个人简介
曾坚阳，国家杰出青年科学基金入选者，科学探索奖入选者，于1999年和2002年分别获得浙江大学的学士和硕士学位。2011年，在美国杜克大学（Duke University）获得计算机科学博士学位。2011年至2012年期间，在杜克大学计算机科学系和杜克医学院从事博士后研究。于2012年12月至2023年5月在清华大学交叉信息研究院（姚班）担任助理教授、长聘制终身副教授，于2023年6月起作为正教授加入西湖大学工学院（生命科学学院兼聘）。
学术成果
曾坚阳课题组的研究方向包括计算生物学，机器学习和大数据分析，长期致力于人工智能和生命科学的交叉学科研究。共发表学术论文80余篇，其中通讯作者论文包括 Nature Machine Intelligence、Nature Communications、 Nature Computational Science、PNAS、Cell Systems、Nucleic Acids Research等，合作作者论文包括Nature等。成果获得“科学探索奖”、ESI高引论文、“吴文俊人工智能自然科学”三等奖、“中国生物信息学十大进展”、“中国生物信息学十大算法和工具”、世界人工智能大会青年优秀论文、国际会议ICIBM 2019最佳论文等荣誉。担任国际期刊IEEE/ACM Transactions on Computational Biology and Bioinformatics的编委、计算生物学领域的国际顶级会议ISMB、RECOMB程序委员会委员、Cell Systems的Advisory Board成员。课题组目前科研方向围绕AI for Life Sciences展开，包括高通量实验方法开发、多组学测序方法开发、基于生物大数据的人工智能/机器学习模型开发、AI驱动的新型治疗方法开发和生物学知识发现等。
代表论文（*代表通信作者）
2. Han Li, Ruotian Zhang, Yaosen Min, Dacheng Ma, Dan Zhao*, and Jianyang Zeng*. A knowledge-guided pre-training framework for improving molecular representation learning. Nature Communications. 2023.
3. Xingang Peng, Yipin Lei, Peiyuan Feng, Lemei Jia, Jianzhu Ma, Dan Zhao*, and Jianyang Zeng*. Characterizing the interaction conformation between T cell receptors and epitopes with deep learning. Nature Machine Intelligence, 2023, 5, 395-4071.
4. Shuya Li, Tingzhong Tian, Ziting Zhang, Ziheng Zou, Dan Zhao*, Jianyang Zeng*. PocketAnchor: Learning Structure-based Pocket Representations for Protein-Ligand Interaction Prediction. Cell Systems. 2023. Cover Article.
5. Yipin Lei, Shuya Li, Ziyi Liu, Fangping Wan, Tingzhong Tian, Shao Li, Dan Zhao*, Jianyang Zeng*. A deep-learning framework for multi-level peptide-protein interaction prediction. Nature Communications, 2021, 12, 5465.
6. Dan Zhao, Weifan Xu, Xiaofan Zhang, XiaotingWang, Enming Yuan, Yuanpeng Xiong, Shenyang Wu, Shuya Li, Nian Wu, Tingzhong Tian, Xiaolong Feng, Hantao Shu, Peng Lang, Xiaokun Shen, Haitao Li, Pilong Li*, Jianyang Zeng*. Understanding the phase separation characteristics of nucleocapsid protein provides a new therapeutic opportunity against SARS-CoV-2. Protein & Cell, 2021, 12(9):734-740.
7. Hantao Shu, Jingtian Zhou, Qiuyu Lian, Han Li, Dan Zhao, Jianyang Zeng*, Jianzhu Ma*. Modeling gene regulatory networks using neural network architectures. Nature Computational Science, 2021, 1, 491-501.
8. Peiyuan Feng, An Xiao, Meng Fang, Fangping Wan, Shuya Li, Peng Lang, Dan Zhao*, Jianyang Zeng*. A novel machine learning based framework for modeling transcription elongation. Proceedings of the National Academy of Sciences (PNAS), 2021, 118(6), e2007450118.
9. Yiyue Ge, Tingzhong Tian, Sulin Huang, Fangping Wan, Jingxin Li, Shuya Li, Hui Yang, Lixiang Hong, Nian Wu, Enming Yuan, Lili Cheng, Yipin Lei, Hantao Shu, Xiaolong Feng, Ziyuan Jiang, Ying Chi, Xiling Guo, Lunbiao Cui, Liang Xiao, Zeng Li, Chunhao Yang, Zehong Miao, Haidong Tang, Ligong Chen, Hainian Zeng, Dan Zhao*, Fengcai Zhu*, Xiaokun Shen*, Jianyang Zeng*. A data-driven drug repositioning framework discovered a potential therapeutic agent targeting COVID-19. Signal Transduction and Targeted Therapy, 2021, 6, 165.
10. Lixiang Hong, Jinjian Lin, Shuya Li, FangpingWan, Hui Yang, Tao Jiang, Dan Zhao*, Jianyang Zeng*. A novel machine learning framework for automated biomedical relation extraction from large-scale literature repositories. Nature Machine Intelligence, 2020, 2, 347-355.
11. Shuya Li, Fangping Wan, Hantao Shu, Tao Jiang, Dan Zhao*, Jianyang Zeng*. MONN: A multi-objective neural network for predicting compound-protein interactions and affinities. Cell Systems, 2020, 10(4):308-322.
12. Ahmed Abbas, Xuan He, Bin Zhou, Guangxiang Zhu, Zishan Ma, Jun-Tao Gao, Michael Q Zhang, Jianyang Zeng*. Integrating Hi-C and FISH data for modeling 3D organizations of chromosomes. Nature Communications, 2019, 10, 2049.
13. Guangxiang Zhu, Wenxuan Deng, Hailin Hu, Rui Ma, Sai Zhang, Jinglin Yang, Jian Peng, Tommy Kaplan, Jianyang Zeng*. Reconstructing spatial organizations of chromosomes through manifold learning. Nucleic Acids Research. 2018, 46 (8), e50.
14. Zhenhai Du, Hui Zheng, Bo Huang, Rui Ma, Jingyi Wu, Xianglin Zhang, Jing He, Yunlong Xiang, Qiujun Wang, Yuanyuan Li, Jing Ma, Xu Zhang, Ke Zhang, Yang Wang, Michael Q. Zhang, Juntao Gao, Jesse R. Dixon, Xiaowo Wang, Jianyang Zeng, Wei Xie*. Allelic reprogramming of 3D chromatin architecture during early mammalian development. Nature, 2017, 547, 232-235.
15. Yunan Luo, Xinbin Zhao, Jingtian Zhou, Jinling Yang, Yanqing Zhang, Wen-hua Kuang, Jian Peng*, Ligong Chen*, Jianyang Zeng*. A network integration approach for drug-target interaction prediction and computational drug repositioning from heterogeneous information. Nature Communications, 2017, 8, 573.
16. Sai Zhang, Hailin Hu, Jingtian Zhou, Xuan He, Tao Jiang, Jianyang Zeng*. Analysis of ribosome stalling and translation elongation dynamics by deep learning. Cell Systems, 2017, 5(3):212-220.
17. Sai Zhang, Jingtian Zhou, Hailin Hu, Haipeng Gong, Ligong Chen, Chao Cheng*, Jianyang Zeng*. A deep learning framework for modeling structural features of RNA-binding protein targets. Nucleic Acids Research, 2016, 44(4):e32.
18. Han Li, Dan Zhao*, Jianyang Zeng*. KPGT: knowledge-guided pre-training of graph transformer for molecular property prediction. Proceedings of the 28th ACM SIGKDD Conference on Knowledge Discovery and Data Mining (KDD), 2022, 857-867.
19. Yichao Zhou, Yuexin Wu, Jianyang Zeng*. Computational protein design uUsing AND/OR branch-and-bound search. International Conference on Research in Computational Molecular Biology (RECOMB), 2015.
20. Yichao Zhou, Jianyang Zeng*. Massively Parallel A* Search on a GPU. Proceeding of the Twenty-Ninth AAAI Conference on Artificial Intelligence (AAAI), 2015.
21. Yichao Zhou, Wei Xu, Bruce R. Donald, Jianyang Zeng*. An efficient parallel algorithm for accelerating computational protein design. Proceedings of the 22nd Annual International Conference on Intelligent Systems for Molecular Biology (ISMB), 2014.
22. Yuhao Wang, Jianyang Zeng*. Predicting drug-target interactions using restricted Boltzmann machines. Proceedings of the 21nd Annual International Conference on Intelligent Systems for Molecular Biology (ISMB), 2013.
联系方式
电子邮箱：zengjy@westlake.edu.cn
研究系列人员招聘信息：https://www.westlake.edu.cn/Careers/OpenPositions/202304/t20230424_27603.shtml
博士后招聘信息：https://www.westlake.edu.cn/Careers/OpenPositions/202304/t20230424_27601.shtml
博士生招聘信息：https://www.westlake.edu.cn/admissions_aid/graduate/
实验室助理招聘信息：https://www.westlake.edu.cn/Careers/OpenPositions/202304/t20230424_27603.shtml