ] [ Software ]
  • Han GH, Ye ML, Jiang XN, Chen R, Ren J, Xue Y, Wang FJ, Song CX, Yao XB, Zou HF. Comprehensive and Reliable Phosphorylation Site Mapping of Individual Phosphoproteins by Combination of Multiple Stage Mass Spectrometric Analysis with a Target-Decoy Database Search. Analytical Chemistry. 2009;81(14):5794-5805.
    [ Abstract ] [ Full Text ]
  • 2008

  • 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.
    [ Abstract ] [ Full Text ] [ Software ] [ ESI HCP ]
  • 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.
    [ Abstract ] [ Full Text ] [ Software ]
  • Gao XJ, Jin CJ, Ren J, Yao XB, Xue Y. Proteome-wide prediction of PKA phosphorylation sites in eukaryotic kingdom. Genomics. 2008;92(6):457-463.
    [ Abstract ] [ Full Text ]