GPS: a comprehensive www server for phosphorylation sites prediction. - Yu Xue 001; Fengfeng Zhou; Minjie Zhu; Kashif Ahmed; Guoliang Chen 001; Xuebiao Yao (Nucleic Acids Res., 2005)

HSPPIP: An Online Tool for Prediction of Protein-Protein Interactions in Humans. - Yu Xue 001; Changjiang Jin; Xuebiao Yao (ICIC (3), 2006)

CSS-Palm: palmitoylation site prediction with a clustering and scoring strategy (CSS). - Fengfeng Zhou; Yu Xue 001; Xuebiao Yao; Ying Xu 001 (Bioinform., 2006)

NBA-Palm: prediction of palmitoylation site implemented in Naïve Bayes algorithm. - Yu Xue 001; Hu Chen; Changjiang Jin; Zhirong Sun; Xuebiao Yao (BMC Bioinform., 2006)

PPSP: prediction of PK-specific phosphorylation site with Bayesian decision theory. - Yu Xue 001; Ao Li 001; Lirong Wang; Huanqing Feng; Xuebiao Yao (BMC Bioinform., 2006)

MeMo: a web tool for prediction of protein methylation modifications. - Hu Chen; Yu Xue 001; Ni Huang; Xuebiao Yao; Zhirong Sun (Nucleic Acids Res., 2006)

SUMOsp: a web server for sumoylation site prediction. - Yu Xue 001; Fengfeng Zhou; Chuanhai Fu; Ying Xu 001; Xuebiao Yao (Nucleic Acids Res., 2006)

Proteome-Wide Analysis of Amino Acid Absence in Composition and Plasticity. - YuZhong Zhao; Yun Xu; ZhiHao Wang; Changjiang Jin; Xinjiao Gao; Yu Xue 001; Xuebiao Yao (ICIC (1), 2008)

MiCroKit 3.0: an integrated database of midbody, centrosome and kinetochore. - Jian Ren 002; Zexian Liu; Xinjiao Gao; Changjiang Jin; Mingliang Ye; Hanfa Zou; Longping Wen; Zhaolei Zhang; Yu Xue 001; Xuebiao Yao (Nucleic Acids Res., 2010)

Prediction of novel pre-microRNAs with high accuracy through boosting and SVM. - Yuanwei Zhang; Yifan Yang 001; Huan Zhang; Xiaohua Jiang; Bo Xu; Yu Xue 001; Yunxia Cao; Qian Zhai; Yong Zhai; Mingqing Xu; Howard J. Cooke; Qinghua Shi (Bioinform., 2011)

CPLA 1.0: an integrated database of protein lysine acetylation. - Zexian Liu; Jun Cao; Xinjiao Gao; Yanhong Zhou; Longping Wen; Xiangjiao Yang; Xuebiao Yao; Jian Ren 002; Yu Xue 001 (Nucleic Acids Res., 2011)

CPSS: a computational platform for the analysis of small RNA deep sequencing data. - Yuanwei Zhang; Bo Xu; Yifan Yang 001; Rongjun Ban; Huan Zhang; Xiaohua Jiang; Howard J. Cooke; Yu Xue 001; Qinghua Shi (Bioinform., 2012)

Systematic analysis of the Plk-mediated phosphoregulation in eukaryotes. - Zexian Liu; Jian Ren 002; Jun Cao; Jiang He; Xuebiao Yao; Changjiang Jin; Yu Xue 001 (Briefings Bioinform., 2013)

UUCD: a family-based database of ubiquitin and ubiquitin-like conjugation. - Tianshun Gao; Zexian Liu; Yongbo Wang; Han Cheng; Qing Yang; Anyuan Guo; Jian Ren 002; Yu Xue 001 (Nucleic Acids Res., 2013)

dbPPT: a comprehensive database of protein phosphorylation in plants. - Han Cheng; Wankun Deng; Yongbo Wang; Jian Ren 002; Zexian Liu; Yu Xue 001 (Database J. Biol. Databases Curation, 2014)

CPLM: a database of protein lysine modifications. - Zexian Liu; Yongbo Wang; Tianshun Gao; Zhicheng Pan; Han Cheng; Qing Yang; Zhongyi Cheng; Anyuan Guo; Jian Ren 002; Yu Xue 001 (Nucleic Acids Res., 2014)

EKPD: a hierarchical database of eukaryotic protein kinases and protein phosphatases. - Yongbo Wang; Zexian Liu; Han Cheng; Tianshun Gao; Zhicheng Pan; Qing Yang; Anyuan Guo; Yu Xue 001 (Nucleic Acids Res., 2014)

GPS-SUMO: a tool for the prediction of sumoylation sites and SUMO-interaction motifs. - Qi Zhao; Yubin Xie; Yueyuan Zheng; Shuai Jiang; Wenzhong Liu; Weiping Mu; Zexian Liu; Yong Zhao 013; Yu Xue 001; Jian Ren 002 (Nucleic Acids Res., 2014)

dbPSP: a curated database for protein phosphorylation sites in prokaryotes. - Zhicheng Pan; Bangshan Wang; Ying Zhang 052; Yongbo Wang; Shahid Ullah; Jian Ren 002; Zexian Liu; Yu Xue 001 (Database J. Biol. Databases Curation, 2015)

IBS: an illustrator for the presentation and visualization of biological sequences. - Wenzhong Liu; Yubin Xie; Jiyong Ma; Xiaotong Luo; Peng Nie; Zhixiang Zuo; Urs Lahrmann; Qi Zhao; Yueyuan Zheng; Yong Zhao 013; Yu Xue 001; Jian Ren 002 (Bioinform., 2015)

MiCroKiTS 4.0: a database of midbody, centrosome, kinetochore, telomere and spindle. - Zhengnan Huang; Lili Ma; Yongbo Wang; Zhicheng Pan; Jian Ren 002; Zexian Liu; Yu Xue 001 (Nucleic Acids Res., 2015)

AnimalTFDB 2.0: a resource for expression, prediction and functional study of animal transcription factors. - Hong-Mei Zhang 008; Teng Liu; Chun-Jie Liu; Shuangyang Song; Xiantong Zhang; Wei Liu 032; Haibo Jia; Yu Xue 001; An-Yuan Guo (Nucleic Acids Res., 2015)

Precision Medicine: What Challenges Are We Facing? - Yu Xue 001; Eric-Wubbo Lameijer; Kai Ye 001; Kunlin Zhang; Suhua Chang; Xiaoyue Wang; Jianmin Wu; Ge Gao; Fangqing Zhao; Jian Li; Chunsheng Han; Shuhua Xu; et al. (Genom. Proteom. Bioinform., 2016)

Computational prediction of methylation types of covalently modified lysine and arginine residues in proteins. - Wankun Deng; Yongbo Wang; Lili Ma; Ying Zhang 052; Shahid Ullah; Yu Xue 001 (Briefings Bioinform., 2017)

CGDB: a database of circadian genes in eukaryotes. - Shujing Li; Ke Shui; Ying Zhang 052; Yongqiang Lv; Wankun Deng; Shahid Ullah; Luoying Zhang; Yu Xue 001 (Nucleic Acids Res., 2017)

WERAM: a database of writers, erasers and readers of histone acetylation and methylation in eukaryotes. - Yang Xu; Shuang Zhang; Shaofeng Lin; Yaping Guo; Wankun Deng; Ying Zhang 052; Yu Xue 001 (Nucleic Acids Res., 2017)

DeepNitro: Prediction of Protein Nitration and Nitrosylation Sites by Deep Learning. - Yubin Xie; Xiaotong Luo; Yupeng Li; Li Chen; Wenbin Ma; Junjiu Huang; Jun Cui; Yong Zhao 013; Yu Xue 001; Zhixiang Zuo; Jian Ren 002 (Genom. Proteom. Bioinform., 2018)

PTMD: A Database of Human Disease-associated Post-translational Modifications. - Hao-Dong Xu; Yongbo Wang; Shaofeng Lin; Wankun Deng; Di Peng; Qinghua Cui; Yu Xue 001 (Genom. Proteom. Bioinform., 2018)

Bioinformatics Commons: The Cornerstone of Life and Health Sciences. - Zhang Zhang 002; Yu Xue 001; Fangqing Zhao (Genom. Proteom. Bioinform., 2018)

Predicting lysine-malonylation sites of proteins using sequence and predicted structural features. - Ghazaleh Taherzadeh; Yuedong Yang; Hao-Dong Xu; Yu Xue 001; Alan Wee-Chung Liew; Yaoqi Zhou (J. Comput. Chem., 2018)

iUUCD 2.0: an update with rich annotations for ubiquitin and ubiquitin-like conjugations. - Jiaqi Zhou 003; Yang Xu; Shaofeng Lin; Yaping Guo; Wankun Deng; Ying Zhang 052; Anyuan Guo; Yu Xue 001 (Nucleic Acids Res., 2018)

iEKPD 2.0: an update with rich annotations for eukaryotic protein kinases, protein phosphatases and proteins containing phosphoprotein-binding domains. - Yaping Guo; Di Peng; Jiaqi Zhou 003; Shaofeng Lin; Chenwei Wang; Wanshan Ning; Hao-Dong Xu; Wankun Deng; Yu Xue 001 (Nucleic Acids Res., 2019)

HybridSucc: A Hybrid-learning Architecture for General and Species-specific Succinylation Site Prediction. - Wanshan Ning; Hao-Dong Xu; Peiran Jiang; Han Cheng; Wankun Deng; Yaping Guo; Yu Xue 001 (Genom. Proteom. Bioinform., 2020)

GPS 5.0: An Update on the Prediction of Kinase-specific Phosphorylation Sites in Proteins. - Chenwei Wang; Hao-Dong Xu; Shaofeng Lin; Wankun Deng; Jiaqi Zhou 003; Ying Zhang 052; Ying Shi; Di Peng; Yu Xue 001 (Genom. Proteom. Bioinform., 2020)

EPSD: a well-annotated data resource of protein phosphorylation sites in eukaryotes. - Shaofeng Lin; Chenwei Wang; Jiaqi Zhou 003; Ying Shi; Chen Ruan; Yiran Tu; Lan Yao; Di Peng; Yu Xue 001 (Briefings Bioinform., 2021)

GPS-Palm: a deep learning-based graphic presentation system for the prediction of S-palmitoylation sites in proteins. - Wanshan Ning; Peiran Jiang; Yaping Guo; Chenwei Wang; Xiaodan Tan; Weizhi Zhang 002; Di Peng; Yu Xue 001 (Briefings Bioinform., 2021)

Database Resources of the National Genomics Data Center, China National Center for Bioinformation in 2021. - Yongbiao Xue; Yiming Bao; Zhang Zhang 002; Wenming Zhao; Jing-Fa Xiao; Shunmin He; Guoqing Zhang 006; Yixue Li; Guoping Zhao; Runsheng Chen; Shuhui Song; Lina Ma; et al. (Nucleic Acids Res., 2021)

GPS-Uber: a hybrid-learning framework for prediction of general and E3-specific lysine ubiquitination sites. - Chenwei Wang; Xiaodan Tan; Dachao Tang; Yujie Gou; Cheng Han; Wanshan Ning; Shaofeng Lin; Weizhi Zhang 002; Miaomiao Chen; Di Peng; Yu Xue 001 (Briefings Bioinform., 2022)

HemI 2.0: an online service for heatmap illustration. - Wanshan Ning; Yuxiang Wei 005; Letian Gao; Cheng Han; Yujie Gou; Shanshan Fu; Dan Liu; Chi Zhang; Xinhe Huang; Sicheng Wu; Di Peng; Chenwei Wang; et al. (Nucleic Acids Res., 2022)

Database Resources of the National Genomics Data Center, China National Center for Bioinformation in 2022. - Yongbiao Xue; Yiming Bao; Zhang Zhang 002; Wenming Zhao; Jing-Fa Xiao; Shunmin He; Guoqing Zhang 006; Yixue Li; Guoping Zhao; Runsheng Chen; Jingyao Zeng; Yadong Zhang; et al. (Nucleic Acids Res., 2022)

CPLM 4.0: an updated database with rich annotations for protein lysine modifications. - Weizhi Zhang 002; Xiaodan Tan; Shaofeng Lin; Yujie Gou; Cheng Han; Chi Zhang; Wanshan Ning; Chenwei Wang; Yu Xue 001 (Nucleic Acids Res., 2022)

AnimalTFDB 4.0: a comprehensive animal transcription factor database updated with variation and expression annotations. - Wen-Kang Shen; Si-Yi Chen; Zi-Quan Gan; Yu-Zhu Zhang; Tao Yue; Miaomiao Chen; Yu Xue 001; Hui Hu; An-Yuan Guo (Nucleic Acids Res., 2023)

Dynamics of a Kuramoto Model with Two-Body and Three-Body Interactions. - Muyang Huang; Yu Xue 001; Haojie Luo; Yi Wang; Yuan Tang; Qiyun Wen (Int. J. Bifurc. Chaos, 2023)

GPS 6.0: an updated server for prediction of kinase-specific phosphorylation sites in proteins. - Miaomiao Chen; Weizhi Zhang 002; Yujie Gou; Danyang Xu; Yuxiang Wei 005; Dan Liu; Cheng Han; Xinhe Huang; Chengzhi Li; Wanshan Ning; Di Peng; Yu Xue 001 (Nucleic Acids Res., 2023)

GPSD: a hybrid learning framework for the prediction of phosphatase-specific dephosphorylation sites. - Cheng Han; Shanshan Fu; Miaomiao Chen; Yujie Gou; Dan Liu; Chi Zhang; Xinhe Huang; Leming Xiao; Miaoying Zhao; Jiayi Zhang; Qiang Xiao; Di Peng; et al. (Briefings Bioinform., 2024)