熊毅

副研究员，博士生导师

生物信息学与生物统计学系
生命科学技术学院
上海交通大学

电子邮箱: xiongyi@sjtu.edu.cn

研究领域: 生物信息与计算、人工智能

研究方向

生物大分子功能预测、序列设计与优化
人工智能驱动的药物、疫苗设计与发现
面向疾病精准诊疗的多组学大数据整合与分析

学习和工作经历

2014.01- 上海交通大学，生物信息学与生物统计学系，助理研究员、副研究员

2012.01-2013.12 普渡大学，生物学系，博士后

2002.09-2011.12 武汉大学，计算机应用技术专业，学士、博士

学术兼职

浦江国家实验室顾问科学家

上海人工智能实验室顾问科学家

BMC Bioinformatics，编委

Interdisciplinary Sciences-Computational Life Sciences，编委

IEEE International Conference on Bioinformatics and Biomedicine (BIBM)，程序委员会委员

中国生物工程学会计算生物学与生物信息学专委会委员

中国计算机学会生物信息学专委会委员

中国人工智能学会生物信息学与人工生命专委会委员

科研项目

主持国家自然科学基金项目

2022.01-2025.12 人工智能驱动的药物相互作用预测方法及发生机制研究，国家自然科学基金面上项目

2017.01-2019.12 基于蛋白质分子表面信息的核酸结合界面的分析和预测，国家自然科学基金青年项目

参与国家重大、重点项目

2023.10-2026.09 基于噬菌体生物传感技术筛选重大肺部疾病无创性鉴别诊断标志物，国家重点研发计划政府间国际科技创新合作专项

2019.01-2023.12 高通量蛋白质组学计算的基础理论与算法，国家自然科学基金重点项目

2016.07-2021.12 蛋白-蛋白相互作用及其网络的理论计算新方法与应用，国家重点研发计划重点专项

学术论文（近五年）

通讯作者（含共同）

Yanyi Chu^†, Yan Zhang^†, Qiankun Wang, Lingfeng Zhang, Xuhong Wang, Yanjing Wang, Dennis Russell Salahub, Qin Xu, Jianmin Wang, Xue Jiang, Yi Xiong^*, Dong-Qing Wei^*. (2022) A transformer-based model to predict peptide-HLA class I binding and optimize mutated peptides for vaccine design. Nature Machine Intelligence 4:300–311. (ESI高被引论文) [PDF]
Yanyi Chu, Aman Chandra Kaushik, Xiangeng Wang, Wei Wang, Yufang Zhang, Xiaoqi Shan, Dennis Russell Salahub, Yi Xiong^*, Dong-Qing Wei^*. (2021) DTI-CDF: a cascade deep forest model towards the prediction of drug-target interactions based on hybrid features. Briefings in Bioinformatics 22(1):451–462. (ESI高被引论文) [PDF]
Jing Zhao, Bowen Zhao, Xiaotong Song, Chujun Lyu , Weizhi Chen, Yi Xiong^*, Dong-Qing Wei^*. (2023) Subtype-DCC: decoupled contrastive clustering method for cancer subtype identification based on multi-omics data. Briefings in Bioinformatics 24(2):bbad025. [PDF]
Shenggeng Lin, Weizhi Chen, Gengwang Chen, Songchi Zhou, Dong-Qing Wei^*, Yi Xiong^*. (2022) MDDI-SCL: predicting multi-type drug-drug interactions via supervised contrastive learning. Journal of Cheminformatics 14:81. [PDF]
Shenggeng Lin, Guangwei Zhang, Dong-Qing Wei^*, Yi Xiong^*. (2022) DeepPSE: prediction of polypharmacy side effects by fusing deep representation of drug pairs and attention mechanism. Computers in Biology and Medicine 149:105984. [PDF]
Shenggeng Lin^†, Yanjing Wang^†, Lingfeng Zhang^†, Yanyi Chu, Yatong Liu, Yitian Fang, Mingming Jiang, Qiankun Wang, Bowen Zhao, Yi Xiong^*, Dong-Qing Wei^*. (2022) MDF-SA-DDI: predicting drug-drug interaction events based on multi-source drug fusion, multi-source feature fusion and transformer self-attention mechanism. Briefings in Bioinformatics 23(1):bbab421. [PDF]
Mingming Jiang, Bowen Zhao, Luosheng Gan, Qiankun Wang, Yanyi Chu, Tianhang Chen, Xueying Mao, Yatong Liu, Yanjing Wang, Xue Jiang, Dong-Qing Wei, Yi Xiong^*. (2021) NeuroPpred-Fuse: an interpretable stacking model for prediction of neuropeptides by fusing sequence information and feature selection methods. Briefings in Bioinformatics 22(6):bbab310. [PDF]
Yanyi Chu, Xuhong Wang, Qiuying Dai, Yanjing Wang, Qiankun Wang, Shaoliang Peng, Xiaoyong Wei, Jingfei Qiu, Dennis Russell Salahub, Yi Xiong^*, Dong-Qing Wei^*. (2021) MDA-GCNFTG: identifying miRNA-disease associations based on graph convolutional networks via graph sampling through the feature and topology graph. Briefings in Bioinformatics 22(6):bbab165. [PDF]
Wei Wang, QiuYing Dai, Fang Li, Yi Xiong^*, Dong-Qing Wei^*. (2021) MLCDForest: multi-label classification with deep forest in disease prediction for long non-coding RNAs. Briefings in Bioinformatics 22(3):bbaa104. [PDF]
Yanyi Chu, Xiaoqi Shan, Tianhang Chen, Mingming Jiang, Yanjing Wang, Qiankun Wang, Dennis Russell Salahub, Yi Xiong^*, Dong-Qing Wei^*. (2021) DTI-MLCD: predicting drug-target interactions using multilabel learning with community detection method. Briefings in Bioinformatics 22(3):bbaa205. [PDF]
Qiuying Dai, Yanyi Chu, Zhiqi Li, Yusong Zhao, Xueying Mao, Yanjing Wang, Yi Xiong^*, Dong-Qing Wei^*. (2021) MDA-CF: predicting miRNA-disease associations based on a cascade forest model by fusing multi-source information. Computers in Biology and Medicine 136:104706. [PDF]
Wei Wang, Xiaoqing Guan, Muhammad Tahir Khan, Yi Xiong^*, Dong-Qing Wei^*. (2020) LMI-DForest: a deep forest model towards the prediction of lncRNA-miRNA interactions. Computational Biology and Chemistry 89:107406. [PDF]
Xiaoqi Shan, Xiangeng Wang, Cheng-Dong Li, Yanyi Chu, Yufang Zhang, Yi Xiong^*, Dong-Qing Wei^*. (2019) Prediction of CYP450 enzyme−substrate selectivity based on the network-based label space division method. Journal of Chemical Information and Modeling 59:4577-4586 [PDF]

合作者

Shaojun Wang, Ronghui You, Yunjia Liu, Yi Xiong, Shanfeng Zhu^*. (2023) NetGO 3.0: protein language model improves large-scale functional annotations. Genomics, Proteomics & Bioinformatics (In press). [PDF]
Song Li, Chao Hu, Song Ke, Chenxing Yang, Jun Chen, Yi Xiong, Hao Liu^*, Liang Hong^*. (2023) LS-MolGen: Ligand-and-Structure Dual-Driven Deep Reinforcement Learning for Target-Specific Molecular Generation Improves Binding Affinity and Novelty. Journal of Chemical Information and Modeling 63:4207–4215 [PDF]
Mingchen Li^†, Liqi Kang^†, Yi Xiong, Yu Guang Wang, Guisheng Fan, Pan Tan^*, Liang Hong^*. (2023) SESNet: sequence-structure feature-integrated deep learning method for data-efficient protein engineering. Journal of Cheminformatics 15(1):12. [PDF]
Zhiqiang Hu^†^*, Wenfeng Liu^†, Chenbin Zhang^†, Jiawen Huang^†, Shaoting Zhang, Huiqun Yu, Yi Xiong, Hao Liu, Song Ke^*, Liang Hong. (2023) SAM-DTA: a sequence-agnostic model for drug-target binding affinity prediction. Briefings in Bioinformatics 24(1):bbac533. [PDF]
Shuwei Yao, Ronghui You, Shaojun Wang, Yi Xiong, Xiaodi Huang, Shanfeng Zhu^*. (2021) NetGO 2.0: improving large-scale protein function prediction with massive sequence, text, domain, family and network information. Nucleic Acids Research 49:W469–W475. [PDF]
Ronghui You, Shuwei Yao, Yi Xiong, Xiaodi Huang, Fengzhu Sun, Hiroshi Mamitsuka, Shanfeng Zhu^*. (2019) NetGO: improving large-scale protein function prediction with massive network information. Nucleic Acids Research 47:W379–W387 [PDF]

学生培养

在读学生

毕业学生

博士

硕士

本科

熊 毅

熊毅