DOG 1.0: illustrator of protein domain structures, Ren J, Wen LP, Gao XJ, Jin CJ, Xue Y, Yao XB, 2009
IBS 2.0: an upgraded illustrator for the visualization of biological sequences, Xie YB, Li HQ, Luo XT, Li HY, Gao QY, Zhang LWY, Teng YY, Zhao Q, Zuo ZX, Ren J, 2022
GPS-SUMO: a tool for the prediction of sumoylation sites and SUMO-interaction motifs, Zhao Q, Xie YB, Zheng YY, Jiang S, Liu WZ, Mu WP, Liu ZX, Zhao Y, Xue Y and Ren J, 2014
IBS: an illustrator for the presentation and visualization of biological sequences, 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, 2015
m6AVar: a database of functional variants involved in m6A modification, Zheng YY, Nie P, Peng D, He ZH, Liu MN, Xie YB, Miao YY, Zuo ZX and Ren J, 2018
BBCancer: an expression atlas of blood-based biomarkers in the early diagnosis of cancers, Zuo ZX, Hu HJ, Xu QX, Luo XT, Peng D, Zhu KY, Zhao Q, Xie YB, Ren J, 2020
CSS-Palm 2.0: an updated software for palmitoylation sites prediction, Ren J, Wen LP, Gao XJ, Jin CJ, Xue Y, Yao XB, 2008
GPS 2.0, a tool to predict kinase-specific phosphorylation sites in hierarchy, Xue Y, Ren J, Gao XJ, Jin CJ, Wen LP, Yao XB, 2008
m6A RNA modification controls autophagy through upregulating ULK1 protein abundance, Jin SH, Zhang XY, Miao YY, Liang PP, Zhu KY, She YC, Wu YX, Liu DA, Huang JJ, Ren J and Cui J, 2018
lnCAR: a comprehensive resource for lncRNAs from Cancer Arrays, Zheng YY, Xu QX, Liu MN, Hu HJ, Xie YB, Zuo ZX, Ren J, 2019
Systematic study of protein sumoylation: Development of a site-specific predictor of SUMOsp 2.0, Ren J, Gao XJ, Jin CJ, Zhu M, Wang XW, Shaw A, Wen LP, Yao XB, Xue Y, 2009
SPENCER: a comprehensive database for small peptides encoded by noncoding RNAs in cancer patients, Luo XT, Huang YT, Li HQ, Luo YH, Zuo ZX, Ren J, Xie YB, 2022
RPS: a comprehensive database of RNAs involved in liquid–liquid phase separation, Liu MN, Li HQ, Luo XT, Cai JY, Chen TJ, Xie YB, Ren J, Zuo ZX, 2022
TIRSF: a web server for screening gene signatures to predict Tumor immunotherapy response, Chen L, Chen TJ, Zhang Y, Lin HC, Wang RH, Wang YH, Li HY, Zuo ZX, Ren J, Xie YB, 2022
RM2Target: a comprehensive database for targets of writers, erasers and readers of RNA modifications, Bao XQ, Zhang Y, Li HQ, Teng YY, Ma LX, Chen ZH, Luo XT, Zheng J, Zhao A, Ren J, Zuo ZX, 2022
GPS-SNO: Computational Prediction of Protein S-Nitrosylation Sites with a Modified GPS Algorithm, Xue Y, Liu ZX, Gao XJ, Jin CJ, Wen LP, Yao XB, Ren J, 2010
GPS 2.1: enhanced prediction of kinase-specific phosphorylation sites with an algorithm of motif length selection, Xue Y, Liu ZX, Cao J, Ma Q, Gao X, Wang QQ, Jin CJ, Zhou YH, Wen LP, Ren J, 2011
DeepPhagy: a deep learning framework for quantitatively measuring autophagy activity in Saccharomyces cerevisiae, Zhang Y, Xie YB, Liu WZ, Deng WK, Peng Di, Wang CW, Xu HD, Ruan C, Deng YJ, Guo YP, Lu CJ, Yi C, Ren J, Xue Y, 2020
RMVar: an updated database of functional variants involved in RNA modifications, Luo XT, Li HQ, Liang JQ, Zhao Q, Xie YB, Ren J, Zuo ZX, 2021
PhosSNP for Systematic Analysis of Genetic Polymorphisms That Influence Protein Phosphorylation, Ren J, Jiang CH, Gao XJ, Liu ZX, Yuan ZN, Jin CJ, Wen LP, Zhang ZL, Xue Y, Yao XB, 2010
MiCroKit 3.0: an integrated database of midbody, centrosome and kinetochore, Ren J, Liu ZX, Gao XJ, Jin CJ, Ye ML, Zou HF, Wen LP, Zhang ZL, Xue Y, Yao XB, 2010
m6ASNP: a tool for annotating genetic variants by m6A function, Jiang S, Xie YB, He ZH, Zhang Y, Zhao YL, Chen L, Zheng YY, Miao YY, Zuo ZX and Ren J, 2018
DeepNitro: Prediction of Protein Nitration and Nitrosylation Sites by Deep Learning, Xie YB, Luo XT, Li YP, Chen L, Ma WB, Huang JJ, Cui J, Zhao Y, Xue Y, Zuo ZX and Ren J, 2018
autoRPA: A web server for constructing cancer staging models by recursive partitioning analysis, Xie YB, Luo XT, Li HQ, Xu QX, He ZH, Zhao Q, Zuo ZX, Ren J, 2020
DeepOMe: A Web Server for the Prediction of 2′-O-Me Sites Based on the Hybrid CNN and BLSTM Architecture, Li HY, Chen L, Huang ZL, Luo XT, Li HQ, Ren J, Xie YB, 2021
PTMsnp: A Web Server for the Identification of Driver Mutations That Affect Protein Post-translational Modification, Peng D, Li HQ, Hu BS, Zhang HW, Chen L, Lin SF, Zuo ZX, Yu Xue, Ren J, Xie YB, 2020
GPS-Lipid: a robust tool for the prediction of multiple lipid modification sites, Xie YB, Zheng YY, Li HY, Luo XT, He ZH, Cao S, Shi Y, Zhao Q, Xue Y, Zuo ZX, Ren J, 2016
CPLA 1.0: an integrated database of protein lysine acetylation, Liu ZX, Cao J, Gao XJ, Zhou YH, Wen LP, Yang X, Yao XB, Ren J, Xue Y, 2011
RPFdb: a database for genome wide information of translated mRNA generated from ribosome profiling, Xie SQ, Nie P, Wang Y, Wang H, Li H, Yang Z, Liu Y, Ren J, Xie Z, 2016
CrossICC: iterative consensus clustering of cross-platform gene expression data without adjusting batch effect, Zhao Q, Sun Y, Liu ZK, Zhang HW, Li XY, Zhu KY, Liu ZX, Ren J, Zuo ZX, 2019
Systematic analysis of protein phosphorylation networks from phosphoproteomic data, Song CX, Ye ML, Jiang XN, Han GH, Songyang Z, Tan YX, Wang HY, Ren J, Xue Y and Zou HF, 2012
Systematic analysis of the Plk-mediated phosphoregulation in eukaryotes, Liu ZX, Ren J, Cao J, He J, Yang Q, Ma Q, Gao XJ, Yao XB, Jin CJ, Xue Y, 2013
Pan-cancer analysis reveals the functional importance of protein lysine modification in cancer development, Chen L, Miao YY, Liu MN, Gao ZJ, Peng D, Zheng YY, Zuo ZX, Xie YB, Ren J, 2018
A Summary of Computational Resources for Protein Phosphorylation, Xue Y, Gao XJ, Cao J, Liu ZX, Jin CJ, Wen LP, Yao XB, Ren J, 2010
An integrated overview of spatiotemporal organization and regulation in mitosis in terms of the proteins in the functional supercomplexes, Zheng YY, Guo JJ, Li X, Xie YB, Hou MM, Fu XY, Dai SK, Diao RC, Miao YY and Ren J, 2014
VirusMap: A visualization database for the influenza A virus, Xie YB, Luo XT, He ZH, Zheng YY, Zuo ZX, Zhao Q, Miao YY and Ren J, 2017
GPS-CCD: A novel computational program for prediction of calpain cleavage sites, Liu ZX, Gao X, Ma Q, Cao J, Ren J, Xue Y, 2011
GPS-YNO2: computational prediction of tyrosine nitration sites in proteins, Liu ZX, Cao J, Ma Q, Gao XJ, Ren J, Xue Y, 2011
GPS-PUP: computational prediction of pupylation sites in prokaryotic proteins, Liu ZX, Ma Q, Cao J, Gao XJ, Ren J, Xue Y, 2011
Computational Analysis of Phosphoproteomics: Progresses and Perspectives, Ren J, Gao XJ, Liu ZX, Cao J, Ma Q, Xue Y, 2011
A de novo substructure generation algorithm for identifying the privileged chemical fragments of liver X receptorβ agonists, Peng H, Liu ZH, Yan X, Ren J and Xu J, 2017
Expression and regulation of long noncoding RNAs during the osteogenic differentiation of periodontal ligament stem cells in the inflammatory microenvironment, Zhang QB, Chen L, Cui SM, Li Y, Zhao Q, Cao W, Lai SX, Yin SJ, Zuo ZX, Ren J, 2017
