Education Background

2008—Present, Ph.D., Computer Application Technology, East China University of Science and Technology
2004—2008, B.E., Computer Science & Technology, East China University of Science and Technology

Research Scopes

1. Drug-target database construction
2. Network pharmacology
3. Bioinformatics
4. Machine Learning

Projects

1. Chemmapper
   ChemMapper is a versatile web-based tool for exploring target pharmacology and chemical relationships against any given small molecules via 3D and 2D similarity method. The platform provides a variety of molecular similarity calculation methods, and integrates information of over 3 million compounds, of which, 400,000 compounds contain biological activity information and corresponding target pharmacology and function annotation. It can be applied to chemical genomics, drug target, multi-pharmacology, virtual screening and skeleton transition study.
   Accessibility: http://lilab.ecust.edu.cn/chemmapper/
2. PTID: Pesticide-Target Interaction Database
   PTID is a web-based database providing association information of pesticides and corresponding potential targets from text mining. The database integrates the annotations for 1 347 pesticides classified into 22 groups, including physicochemical, toxicological, ecotoxicological and other related information. The potential targets for each pesticide in PTID were identified from literatures via the online text mining tool PloySearch. 4 245 target terms was finally mapped onto the pesticides and classified accordingly, with corresponding sequences and SwissProt/TrEMBL annotations provided.
   Accessibility: http://lilab.ecust.edu.cn/ptid/
3. Molecular Surface Generation Based on Iso-contouring Algorithm
   Implemented a method which generates the smooth and high quality triangular surface meshes efficiently. This method has been integrated into the D³Pharma software package.

Publication

1. Jiayu Gong, Xiaofeng Liu, Xianwen Cao, Yanyan Diao, Daqi Gao, Honglin Li and Xuhong Qian. PTID: an integrated web resource and computational tool for agrochemical discovery. Bioinformatics, 2013, 29(2) : 292-294
2. Jiayu Gong, Chaoqian Cai, Xiaofeng Liu, Xin Ku, Hualiang Jiang, Daqi Gao and Honglin Li, ChemMapper: a Versatile Web Server for Exploring Target Pharmacology and Chemical Relationship Based on 3D Molecular Similarity Methods. Bioinformatics, 2013, 29(14) : 1827-1829
3. Chaoqian Cai, Jiayu Gong,, Xiaofeng Liu, Hualiang Jiang, Daqi Gao and Honglin Li. A novel, customizable and optimizable parameter method using spherical harmonics for molecular shape similarity comparisons. Journal of Molecular Modeling, 2012, 18(4), 1597-1610
4. Chuanxin Zou, Jiayu Gong and Honglin Li, An improved sequence based prediction protocol for DNA-binding proteins using SVM and comprehensive feature analysis, BMC Bioinformatics, 2013, 14 (1): 90
5. Li Liu, Xiaofeng Liu, Jiayu Gong, Hualiang Jiang, and Honglin Li. Accelerating All-Atom Normal Mode Analysis with Graphics Processing Unit. Journal of Chemical Theory and Computation ,2011 7(6), 1595-1603
6. Daqi Gao, Jiuming Ji, Jiayu Gong and Chaoqian Cai, Quantitative analysis of different volatile organic compounds using an improved electronic nose, Meas. Sci. Technol., 2012, 23 (10):15103
7. Xiaofeng Liu, Sisheng Ouyang, Biao Yu, Kai Huang, Yabo Liu, Jiayu Gong, Sisuan Zheng, Zhihua Li, Honglin Li, Hualiang Jiang. PharmMapper Server: a web server for potential drug target identification via pharmacophore mapping approach. Nucleic Acids Research,2010,38, W609-W614.