Yang Xu (Yu Xue)

ResearcherID ORCID

Publication Activity (10 Years)

Years Active: 2016-2024
Publications (10 Years): 38

Top Topics

Amyotrophic Lateral Sclerosis

Saccharomyces Cerevisiae

Top Venues

Nature communications

Nucleic acids research

National science review

This page only lists publications with an associated author ORCID identifier.

Publications

Junhong Qin, Xinhe Huang, Shengsong Gou, Sitao Zhang, Yujie Gou, Qian Zhang, Hongyu Chen, Lin Sun, Miaomiao Chen, Dan Liu, Cheng Han, Min Tang, Zihao Feng, Shenghui Niu, Lin Zhao, Yingfeng Tu, Ze-Xian Liu, Weimin Xuan, Lunzhi Dai, Da Jia, Yang Xu
Ketogenic diet reshapes cancer metabolism through lysine β-hydroxybutyrylation. Nature metabolism (2024)
Yujie Gou, Dan Liu, Miaomiao Chen, Yuxiang Wei, Xinhe Huang, Cheng Han, Zihao Feng, Chi Zhang, Teng Lu, Di Peng, Yang Xu
GPS-SUMO 2.0: an updated online service for the prediction of SUMOylation sites and SUMO-interacting motifs. Nucleic acids research 52 (W1) (2024)
Yujie Gou, Dan Liu, Miaomiao Chen, Yuxiang Wei, Xinhe Huang, Cheng Han, Zihao Feng, Chi Zhang, Teng Lu, Di Peng, Yang Xu
GPS-SUMO 2.0: an updated online service for the prediction of SUMOylation sites and SUMO-interacting motifs. Nucleic acids research 52 (W1) (2024)
Di Peng, Liubin Zheng, Dan Liu, Cheng Han, Xin Wang, Yan Yang, Li Song, Miaoying Zhao, Yanfeng Wei, Jiayi Li, Xiaoxue Ye, Yuxiang Wei, Zihao Feng, Xinhe Huang, Miaomiao Chen, Yujie Gou, Yang Xu, Luoying Zhang
Large-language models facilitate discovery of the molecular signatures regulating sleep and activity. Nature communications 15 (1) (2024)
Di Peng, Liubin Zheng, Dan Liu, Cheng Han, Xin Wang, Yan Yang, Li Song, Miaoying Zhao, Yanfeng Wei, Jiayi Li, Xiaoxue Ye, Yuxiang Wei, Zihao Feng, Xinhe Huang, Miaomiao Chen, Yujie Gou, Yang Xu, Luoying Zhang
Large-language models facilitate discovery of the molecular signatures regulating sleep and activity. Nature communications 15 (1) (2024)
Junhong Qin, Xinhe Huang, Shengsong Gou, Sitao Zhang, Yujie Gou, Qian Zhang, Hongyu Chen, Lin Sun, Miaomiao Chen, Dan Liu, Cheng Han, Min Tang, Zihao Feng, Shenghui Niu, Lin Zhao, Yingfeng Tu, Ze-Xian Liu, Weimin Xuan, Lunzhi Dai, Da Jia, Yang Xu
Ketogenic diet reshapes cancer metabolism through lysine β-hydroxybutyrylation. Nature metabolism 6 (8) (2024)
Di Peng, Liubin Zheng, Dan Liu, Cheng Han, Xin Wang, Yan Yang, Li Song, Miaoying Zhao, Yanfeng Wei, Jiayi Li, Xiaoxue Ye, Yuxiang Wei, Zihao Feng, Xinhe Huang, Miaomiao Chen, Yujie Gou, Yang Xu, Luoying Zhang
Large-language models facilitate discovery of the molecular signatures regulating sleep and activity. Nature communications 15 (1) (2024)
Yujie Gou, Dan Liu, Miaomiao Chen, Yuxiang Wei, Xinhe Huang, Cheng Han, Zihao Feng, Chi Zhang, Teng Lu, Di Peng, Yang Xu
GPS-SUMO 2.0: an updated online service for the prediction of SUMOylation sites and SUMO-interacting motifs. Nucleic acids research (2024)
Yujie Gou, Dan Liu, Miaomiao Chen, Yuxiang Wei, Xinhe Huang, Cheng Han, Zihao Feng, Chi Zhang, Teng Lu, Di Peng, Yang Xu
GPS-SUMO 2.0: an updated online service for the prediction of SUMOylation sites and SUMO-interacting motifs. Nucleic acids research 52 (W1) (2024)
Miaomiao Chen, Weizhi Zhang, Yujie Gou, Danyang Xu, Yuxiang Wei, Dan Liu, Cheng Han, Xinhe Huang, Chengzhi Li, Wan-Shan Ning, Di Peng, Yang Xu
GPS 6.0: an updated server for prediction of kinase-specific phosphorylation sites in proteins. Nucleic acids research (2023)
Ke Shui, Chenwei Wang, Xuedi Zhang, Shanshan Ma, Qinyu Li, Wan-Shan Ning, Weizhi Zhang, Miaomiao Chen, Di Peng, Hui Hu, Zheng Fang, An-Yuan Guo, Guanjun Gao, Mingliang Ye, Luoying Zhang, Yang Xu
Small-sample learning reveals propionylation in determining global protein homeostasis. Nature communications 14 (1) (2023)
Ke Shui, Chenwei Wang, Xuedi Zhang, Shanshan Ma, Qinyu Li, Wan-Shan Ning, Weizhi Zhang, Miaomiao Chen, Di Peng, Hui Hu, Zheng Fang, An-Yuan Guo, Guanjun Gao, Mingliang Ye, Luoying Zhang, Yang Xu
Small-sample learning reveals propionylation in determining global protein homeostasis. Nature communications 14 (1) (2023)
Ke Shui, Chenwei Wang, Xuedi Zhang, Shanshan Ma, Qinyu Li, Wan-Shan Ning, Weizhi Zhang, Miaomiao Chen, Di Peng, Hui Hu, Zheng Fang, An-Yuan Guo, Guanjun Gao, Mingliang Ye, Luoying Zhang, Yang Xu
Small-sample learning reveals propionylation in determining global protein homeostasis. Nature communications 14 (1) (2023)
Chenwei Wang, Xiaodan Tan, Dachao Tang, Yujie Gou, Cheng Han, Wan-Shan Ning, Shaofeng Lin, Weizhi Zhang, Miaomiao Chen, Di Peng, Yang Xu
GPS-Uber: a hybrid-learning framework for prediction of general and E3-specific lysine ubiquitination sites. Briefings in bioinformatics 23 (2) (2022)
Wan-Shan Ning, Yuxiang Wei, Letian Gao, Cheng Han, Yujie Gou, Shanshan Fu, Dan Liu, Chi Zhang, Xinhe Huang, Sicheng Wu, Di Peng, Chenwei Wang, Yang Xu
HemI 2.0: an online service for heatmap illustration. Nucleic acids research (2022)
Yanan Cao, Lingling Chen, Hua Chen, Yupeng Cun, Xiaofeng Dai, Hongli Du, Feng Gao, Fengbiao Guo, Ya-Long Guo, Pei Hao, Shunmin He, Shunping He, XiongLei He, Zheng Hu, Boon-Peng Hoh, Xin Jin, Qian Jiang, Qinghua Jiang, Asifullah Khan, Hong-Zhi Kong, Jin-Chen Li, Shuai Cheng Li, Ying Li, Qiang Lin, Jianquan Liu, Qi Liu, Jian Lu, Xuemei Lu, Shujin Luo, Qinghua Nie, Zilong Qiu, Tieliu Shi, Xiaofeng Song, Jianzhong Su, Sheng-Ce Tao, Chaolong Wang, Chuan-Chao Wang, Guo-Dong Wang, Ji-Guang Wang, Qi Wu, Shaoyuan Wu, Shuhua Xu, Yang Xu, Wenjun Yang, Zhaohui Yang, Kai Ye, Yuan-Nong Ye, Li Yu, Fangqing Zhao, Yiqiang Zhao, Weiwei Zhai, Dandan Zhang, Liye Zhang, Hou-Feng Zheng, Qi Zhou, Tianqi Zhu, Ya-Ping Zhang
Was Wuhan the early epicenter of the COVID-19 pandemic?-A critique. National science review 10 (4) (2022)
Wen-Kang Shen, Si-Yi Chen, Zi-Quan Gan, Yu-Zhu Zhang, Tao Yue, Miao-Miao Chen, Yang Xu, Hui Hu, An-Yuan Guo
AnimalTFDB 4.0: a comprehensive animal transcription factor database updated with variation and expression annotations. Nucleic acids research (2022)
Yanan Cao, Lingling Chen, Hua Chen, Yupeng Cun, Xiaofeng Dai, Hongli Du, Feng Gao, Fengbiao Guo, Ya-Long Guo, Pei Hao, Shunmin He, Shunping He, XiongLei He, Zheng Hu, Boon-Peng Hoh, Xin Jin, Qian Jiang, Qinghua Jiang, Asifullah Khan, Hong-Zhi Kong, Jin-Chen Li, Shuai Cheng Li, Ying Li, Qiang Lin, Jianquan Liu, Qi Liu, Jian Lu, Xuemei Lu, Shujin Luo, Qinghua Nie, Zilong Qiu, Tieliu Shi, Xiaofeng Song, Jianzhong Su, Sheng-Ce Tao, Chaolong Wang, Chuan-Chao Wang, Guo-Dong Wang, Ji-Guang Wang, Qi Wu, Shaoyuan Wu, Shuhua Xu, Yang Xu, Wenjun Yang, Zhaohui Yang, Kai Ye, Yuan-Nong Ye, Li Yu, Fangqing Zhao, Yiqiang Zhao, Weiwei Zhai, Dandan Zhang, Liye Zhang, Hou-Feng Zheng, Qi Zhou, Tianqi Zhu, Ya-Ping Zhang
Was Wuhan the early epicenter of the COVID-19 pandemic?-A critique. National science review 10 (4) (2022)
Yanan Cao, Lingling Chen, Hua Chen, Yupeng Cun, Xiaofeng Dai, Hongli Du, Feng Gao, Fengbiao Guo, Ya-Long Guo, Pei Hao, Shunmin He, Shunping He, XiongLei He, Zheng Hu, Boon-Peng Hoh, Xin Jin, Qian Jiang, Qinghua Jiang, Asifullah Khan, Hong-Zhi Kong, Jin-Chen Li, Shuai Cheng Li, Ying Li, Qiang Lin, Jianquan Liu, Qi Liu, Jian Lu, Xuemei Lu, Shujin Luo, Qinghua Nie, Zilong Qiu, Tieliu Shi, Xiaofeng Song, Jianzhong Su, Sheng-Ce Tao, Chaolong Wang, Chuan-Chao Wang, Guo-Dong Wang, Ji-Guang Wang, Qi Wu, Shaoyuan Wu, Shuhua Xu, Yang Xu, Wenjun Yang, Zhaohui Yang, Kai Ye, Yuan-Nong Ye, Li Yu, Fangqing Zhao, Yiqiang Zhao, Weiwei Zhai, Dandan Zhang, Liye Zhang, Hou-Feng Zheng, Qi Zhou, Tianqi Zhu, Ya-Ping Zhang
Was Wuhan the early epicenter of the COVID-19 pandemic?-A critique. National science review 10 (4) (2022)
Yanan Cao, Lingling Chen, Hua Chen, Yupeng Cun, Xiaofeng Dai, Hongli Du, Feng Gao, Fengbiao Guo, Ya-Long Guo, Pei Hao, Shunmin He, Shunping He, XiongLei He, Zheng Hu, Boon-Peng Hoh, Xin Jin, Qian Jiang, Qinghua Jiang, Asifullah Khan, Hong-Zhi Kong, Jin-Chen Li, Shuai Cheng Li, Ying Li, Qiang Lin, Jianquan Liu, Qi Liu, Jian Lu, Xuemei Lu, Shujin Luo, Qinghua Nie, Zilong Qiu, Tieliu Shi, Xiaofeng Song, Jianzhong Su, Sheng-Ce Tao, Chaolong Wang, Chuan-Chao Wang, Guo-Dong Wang, Ji-Guang Wang, Qi Wu, Shaoyuan Wu, Shuhua Xu, Yang Xu, Wenjun Yang, Zhaohui Yang, Kai Ye, Yuan-Nong Ye, Li Yu, Fangqing Zhao, Yiqiang Zhao, Weiwei Zhai, Dandan Zhang, Liye Zhang, Hou-Feng Zheng, Qi Zhou, Tianqi Zhu, Ya-Ping Zhang
Was Wuhan the early epicenter of the COVID-19 pandemic?-A critique. National science review 10 (4) (2022)
Yang Xu
Cutting-Edge Methods for Better Understanding Cells. Cells 11 (21) (2022)
Yangyang Yuan, Chenwei Wang, Xuran Zhuang, Shaofeng Lin, Miaomiao Luo, Wankun Deng, Jiaqi Zhou, Lihui Liu, Lina Mao, Wenbo Peng, Jian Chen, Qiangsong Wang, Yi-Lai Shu, Yang Xu, Pengyu Huang
PIM1 promotes hepatic conversion by suppressing reprogramming-induced ferroptosis and cell cycle arrest. Nature communications 13 (1) (2022)
Dachao Tang, Cheng Han, Shaofeng Lin, Xiaodan Tan, Weizhi Zhang, Di Peng, Chenwei Wang, Yang Xu
iPCD: A Comprehensive Data Resource of Regulatory Proteins in Programmed Cell Death. Cells 11 (13) (2022)
Weizhi Zhang, Zhu Han, Yang Xu, Da Jia
iCAL: a new pipeline to investigate autophagy selectivity and cancer. Autophagy 17 (7) (2021)
Zhu Han, Weizhi Zhang, Wan-Shan Ning, Chenwei Wang, Wankun Deng, Zhidan Li, Zehua Shang, Xiaofei Shen, Xiaohui Liu, Otto Baba, Tsuyoshi Morita, Lu Chen, Yang Xu, Da Jia
Model-based analysis uncovers mutations altering autophagy selectivity in human cancer. Nature communications 12 (1) (2021)
Wen-Jun Li, Chen-Wei Wang, Li Tao, Yong-Hong Yan, Mei-Jun Zhang, Ze-Xian Liu, Yu-Xin Li, Han-Qing Zhao, Xue-Mei Li, Xian-Dong He, Yang Xu, Meng-Qiu Dong
Insulin signaling regulates longevity through protein phosphorylation in Caenorhabditis elegans. Nature communications 12 (1) (2021)
Weizhi Zhang, Xiaodan Tan, Shaofeng Lin, Yujie Gou, Cheng Han, Chi Zhang, Wan-Shan Ning, Chenwei Wang, Yang Xu
CPLM 4.0: an updated database with rich annotations for protein lysine modifications. Nucleic acids research (2021)
Di Peng, Chen Ruan, Shanshan Fu, Chengwen He, Jing-Zhen Song, Hui Li, Yiran Tu, Dachao Tang, Lan Yao, Shaofeng Lin, Ying Shi, Weizhi Zhang, Hao Zhou, Le Zhu, Cong Ma, Cheng Chang, Jie Ma, Zhiping Xie, Chenwei Wang, Yang Xu
Atg9-centered multi-omics integration reveals new autophagy regulators in Saccharomyces cerevisiae. Autophagy (2021)
Yang Qiu, Di Wu, Wan-Shan Ning, Jiqian Xu, Ting Shu, Muhan Huang, Rong Chen, Jiancheng Zhang, Yang Han, Qingyu Yang, Ruiting Li, Xiaobo Yang, Yaxin Wang, Xiaojing Zou, Shangwen Pan, Chaolin Huang, Yang Xu, You Shang, Xi Zhou
Post-mortem tissue proteomics reveals the pathogenesis of multi-organ injuries of COVID-19. National science review 8 (11) (2021)
Xinyu Mei, Dashi Qi, Ting Zhang, Ying Zhao, Li Jin, Junli Hou, Jianhua Wang, Yan Lin, Yang Xu, Pingping Zhu, Ze-Xian Liu, Lei Huang, Ji Nie, Wen Si, Jingyi Ma, Jianhong Ye, Richard H Finnell, Hexige Saiyin, Hong-Yan Wang, Jianyuan Zhao, Shimin Zhao, Wei Xu
Inhibiting MARSs reduces hyperhomocysteinemia-associated neural tube and congenital heart defects. EMBO molecular medicine 12 (3) (2020)
Chen Ruan, Chenwei Wang, Xuanqing Gong, Ying Zhang, Wankun Deng, Jiaqi Zhou, Dengtong Huang, Zining Wang, Qiong Zhang, An-Yuan Guo, Jia-Hong Lu, Jinhao Gao, Di Peng, Yang Xu
An integrative multi-omics approach uncovers the regulatory role of CDK7 and CDK4 in autophagy activation induced by silica nanoparticles. Autophagy 17 (6) (2020)
Yaping Guo, Wan-Shan Ning, Peiran Jiang, Shaofeng Lin, Chenwei Wang, Xiaodan Tan, Lan Yao, Di Peng, Yang Xu
GPS-PBS: A Deep Learning Framework to Predict Phosphorylation Sites that Specifically Interact with Phosphoprotein-Binding Domains. Cells 9 (5) (2020)
Chenwei Wang, Ke Shui, Shanshan Ma, Shaofeng Lin, Ying Zhang, Bo Wen, Wankun Deng, Haodong Xu, Hui Hu, An-Yuan Guo, Yang Xu, Luoying Zhang
Integrated omics in Drosophila uncover a circadian kinome. Nature communications 11 (1) (2020)
Xin Yong, Lin Zhao, Wankun Deng, Hongbin Sun, Xue Zhou, Lejiao Mao, Wenfeng Hu, Xiaofei Shen, Qingxiang Sun, Daniel D Billadeau, Yang Xu, Da Jia
Mechanism of cargo recognition by retromer-linked SNX-BAR proteins. PLoS biology 18 (3) (2020)
Wan-Shan Ning, Shijun Lei, Jingjing Yang, Yukun Cao, Peiran Jiang, Qianqian Yang, Jiao Zhang, Xiaobei Wang, Fenghua Chen, Zhi Geng, Liang Xiong, Hongmei Zhou, Yaping Guo, Yulan Zeng, Heshui Shi, Lin Wang, Yang Xu, Zheng Wang
Open resource of clinical data from patients with pneumonia for the prediction of COVID-19 outcomes via deep learning. Nature biomedical engineering 4 (12) (2020)
Ying Zhang, Yubin Xie, Wenzhong Liu, Wankun Deng, Di Peng, Chenwei Wang, Haodong Xu, Chen Ruan, Yongjie Deng, Yaping Guo, Chenjun Lu, Cong Yi, Jian Ren, Yang Xu
DeepPhagy: a deep learning framework for quantitatively measuring autophagy activity in Saccharomyces cerevisiae. Autophagy 16 (4) (2019)
Gebreamlak Bezabih, Han Cheng, Bin Han, Mao Feng, Yang Xu, Han Hu, Jianke Li
Phosphoproteome Analysis Reveals Phosphorylation Underpinnings in the Brains of Nurse and Forager Honeybees (Apis mellifera). Scientific reports 7 (1) (2017)
Yang Xu, Shuang Zhang, Shaofeng Lin, Yaping Guo, Wankun Deng, Ying Zhang
WERAM: a database of writers, erasers and readers of histone acetylation and methylation in eukaryotes. Nucleic acids research 45 (D1) (2016)