Yu Xue - RankMe

46 papers Journal 44Unranked 2

Year	Rank	Type	Title / Venue / Authors
2025	J	`jnl`	EPSD 2.0: An Updated Database of Protein Phosphorylation Sites Across Eukaryotic Species. Genom. Proteom. Bioinform. Miaomiao Chen, Yujie Gou, Ming Lei, Leming Xiao, Miaoying Zhao, Xinhe Huang, Dan Liu, Zihao Feng, Di Peng, Yu Xue
2025	J	`jnl`	GPSD: a hybrid learning framework for the prediction of phosphatase-specific dephosphorylation sites. Briefings Bioinform. Cheng Han, Shanshan Fu, Miaomiao Chen, Yujie Gou, Dan Liu, Chi Zhang, Xinhe Huang, Leming Xiao, Miaoying Zhao, Jiayi Zhang, Qiang Xiao, Di Peng, Yu Xue
2025	J	`jnl`	Taiji: A DPU Memory Elasticity Solution for In-production Cloud Environments. CoRR Hao Zheng, Longxiang Wang, Yu Xue, Qiang Wang, Yibin Shen, Xiaoshe Dong, Bang Di, Jia Wei, Shenyu Dong, Xingjun Zhang, Weichen Chen, Zhao Han, Sanqian Zhao, Dongdong Huang, Jie Qi, Yifan Yang, Zhao Gao, Yi Wang, Jinhu Li, Xudong Ren, Min He, Hang Yang, Xiao Zheng, Haijiao Hao, Jiesheng Wu
2023	J	`jnl`	AnimalTFDB 4.0: a comprehensive animal transcription factor database updated with variation and expression annotations. Nucleic Acids Res. Wen-Kang Shen, Si-Yi Chen, Zi-Quan Gan, Yu-Zhu Zhang, Tao Yue, Miaomiao Chen, Yu Xue, Hui Hu, An-Yuan Guo
2023	J	`jnl`	Dynamics of a Kuramoto Model with Two-Body and Three-Body Interactions. Int. J. Bifurc. Chaos Muyang Huang, Yu Xue, Haojie Luo, Yi Wang, Yuan Tang, Qiyun Wen
2023	J	`jnl`	GPS 6.0: an updated server for prediction of kinase-specific phosphorylation sites in proteins. Nucleic Acids Res. Miaomiao Chen, Weizhi Zhang, Yujie Gou, Danyang Xu, Yuxiang Wei, Dan Liu, Cheng Han, Xinhe Huang, Chengzhi Li, Wanshan Ning, Di Peng, Yu Xue
2022	J	`jnl`	CPLM 4.0: an updated database with rich annotations for protein lysine modifications. Nucleic Acids Res. Weizhi Zhang, Xiaodan Tan, Shaofeng Lin, Yujie Gou, Cheng Han, Chi Zhang, Wanshan Ning, Chenwei Wang, Yu Xue
2022	J	`jnl`	GPS-Uber: a hybrid-learning framework for prediction of general and E3-specific lysine ubiquitination sites. Briefings Bioinform. Chenwei Wang, Xiaodan Tan, Dachao Tang, Yujie Gou, Cheng Han, Wanshan Ning, Shaofeng Lin, Weizhi Zhang, Miaomiao Chen, Di Peng, Yu Xue
2022	J	`jnl`	HemI 2.0: an online service for heatmap illustration. Nucleic Acids Res. Wanshan Ning, Yuxiang Wei, Letian Gao, Cheng Han, Yujie Gou, Shanshan Fu, Dan Liu, Chi Zhang, Xinhe Huang, Sicheng Wu, Di Peng, Chenwei Wang, Yu Xue
2021	J	`jnl`	Database Resources of the National Genomics Data Center, China National Center for Bioinformation in 2021. Nucleic Acids Res. Yongbiao Xue, Yiming Bao, Zhang Zhang, Wenming Zhao, Jing-Fa Xiao, Shunmin He, Guoqing Zhang, Yixue Li, Guoping Zhao, Runsheng Chen, Shuhui Song, Lina Ma, Dong Zou, Dongmei Tian, Cuiping Li, Junwei Zhu, Zheng Gong, Meili Chen, Anke Wang, Yingke Ma, Mengwei Li, Xufei Teng, Ying Cui, Guangya Duan, Mochen Zhang, Tong Jin, Chengmin Shi, Zhenglin Du, Yadong Zhang, Chuandong Liu, Rujiao Li, Jingyao Zeng, Lili Hao, Shuai Jiang, Hua Chen, Dali Han, Tao Zhang, Wang Kang, Fei Yang, Jing Qu, Weiqi Zhang, Guanghui Liu, Lin Liu, Yang Zhang, Guangyi Niu, Tongtong Zhu, Changrui Feng, Xiaonan Liu, Yuansheng Zhang, Zhao Li, Ruru Chen, Qianpeng Li, Zhongyi Hua, Chao Jiang, Ziyuan Chen, Fangshu He, Yuyang Zhao, Yan Jin, Luqi Huang, Yuan Yuan, Chenfen Zhou, Qingwei Xu, Sheng He, Wei Ye, Ruifang Cao, Pengyu Wang, Yunchao Ling, Xing Yan, Qingzhong Wang, Qiang Du, Wenting Zong, Hongen Kang, Zhuang Xiong, Wendi Huan, Sirui Zhang, Qiguang Xia, Xiaojuan Fan, Zefeng Wang, Xu Chen, Tingting Chen, Sisi Zhang, Bixia Tang, Lili Dong, Zhewen Zhang, Zhonghuang Wang, Hailong Kang, Yanqing Wang, Song Wu, Ming Chen, Chang Liu, Yujia Xiong, Xueying Shao, Yanyan Li, Honghong Zhou, Xiaomin Chen, Yu Zheng, Quan Kang, Di Hao, LiLi Zhang, Huaxia Luo, Yajing Hao, Peng Zhang, Zhi Nie, Shuhuan Yu, Jian Sang, Zhaohua Li, Xiangquan Zhang, Qing Zhou, Shuang Zhai, Yaping Zhang, Guodong Wang, Qianghui Zhu, Xin Li, Menghua Li, Jun Yan, Chen Li, Zhennan Wang, Xiangfeng Wang, Yuanming Liu, Hong Luo, Xiaoyuan Wu, Hai-Chun Jing, Lianhe Zhao, Jiajia Wang, Tinrui Song, Yi Zhao, Furrukh Mehmood, Shahid Ali, Amjad Ali, Shoaib Saleem, Irfan Hussain, Amir Ali Abbasi, Zhixiang Zuo, Jian Ren, Xinxin Zhang, Yun Xiao, Xia Li, Yiran Tu, Yu Xue, Wanying Wu, Peifeng Ji, Fangqing Zhao, Xianwen Meng, Di Peng, Hao Luo, Feng Gao, Wanshan Ning, Shaofeng Lin, Teng Liu, An-Yuan Guo, Hao Yuan, Yong E. Zhang, Xiaodan Tan, Weizhi Zhang, Yubin Xie, Chenwei Wang, Chun-Jie Liu, De-Chang Yang, Feng Tian, Ge Gao, Dachao Tang, Lan Yao, Qinghua Cui, Ni A. An, Chuan-Yun Li, Xiaotong Luo
2021	J	`jnl`	EPSD: a well-annotated data resource of protein phosphorylation sites in eukaryotes. Briefings Bioinform. Shaofeng Lin, Chenwei Wang, Jiaqi Zhou, Ying Shi, Chen Ruan, Yiran Tu, Lan Yao, Di Peng, Yu Xue
2021	J	`jnl`	GPS-Palm: a deep learning-based graphic presentation system for the prediction of S-palmitoylation sites in proteins. Briefings Bioinform. Wanshan Ning, Peiran Jiang, Yaping Guo, Chenwei Wang, Xiaodan Tan, Weizhi Zhang, Di Peng, Yu Xue
2020	J	`jnl`	GPS 5.0: An Update on the Prediction of Kinase-specific Phosphorylation Sites in Proteins. Genom. Proteom. Bioinform. Chenwei Wang, Hao-Dong Xu, Shaofeng Lin, Wankun Deng, Jiaqi Zhou, Ying Zhang, Ying Shi, Di Peng, Yu Xue
2020	J	`jnl`	HybridSucc: A Hybrid-learning Architecture for General and Species-specific Succinylation Site Prediction. Genom. Proteom. Bioinform. Wanshan Ning, Hao-Dong Xu, Peiran Jiang, Han Cheng, Wankun Deng, Yaping Guo, Yu Xue
2019	J	`jnl`	iEKPD 2.0: an update with rich annotations for eukaryotic protein kinases, protein phosphatases and proteins containing phosphoprotein-binding domains. Nucleic Acids Res. Yaping Guo, Di Peng, Jiaqi Zhou, Shaofeng Lin, Chenwei Wang, Wanshan Ning, Hao-Dong Xu, Wankun Deng, Yu Xue
2018	J	`jnl`	Bioinformatics Commons: The Cornerstone of Life and Health Sciences. Genom. Proteom. Bioinform. Zhang Zhang, Yu Xue, Fangqing Zhao
2018	J	`jnl`	DeepNitro: Prediction of Protein Nitration and Nitrosylation Sites by Deep Learning. Genom. Proteom. Bioinform. Yubin Xie, Xiaotong Luo, Yupeng Li, Li Chen, Wenbin Ma, Junjiu Huang, Jun Cui, Yong Zhao, Yu Xue, Zhixiang Zuo, Jian Ren
2018	J	`jnl`	PTMD: A Database of Human Disease-associated Post-translational Modifications. Genom. Proteom. Bioinform. Hao-Dong Xu, Yongbo Wang, Shaofeng Lin, Wankun Deng, Di Peng, Qinghua Cui, Yu Xue
2018	J	`jnl`	Predicting lysine-malonylation sites of proteins using sequence and predicted structural features. J. Comput. Chem. Ghazaleh Taherzadeh, Yuedong Yang, Hao-Dong Xu, Yu Xue, Alan Wee-Chung Liew, Yaoqi Zhou
2018	J	`jnl`	iUUCD 2.0: an update with rich annotations for ubiquitin and ubiquitin-like conjugations. Nucleic Acids Res. Jiaqi Zhou, Yang Xu, Shaofeng Lin, Yaping Guo, Wankun Deng, Ying Zhang, Anyuan Guo, Yu Xue
2017	J	`jnl`	CGDB: a database of circadian genes in eukaryotes. Nucleic Acids Res. Shujing Li, Ke Shui, Ying Zhang, Yongqiang Lv, Wankun Deng, Shahid Ullah, Luoying Zhang, Yu Xue
2017	J	`jnl`	Computational prediction of methylation types of covalently modified lysine and arginine residues in proteins. Briefings Bioinform. Wankun Deng, Yongbo Wang, Lili Ma, Ying Zhang, Shahid Ullah, Yu Xue
2017	J	`jnl`	WERAM: a database of writers, erasers and readers of histone acetylation and methylation in eukaryotes. Nucleic Acids Res. Yang Xu, Shuang Zhang, Shaofeng Lin, Yaping Guo, Wankun Deng, Ying Zhang, Yu Xue
2016	J	`jnl`	Precision Medicine: What Challenges Are We Facing? Genom. Proteom. Bioinform. Yu Xue, Eric-Wubbo Lameijer, Kai Ye, Kunlin Zhang, Suhua Chang, Xiaoyue Wang, Jianmin Wu, Ge Gao, Fangqing Zhao, Jian Li, Chunsheng Han, Shuhua Xu, Jing-Fa Xiao, Xuerui Yang, Xiaomin Ying, Xuegong Zhang, Wei-Hua Chen, Yun Liu, Zhang Zhang, Kun Huang, Jun Yu
2015	J	`jnl`	AnimalTFDB 2.0: a resource for expression, prediction and functional study of animal transcription factors. Nucleic Acids Res. Hong-Mei Zhang, Teng Liu, Chun-Jie Liu, Shuangyang Song, Xiantong Zhang, Wei Liu, Haibo Jia, Yu Xue, An-Yuan Guo
2015	J	`jnl`	IBS: an illustrator for the presentation and visualization of biological sequences. Bioinform. Wenzhong Liu, Yubin Xie, Jiyong Ma, Xiaotong Luo, Peng Nie, Zhixiang Zuo, Urs Lahrmann, Qi Zhao, Yueyuan Zheng, Yong Zhao, Yu Xue, Jian Ren
2015	J	`jnl`	MiCroKiTS 4.0: a database of midbody, centrosome, kinetochore, telomere and spindle. Nucleic Acids Res. Zhengnan Huang, Lili Ma, Yongbo Wang, Zhicheng Pan, Jian Ren, Zexian Liu, Yu Xue
2015	J	`jnl`	dbPSP: a curated database for protein phosphorylation sites in prokaryotes. Database J. Biol. Databases Curation Zhicheng Pan, Bangshan Wang, Ying Zhang, Yongbo Wang, Shahid Ullah, Jian Ren, Zexian Liu, Yu Xue
2014	J	`jnl`	CPLM: a database of protein lysine modifications. Nucleic Acids Res. Zexian Liu, Yongbo Wang, Tianshun Gao, Zhicheng Pan, Han Cheng, Qing Yang, Zhongyi Cheng, Anyuan Guo, Jian Ren, Yu Xue
2014	J	`jnl`	EKPD: a hierarchical database of eukaryotic protein kinases and protein phosphatases. Nucleic Acids Res. Yongbo Wang, Zexian Liu, Han Cheng, Tianshun Gao, Zhicheng Pan, Qing Yang, Anyuan Guo, Yu Xue
2014	J	`jnl`	GPS-SUMO: a tool for the prediction of sumoylation sites and SUMO-interaction motifs. Nucleic Acids Res. Qi Zhao, Yubin Xie, Yueyuan Zheng, Shuai Jiang, Wenzhong Liu, Weiping Mu, Zexian Liu, Yong Zhao, Yu Xue, Jian Ren
2014	J	`jnl`	dbPPT: a comprehensive database of protein phosphorylation in plants. Database J. Biol. Databases Curation Han Cheng, Wankun Deng, Yongbo Wang, Jian Ren, Zexian Liu, Yu Xue
2013	J	`jnl`	Systematic analysis of the Plk-mediated phosphoregulation in eukaryotes. Briefings Bioinform. Zexian Liu, Jian Ren, Jun Cao, Jiang He, Xuebiao Yao, Changjiang Jin, Yu Xue
2013	J	`jnl`	UUCD: a family-based database of ubiquitin and ubiquitin-like conjugation. Nucleic Acids Res. Tianshun Gao, Zexian Liu, Yongbo Wang, Han Cheng, Qing Yang, Anyuan Guo, Jian Ren, Yu Xue
2012	J	`jnl`	CPSS: a computational platform for the analysis of small RNA deep sequencing data. Bioinform. Yuanwei Zhang, Bo Xu, Yifan Yang, Rongjun Ban, Huan Zhang, Xiaohua Jiang, Howard J. Cooke, Yu Xue, Qinghua Shi
2011	J	`jnl`	CPLA 1.0: an integrated database of protein lysine acetylation. Nucleic Acids Res. Zexian Liu, Jun Cao, Xinjiao Gao, Yanhong Zhou, Longping Wen, Xiangjiao Yang, Xuebiao Yao, Jian Ren, Yu Xue
2011	J	`jnl`	Prediction of novel pre-microRNAs with high accuracy through boosting and SVM. Bioinform. Yuanwei Zhang, Yifan Yang, Huan Zhang, Xiaohua Jiang, Bo Xu, Yu Xue, Yunxia Cao, Qian Zhai, Yong Zhai, Mingqing Xu, Howard J. Cooke, Qinghua Shi
2010	J	`jnl`	MiCroKit 3.0: an integrated database of midbody, centrosome and kinetochore. Nucleic Acids Res. Jian Ren, Zexian Liu, Xinjiao Gao, Changjiang Jin, Mingliang Ye, Hanfa Zou, Longping Wen, Zhaolei Zhang, Yu Xue, Xuebiao Yao
2008	—	`conf`	Proteome-Wide Analysis of Amino Acid Absence in Composition and Plasticity. ICIC (1) Yuzhong Zhao, Yun Xu, Zhihao Wang, Changjiang Jin, Xinjiao Gao, Yu Xue, Xuebiao Yao
2006	J	`jnl`	CSS-Palm: palmitoylation site prediction with a clustering and scoring strategy (CSS). Bioinform. Fengfeng Zhou, Yu Xue, Xuebiao Yao, Ying Xu
2006	—	`conf`	HSPPIP: An Online Tool for Prediction of Protein-Protein Interactions in Humans. ICIC (3) Yu Xue, Changjiang Jin, Xuebiao Yao
2006	J	`jnl`	MeMo: a web tool for prediction of protein methylation modifications. Nucleic Acids Res. Hu Chen, Yu Xue, Ni Huang, Xuebiao Yao, Zhirong Sun
2006	J	`jnl`	NBA-Palm: prediction of palmitoylation site implemented in Naïve Bayes algorithm. BMC Bioinform. Yu Xue, Hu Chen, Changjiang Jin, Zhirong Sun, Xuebiao Yao
2006	J	`jnl`	PPSP: prediction of PK-specific phosphorylation site with Bayesian decision theory. BMC Bioinform. Yu Xue, Ao Li, Lirong Wang, Huanqing Feng, Xuebiao Yao
2006	J	`jnl`	SUMOsp: a web server for sumoylation site prediction. Nucleic Acids Res. Yu Xue, Fengfeng Zhou, Chuanhai Fu, Ying Xu, Xuebiao Yao
2005	J	`jnl`	GPS: a comprehensive www server for phosphorylation sites prediction. Nucleic Acids Res. Yu Xue, Fengfeng Zhou, Minjie Zhu, Kashif Ahmed, Guoliang Chen, Xuebiao Yao