Feng Zhu

Publication Activity (10 Years)

Years Active: 2010-2024
Publications (10 Years): 68

Top Topics

Protein Functional

Computational Chemistry

Top Venues

Briefings Bioinform.

Nucleic Acids Res.

J. Chem. Inf. Model.

Comput. Biol. Medicine

Publications

Kenneth M. Merz Jr., Yee-Siew Choong, Zoe Cournia, Olexandr Isayev, Thereza A. Soares, Guo-Wei Wei, Feng Zhu
Editorial: Machine Learning in Materials Science. J. Chem. Inf. Model. 64 (10) (2024)
Kuerbannisha Amahong, Wei Zhang, Yu-Hong Liu, Teng Li, Shijie Huang, Lianyi Han, Lin Tao, Feng Zhu
RVvictor: Virus RNA-directed molecular interactions for RNA virus infection. Comput. Biol. Medicine 169 (2024)
Zhao Zhang, Fengcheng Li, Zixin Duan, Chaoqun Shi, Xiaona Wang, Feng Zhu, Weiwei Xue
OPTICS: An interactive online platform for photosensory and bio-functional proteins in optogenetic systems. Comput. Biol. Medicine 178 (2024)
Kenneth M. Merz Jr., Guo-Wei Wei, Feng Zhu
Editorial: Machine Learning in Bio-cheminformatics. J. Chem. Inf. Model. 64 (7) (2024)
Wei Zhang, Minjie Mou, Wei Hu, Mingkun Lu, Hanyu Zhang, Hongning Zhang, Yongchao Luo, Hongquan Xu, Lin Tao, Haibin Dai, Jianqing Gao, Feng Zhu
MOINER: A Novel Multiomics Early Integration Framework for Biomedical Classification and Biomarker Discovery. J. Chem. Inf. Model. 64 (7) (2024)
Lingyan Zheng, Shuiyang Shi, Xiuna Sun, Mingkun Lu, Yang Liao, Sisi Zhu, Hongning Zhang, Ziqi Pan, Pan Fang, Zhenyu Zeng, Honglin Li, Zhaorong Li, Weiwei Xue, Feng Zhu
MoDAFold: a strategy for predicting the structure of missense mutant protein based on AlphaFold2 and molecular dynamics. Briefings Bioinform. 25 (2) (2024)
Kenneth M. Merz Jr., Guo-Wei Wei, Feng Zhu
Editorial: Cutting-Edge Methodologies in Omics Data Analysis. J. Chem. Inf. Model. 64 (13) (2024)
Hong-Quan Xu, Wei Zhang, Ying Zhou, Zi-Xuan Yue, Tian-Ci Yan, Yuanyuan Zhang, Yu-Hong Liu, Yan-Feng Hong, Shuiping Liu, Feng Zhu, Lin Tao
Systematic Description of the Content Variation of Natural Products (NPs): To Prompt the Yield of High-Value NPs and the Discovery of New Therapeutics. J. Chem. Inf. Model. 63 (5) (2023)
Hongning Zhang, Mingkun Lu, Gaole Lin, Lingyan Zheng, Wei Zhang, Zhijian Xu, Feng Zhu
SoCube: an innovative end-to-end doublet detection algorithm for analyzing scRNA-seq data. Briefings Bioinform. 24 (3) (2023)
Shengzhe Deng, Haiwei Zhang, Rongpei Gou, Ding Luo, Zerong Liu, Feng Zhu, Weiwei Xue
Structure-Based Discovery of a Novel Allosteric Inhibitor against Human Dopamine Transporter. J. Chem. Inf. Model. 63 (14) (2023)
Wei Hu, Wei Zhang, Ying Zhou, Yongchao Luo, Xiuna Sun, Huimin Xu, Shuiyang Shi, Teng Li, Yichao Xu, Qianqian Yang, Yunqing Qiu, Feng Zhu, Haibin Dai
MecDDI: Clarified Drug-Drug Interaction Mechanism Facilitating Rational Drug Use and Potential Drug-Drug Interaction Prediction. J. Chem. Inf. Model. 63 (5) (2023)
Kenneth M. Merz Jr., Guo-Wei Wei, Feng Zhu
Editorial: Machine Learning in Bio-cheminformatics. J. Chem. Inf. Model. 63 (1) (2023)
Xiuna Sun, Yintao Zhang, Hanyang Li, Ying Zhou, Shuiyang Shi, Zhen Chen, Xin He, Hanyu Zhang, Fengcheng Li, Jiayi Yin, Minjie Mou, Yunzhu Wang, Yunqing Qiu, Feng Zhu
DRESIS: the first comprehensive landscape of drug resistance information. Nucleic Acids Res. 51 (D1) (2023)
Hong-Quan Xu, Huan Xiao, Jin-Hui Bu, Yan-Feng Hong, Yu-Hong Liu, Zi-Yue Tao, Shu-Fan Ding, Yi-Tong Xia, E. Wu, Zhen Yan, Wei Zhang, Gong-Xing Chen, Feng Zhu, Lin Tao
EMNPD: a comprehensive endophytic microorganism natural products database for prompt the discovery of new bioactive substances. J. Cheminformatics 15 (1) (2023)
Yongchao Luo, Panpan Wang, Minjie Mou, Hanqi Zheng, Jiajun Hong, Lin Tao, Feng Zhu
A novel strategy for designing the magic shotguns for distantly related target pairs. Briefings Bioinform. 24 (1) (2023)
Kenneth M. Merz Jr., Guo-Wei Wei, Feng Zhu
Editorial: Harnessing the Power of Large Language Model-Based Chatbots for Scientific Discovery. J. Chem. Inf. Model. 63 (17) (2023)
Yunxia Wang, Zhen Chen, Ziqi Pan, Shijie Huang, Jin Liu, Weiqi Xia, Hongning Zhang, Mingyue Zheng, Honglin Li, Tingjun Hou, Feng Zhu
RNAincoder: a deep learning-based encoder for RNA and RNA-associated interaction. Nucleic Acids Res. 51 (W1) (2023)
Wei Hu, Tingting Jin, Ziqi Pan, Huimin Xu, Lingyan Yu, Tingting Chen, Wei Zhang, Huifang Jiang, Wenjun Yang, Junjun Xu, Feng Zhu, Haibin Dai
An interpretable ensemble learning model facilitates early risk stratification of ischemic stroke in intensive care unit: Development and external validation of ICU-ISPM. Comput. Biol. Medicine 166 (2023)
Jianbo Fu, Qingxia Yang, Yongchao Luo, Song Zhang, Jing Tang, Ying Zhang, Hongning Zhang, Hanxiang Xu, Feng Zhu
Label-free proteome quantification and evaluation. Briefings Bioinform. 24 (1) (2023)
Shuiping Liu, Lu Chen, Yintao Zhang, Ying Zhou, Ying He, Zhen Chen, Shasha Qi, Jinyu Zhu, Xudong Chen, Hao Zhang, Yongchao Luo, Yunqing Qiu, Lin Tao, Feng Zhu
M6AREG: m6A-centered regulation of disease development and drug response. Nucleic Acids Res. 51 (D1) (2023)
Fengcheng Li, Jiayi Yin, Mingkun Lu, Minjie Mou, Zhaorong Li, Zhenyu Zeng, Ying Tan, Shanshan Wang, Xinyi Chu, Haibin Dai, Tingjun Hou, Su Zeng, Yuzong Chen, Feng Zhu
DrugMAP: molecular atlas and pharma-information of all drugs. Nucleic Acids Res. 51 (D1) (2023)
Kuerbannisha Amahong, Wei Zhang, Ying Zhou, Song Zhang, Jiayi Yin, Fengcheng Li, Hong-Quan Xu, Tian-Ci Yan, Zi-Xuan Yue, Yu-Hong Liu, Tingjun Hou, Yunqing Qiu, Lin Tao, Lianyi Han, Feng Zhu
CovInter: interaction data between coronavirus RNAs and host proteins. Nucleic Acids Res. 51 (D1) (2023)
Xueni Sun, Yintao Zhang, Ying Zhou, Xichen Lian, Lili Yan, Ting Pan, Ting Jin, Han Xie, Zimao Liang, Wenqi Qiu, Jianxin Wang, Zhaorong Li, Feng Zhu, Xinbing Sui
NPCDR: natural product-based drug combination and its disease-specific molecular regulation. Nucleic Acids Res. 50 (D1) (2022)
Guo-Wei Wei, Feng Zhu, Kenneth M. Merz Jr.
Editorial on Machine Learning. J. Chem. Inf. Model. 62 (17) (2022)
Chenyang Zhang, Minjie Mou, Ying Zhou, Wei Zhang, Xichen Lian, Shuiyang Shi, Mingkun Lu, Huaicheng Sun, Fengcheng Li, Yunxia Wang, Zhenyu Zeng, Zhaorong Li, Bing Zhang, Yunqing Qiu, Feng Zhu, Jianqing Gao
Biological activities of drug inactive ingredients. Briefings Bioinform. 23 (5) (2022)
Xiaona Wang, Fengcheng Li, Wenqi Qiu, Binbin Xu, Yanlin Li, Xichen Lian, Hongyan Yu, Zhao Zhang, Jianxin Wang, Zhaorong Li, Weiwei Xue, Feng Zhu
SYNBIP: synthetic binding proteins for research, diagnosis and therapy. Nucleic Acids Res. 50 (D1) (2022)
Tingting Fu, Fengcheng Li, Yang Zhang, Jiayi Yin, Wenqi Qiu, Xuedong Li, Xingang Liu, Wenwen Xin, Chengzhao Wang, Lushan Yu, Jianqing Gao, Qingchuan Zheng, Su Zeng, Feng Zhu
VARIDT 2.0: structural variability of drug transporter. Nucleic Acids Res. 50 (D1) (2022)
Qingxia Yang, Bo Li, Panpan Wang, Jicheng Xie, Yuhao Feng, Ziqiang Liu, Feng Zhu
LargeMetabo: an out-of-the-box tool for processing and analyzing large-scale metabolomic data. Briefings Bioinform. 23 (6) (2022)
Weiqi Xia, Lingyan Zheng, Jiebin Fang, Fengcheng Li, Ying Zhou, Zhenyu Zeng, Bing Zhang, Zhaorong Li, Honglin Li, Feng Zhu
PFmulDL: a novel strategy enabling multi-class and multi-label protein function annotation by integrating diverse deep learning methods. Comput. Biol. Medicine 145 (2022)
Song Zhang, Kuerbannisha Amahong, Chenyang Zhang, Fengcheng Li, Jianqing Gao, Yunqing Qiu, Feng Zhu
RNA-RNA interactions between SARS-CoV-2 and host benefit viral development and evolution during COVID-19 infection. Briefings Bioinform. 23 (1) (2022)
Fengcheng Li, Ying Zhou, Ying Zhang, Jiayi Yin, Yunqing Qiu, Jianqing Gao, Feng Zhu
POSREG: proteomic signature discovered by simultaneously optimizing its reproducibility and generalizability. Briefings Bioinform. 23 (2) (2022)
Fengcheng Li, Jiayi Yin, Mingkun Lu, Qingxia Yang, Zhenyu Zeng, Bing Zhang, Zhaorong Li, Yunqing Qiu, Haibin Dai, Yuzong Chen, Feng Zhu
ConSIG: consistent discovery of molecular signature from OMIC data. Briefings Bioinform. 23 (4) (2022)
Guo-Wei Wei, Thereza A. Soares, Habibah A. Wahab, Feng Zhu
Computational Chemistry in Asia. J. Chem. Inf. Model. 62 (21) (2022)
Ying Zhou, Yintao Zhang, Xichen Lian, Fengcheng Li, Chaoxin Wang, Feng Zhu, Yunqing Qiu, Yuzong Chen
Therapeutic target database update 2022: facilitating drug discovery with enriched comparative data of targeted agents. Nucleic Acids Res. 50 (D1) (2022)
Song Zhang, Xiuna Sun, Minjie Mou, Kuerbannisha Amahong, Huaicheng Sun, Wei Zhang, Shuiyang Shi, Zhaorong Li, Jianqing Gao, Feng Zhu
REGLIV: Molecular regulation data of diverse living systems facilitating current multiomics research. Comput. Biol. Medicine 148 (2022)
Minjie Mou, Ziqi Pan, Mingkun Lu, Huaicheng Sun, Yunxia Wang, Yongchao Luo, Feng Zhu
Application of Machine Learning in Spatial Proteomics. J. Chem. Inf. Model. 62 (23) (2022)
Hanyu Zhang, Yunxia Wang, Ziqi Pan, Xiuna Sun, Minjie Mou, Bing Zhang, Zhaorong Li, Honglin Li, Feng Zhu
ncRNAInter: a novel strategy based on graph neural network to discover interactions between lncRNA and miRNA. Briefings Bioinform. 23 (6) (2022)
Jing Tang, Yongheng Wang, Jianbo Fu, Xianglu Wu, Zhijie Han, Chuan Wang, Maiyuan Guo, Yingxiong Wang, Yubin Ding, Bo Yang, Feng Zhu
Functional characterization of disease/comorbidity-associated lncRNA. Quant. Biol. 9 (4) (2021)
Jiayi Yin, Fengcheng Li, Ying Zhou, Minjie Mou, Yinjing Lu, Kangli Chen, Jia Xue, Yongchao Luo, Jianbo Fu, Xu He, Jianqing Gao, Su Zeng, Lushan Yu, Feng Zhu
INTEDE: interactome of drug-metabolizing enzymes. Nucleic Acids Res. 49 (Database-Issue) (2021)
Song Zhang, Ying Zhou, Yanan Wang, Zhengwen Wang, Qitao Xiao, Ying Zhang, Yan Lou, Yunqing Qiu, Feng Zhu
The mechanistic, diagnostic and therapeutic novel nucleic acids for hepatocellular carcinoma emerging in past score years. Briefings Bioinform. 22 (2) (2021)
Wan Xiang Shen, Xian Zeng, Feng Zhu, Ya li Wang, Chu Qin, Ying Tan, Yu Yang Jiang, Yu Zong Chen
Out-of-the-box deep learning prediction of pharmaceutical properties by broadly learned knowledge-based molecular representations. Nat. Mach. Intell. 3 (4) (2021)
Jing Tang, Minjie Mou, Yunxia Wang, Yongchao Luo, Feng Zhu
MetaFS: Performance assessment of biomarker discovery in metaproteomics. Briefings Bioinform. 22 (3) (2021)
Song Zhang, Kuerbannisha Amahong, Xiuna Sun, Xichen Lian, Jin Liu, Huaicheng Sun, Yan Lou, Feng Zhu, Yunqing Qiu
The miRNA: a small but powerful RNA for COVID-19. Briefings Bioinform. 22 (2) (2021)
Jing Tang, Xianglu Wu, Minjie Mou, Chuan Wang, Lidan Wang, Fengcheng Li, Maiyuan Guo, Jiayi Yin, Wenqin Xie, Xiaona Wang, Yingxiong Wang, Yubin Ding, Weiwei Xue, Feng Zhu
GIMICA: host genetic and immune factors shaping human microbiota. Nucleic Acids Res. 49 (Database-Issue) (2021)
Jianbo Fu, Ying Zhang, Jin Liu, Xichen Lian, Jing Tang, Feng Zhu
Pharmacometabonomics: data processing and statistical analysis. Briefings Bioinform. 22 (5) (2021)
Chao Shen, Zhe Wang, Xiaojun Yao, Youyong Li, Tailong Lei, Ercheng Wang, Lei Xu, Feng Zhu, Dan Li, Tingjun Hou
Comprehensive assessment of nine docking programs on type II kinase inhibitors: prediction accuracy of sampling power, scoring power and screening power. Briefings Bioinform. 21 (1) (2020)
Qingxia Yang, Yunxia Wang, Ying Zhang, Fengcheng Li, Weiqi Xia, Ying Zhou, Yunqing Qiu, Honglin Li, Feng Zhu
NOREVA: enhanced normalization and evaluation of time-course and multi-class metabolomic data. Nucleic Acids Res. 48 (Webserver-Issue) (2020)
Zhijie Han, Weiwei Xue, Lin Tao, Yan Lou, Yunqing Qiu, Feng Zhu
Genome-wide identification and analysis of the eQTL lncRNAs in multiple sclerosis based on RNA-seq data. Briefings Bioinform. 21 (3) (2020)
Jiayi Yin, Wen Sun, Fengcheng Li, Jiajun Hong, Xiaoxu Li, Ying Zhou, Yinjing Lu, Mengzhi Liu, Xue Zhang, Na Chen, Xiuping Jin, Jia Xue, Su Zeng, Lushan Yu, Feng Zhu
VARIDT 1.0: variability of drug transporter database. Nucleic Acids Res. 48 (Database-Issue) (2020)
Ying Hong Li, Xiao Xu Li, Jiajun Hong, Yunxia Wang, Jianbo Fu, Hong Yang, Chun Yan Yu, Feng Cheng Li, Jie Hu, Weiwei Xue, Yu Yang Jiang, Yu Zong Chen, Feng Zhu
Clinical trials, progression-speed differentiating features and swiftness rule of the innovative targets of first-in-class drugs. Briefings Bioinform. 21 (2) (2020)
Yunxia Wang, Song Zhang, Fengcheng Li, Ying Zhou, Ying Zhang, Zhengwen Wang, Runyuan Zhang, Jiang Zhu, Yuxiang Ren, Ying Tan, Chu Qin, Yinghong Li, Xiaoxu Li, Yuzong Chen, Feng Zhu
Therapeutic target database 2020: enriched resource for facilitating research and early development of targeted therapeutics. Nucleic Acids Res. 48 (Database-Issue) (2020)
Jiayi Yin, Wen Sun, Feng Cheng Li, Jiajun Hong, Xiao Xu Li, Ying Zhou, Yinjing Lu, Mengzhi Liu, Xue Zhang, Na Chen, Xiuping Jin, Jia Xue, Su Zeng, Lushan Yu, Feng Zhu
VARIDT 1.0: variability of drug transporter database (Corrigendum). Nucleic Acids Res. 48 (Database-Issue) (2020)
Jiajun Hong, Yongchao Luo, Minjie Mou, Jianbo Fu, Yang Zhang, Weiwei Xue, Tian Xie, Lin Tao, Yan Lou, Feng Zhu
Convolutional neural network-based annotation of bacterial type IV secretion system effectors with enhanced accuracy and reduced false discovery. Briefings Bioinform. 21 (5) (2020)
Qingxia Yang, Bo Li, Jing Tang, Xuejiao Cui, Yunxia Wang, Xiaofeng Li, Jie Hu, Yuzong Chen, Weiwei Xue, Yan Lou, Yunqing Qiu, Feng Zhu
Consistent gene signature of schizophrenia identified by a novel feature selection strategy from comprehensive sets of transcriptomic data. Briefings Bioinform. 21 (3) (2020)
Jing Tang, Jianbo Fu, Yunxia Wang, Bo Li, Yinghong Li, Qingxia Yang, Xuejiao Cui, Jiajun Hong, Xiaofeng Li, Yuzong Chen, Weiwei Xue, Feng Zhu
ANPELA: analysis and performance assessment of the label-free quantification workflow for metaproteomic studies. Briefings Bioinform. 21 (2) (2020)
Jiajun Hong, Yongchao Luo, Yang Zhang, Junbiao Ying, Weiwei Xue, Tian Xie, Lin Tao, Feng Zhu
Protein functional annotation of simultaneously improved stability, accuracy and false discovery rate achieved by a sequence-based deep learning. Briefings Bioinform. 21 (4) (2020)
Jing Tang, Yunxia Wang, Jianbo Fu, Ying Zhou, Yongchao Luo, Ying Zhang, Bo Li, Qingxia Yang, Weiwei Xue, Yan Lou, Yunqing Qiu, Feng Zhu
A critical assessment of the feature selection methods used for biomarker discovery in current metaproteomics studies. Briefings Bioinform. 21 (4) (2020)
Qingxia Yang, Jiajun Hong, Yi Li, Weiwei Xue, Song Li, Hui Yang, Feng Zhu
A novel bioinformatics approach to identify the consistently well-performing normalization strategy for current metabolomic studies. Briefings Bioinform. 21 (6) (2020)
Zhe Wang, Xuwen Wang, Youyong Li, Tailong Lei, Ercheng Wang, Dan Li, Yu Kang, Feng Zhu, Tingjun Hou
farPPI: a webserver for accurate prediction of protein-ligand binding structures for small-molecule PPI inhibitors by MM/PB(GB)SA methods. Bioinform. 35 (10) (2019)
Chu Qin, Ying Tan, Shangying Chen, Xian Zeng, Xingxing Qi, Tian Jin, Huan Shi, Yiwei Wan, Yu Chen, Jingfeng Li, Weidong He, Yali Wang, Peng Zhang, Feng Zhu, Hongping Zhao, Yu Yang Jiang, Yuzong Chen
Clustering Bioactive Molecules in 3D Chemical Space with Unsupervised Deep Learning. CoRR (2019)
Gaoqi Weng, Ercheng Wang, Zhe Wang, Hui Liu, Feng Zhu, Dan Li, Tingjun Hou
HawkDock: a web server to predict and analyze the protein-protein complex based on computational docking and MM/GBSA. Nucleic Acids Res. 47 (Webserver-Issue) (2019)
Ying Hong Li, Chun Yan Yu, Xiao Xu Li, Peng Zhang, Jing Tang, Qingxia Yang, Tingting Fu, Xiaoyu Zhang, Xuejiao Cui, Gao Tu, Yang Zhang, Shuang Li, Fengyuan Yang, Qiu Sun, Chu Qin, Xian Zeng, Zhe Chen, Yu Zong Chen, Feng Zhu
Therapeutic target database update 2018: enriched resource for facilitating bench-to-clinic research of targeted therapeutics. Nucleic Acids Res. 46 (Database-Issue) (2018)
Jun Shang, Ben Hu, Junmei Wang, Feng Zhu, Yu Kang, Dan Li, Huiyong Sun, De-Xin Kong, Tingjun Hou
Cheminformatic Insight into the Differences between Terrestrial and Marine Originated Natural Products. J. Chem. Inf. Model. 58 (6) (2018)
Shuang Li, Xuejiao Cui, Feng Zhu
The Comprehensive Assessment of the Normalization Methods Applied to Metabolomics Data. ICBBS (2018)
Peng Zhang, Lin Tao, Xian Zeng, Chu Qin, Shangying Chen, Feng Zhu, Zerong Li, Yu Yang Jiang, Weiping Chen, Yuzong Chen
A protein network descriptor server and its use in studying protein, disease, metabolic and drug targeted networks. Briefings Bioinform. 18 (6) (2017)
Ting Feng, Fu Chen, Yu Kang, Huiyong Sun, Hui Liu, Dan Li, Feng Zhu, Tingjun Hou
HawkRank: a new scoring function for protein-protein docking based on weighted energy terms. J. Cheminformatics 9 (1) (2017)
Bo Li, Jing Tang, Qingxia Yang, Shuang Li, Xuejiao Cui, Yinghong Li, Yuzong Chen, Weiwei Xue, Xiaofeng Li, Feng Zhu
NOREVA: normalization and evaluation of MS-based metabolomics data. Nucleic Acids Res. 45 (Webserver-Issue) (2017)
Hong Yang, Chu Qin, Ying Hong Li, Lin Tao, Jin Zhou, Chun Yan Yu, Feng Xu, Zhe Chen, Feng Zhu, Yu Zong Chen
Therapeutic target database update 2016: enriched resource for bench to clinical drug target and targeted pathway information. Nucleic Acids Res. 44 (Database-Issue) (2016)
Yanping Jing, Bo Li, Na Chen, Xiaofeng Li, Jie Hu, Feng Zhu
The Discrimination of Learning Styles by Bayes-Based Statistics: an Extended Study on ILS System. Control. Intell. Syst. 43 (2) (2015)
Chu Qin, Cheng Zhang, Feng Zhu, Feng Xu, Shangying Chen, Peng Zhang, Ying Hong Li, Sheng-Yong Yang, Yu-Quan Wei, Lin Tao, Yu Zong Chen
Therapeutic target database update 2014: a resource for targeted therapeutics. Nucleic Acids Res. 42 (Database-Issue) (2014)
Feng Zhu, Zhe Shi, Chu Qin, Lin Tao, Xin Liu, Feng Xu, Li Zhang, Yang Song, Xianghui Liu, Jing-Xian Zhang, Bu-Cong Han, Peng Zhang, Yuzong Chen
Therapeutic target database update 2012: a resource for facilitating target-oriented drug discovery. Nucleic Acids Res. 40 (Database-Issue) (2012)
Feng Zhu, Bu-Cong Han, Pankaj Kumar, Xianghui Liu, Xiao Hua Ma, XiaoNa Wei, Lu Huang, Yangfan Guo, LianYi Han, ChanJuan Zheng, Yu Zong Chen
Update of TTD: Therapeutic Target Database. Nucleic Acids Res. 38 (Database-Issue) (2010)