熊毅 - 上海交通大学 - 生命科学技术学院

个人简介

2006年获武汉大学软件工程专业工学学士学位，2011年获武汉大学计算机应用技术专业生物信息学方向工学博士学位（硕博连读）。博士期间（2009年-2011年）在上海交通大学生物信息学和生物统计学系交流学习两年，2012年-2013年赴美国普渡大学生物系Daisuke Kihara教授实验室从事博士后科研工作。自2014年参加工作以来，先后主持教育部留学回国人员科研启动基金、国家自然科学基金青年项目、上海市智能信息处理重点实验室开放基金等课题，并作为项目骨干参与国家重点研发计划、国家自然科学基金重点项目、面上项目等课题。

研究领域

主要从事蛋白质、药物相关的计算模型的研究，以及生物信息学工具、数据库开发，研究兴趣主要包括：1) 蛋白质结构生物信息学（蛋白质-核酸相互作用界面的分析与预测，蛋白质-蛋白质、蛋白质-配体等相互作）；2) 健康医疗大数据挖掘与分析（药物组合预测、药物代谢酶CYP450、药物-靶标关系等）；3) 机器学习及其在生物信息学分类问题中的应用。

近期论文

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Yi Xiong, Qiankun Wang, Junchen Yang, Xiaolei Zhu*, Dong-Qing Wei*. (2018) PredT4SE-Stack: prediction of bacterial type IV secreted effectors from protein sequences using a stacked ensemble method. Frontiers in Microbiology (2017 IF: 4.019) (In press) Yi Xiong, Yanhua Qiao, Daisuke Kihara, Xiaolei Zhu*, Dong-Qing Wei*. (2018) Survey of Machine Learning Techniques for Prediction of the Isoform Specificity of Cytochrome P450 Substrates. Current Drug Metabolism (2017 IF: 2.655) (In press) Huiyuan Zhang, Qin Xu, Yi Xiong, Shaoliang Peng, Kotni Meena Kumari, Dong-Qing Wei*. (2018) Membrane Defect and Water Leakage Caused by Passive Calcium Permeation. Journal of Molecular Liquids (2017 IF: 4.513) (In press) Jingjing He, Ting Fang, Zizheng Zhang, Bei Huang, Xiaolei Zhu*, Yi Xiong*. (2018) PseUI: Pseudouridine sites identification based on RNA sequence information. BMC Bioinformatics 19: 306. (2017 IF: 2.213) Ronghui You, Zihan Zhang, Yi Xiong, Fengzhu Sun, Hiroshi Mamitsuka, Shanfeng Zhu*. (2018) GOLabeler: Improving Sequence-Based Large-Scale Protein Function Prediction by Learning to Rank. Bioinformatics (2017 IF: 5.481) Ling Liu†, Yi Xiong†, Hongyun Gao, Dong-Qing Wei, Julie C Mitchell*, Xiaolei Zhu*. (2018) dbAMEPNI: a Database of Alanine Mutagenic Effects for Protein-Nucleic Acid Interactions. Database-The Journal of Biological Databases and Curation (2017 IF: 3.978) (Co-first authors) Yi Xiong, Xiaolei Zhu, Hao Dai, Dong-Qing Wei. (2018) Survey of Computational Approaches for Prediction of DNA-Binding Residues on Protein Surfaces. Computational Systems Biology: Methods and Protocols, Methods in Molecular Biology, Tao Huang (ed.), Springer. vol. 1754:223-234. Li-Yue Bai, Hao Dai, Qin Xu, Muhammad Junaid, Shao-Liang Peng, Xiaolei Zhu, Yi Xiong*, Dong-Qing Wei*. (2018) Prediction of Effective Drug Combinations by an Improved Naïve Bayesian Algorithm. International Journal of Molecular Sciences 19(2), 467. (2017 IF: 3.687) Yanhua Qiao†, Yi Xiong†, Hongyun Gao, Xiaolei Zhu*, Peng Chen*. (2018) Protein-Protein Interface Hot Spots Prediction Based on a Hybrid Feature Selection Strategy. BMC Bioinformatics 19: 14. (2017 IF: 2.213) (Co-first authors) Haojie Jin†, Cun Wang†, Guangzhi Jin†, Haoyu Ruan, Dishui Gu, Lin Wei, Hui Wang, Ning Wang, Einthavy Arunachalam, Yurong Zhang, Xuan Deng, Chen Yang, Yi Xiong, Hugang Feng, Ming Yao, Jingyuan Fang, Jianren Gu, Wenming Cong*, Wenxin Qin*. (2017) Regulator of Calcineurin 1 Gene Isoform 4, Downregulated in Hepatocellular Carcinoma, Prevents Proliferation, Migration, and Invasive Activity of Cancer Cells and Growth of Orthotopic Tumors by Inhibiting Nuclear Translocation of NFAT1. Gastroenterology 153: 799-811 e33. (2017 IF: 20.773) Qian Xu, Yi Xiong*, Hao Dai, Kotni Meena Kumari, Qin Xu, Hong-Yu Ou, Dong-Qing Wei. (2017) PDC-SGB: Prediction of Effective Drug Combinations using a Stochastic Gradient Boosting Algorithm. Journal of Theoretical Biology 417：1-7. (2017 IF: 1.833) Hao Dai, Qin Xu*, Yi Xiong*, Wei-Lin Liu, Dong-Qing Wei*. (2016) Improved Prediction of Michaelis Constants in CYP450-Mediated Reactions by Resilient Back Propagation Algorithm. Current Drug Metabolism 17(7)：673-680. (2016 IF: 2.659) Hui-Yuan Zhang, Qin Xu*, Fang Li, Pei-Chuan Tian, Ying-Hao Wang, Yi Xiong, Yong-Hong Zhang, Dong-Qing Wei*. (2016) Recent Progresses of Simulations on Passive Membrane Permeations in China. Molecular Simulation 42(10): 799-808. (2016 IF: 1.254) Juan Esquivel-Rodríguez†, Yi Xiong†, Xusi Han, Shuomeng Guang, Charles Christoffer, Daisuke Kihara*. (2015) Navigating 3D Electron Microscopy Maps with EM-SURFER. BMC Bioinformatics 16: 181. (2015 IF: 2.435) (Co-first authors) Li Li, Yi Xiong*, Zhuo-Yu Zhang, Quan Guo, Qin Xu, Hien-Haw Liow, Yong-Hong Zhang*, Dong-Qing Wei.(2015) Improved Feature-based Prediction of SNPs in Human Cytochrome P450 Enzymes. Interdisciplinary Sciences-Computational Life Sciences 7: 65-77. (2015 IF: 0.853) Xiaolei Zhu, Yi Xiong, Daisuke Kihara*. (2015) Large-scale Binding Ligand Prediction by Improved Patch-based Method Patch-Surfer2.0. Bioinformatics 31(5): 707-713. (2015 IF: 5.766) Yi Xiong, Juan Esquivel-Rodriguez, Lee Sael, and Daisuke Kihara. (2014) 3D-SURFER 2.0: Web Platform for Real-time Search and Characterization of Protein Surfaces. Protein Structure Prediction, Methods in Molecular Biology, Daisuke Kihara (ed.), Springer. vol. 1137:105-117. Uma K. Aryal, Yi Xiong, Zachary McBride, Daisuke Kihara, Jun Xie, Mark C. Hall, Daniel B. Szymanski*. (2014) A Proteomic Strategy for Global Analysis of Plant Protein Complexes. Plant Cell 26: 3867-3882. (2014 IF: 9.338) Yifan Sun, Yi Xiong*, Qian Xu, Dong-Qing Wei*. (2014) A Hadoop-based Method to Predict Potential Effective Drug Combination. BioMed Research International 2014: 196858. (2014 IF: 1.579) (Co-first authors) Wei Wang, Juan Liu*, Yi Xiong, Lida Zhu, Xionghui Zhou. (2014) Analysis and Classification of DNA-binding Sites in Single-stranded and Double-stranded DNA-binding Proteins using Protein Information. IET Systems Biology 8(4): 176-183. (2014 IF: 1.059)