个人简历

Employment\r
Associate Professor (with tenure), IIIS, Tsinghua University, Dec. 2018 - Present;\r
Tenure-Track Assistant Professor, IIIS, Tsinghua University, Dec. 2012 - Dec. 2018;\r
Postdoctoral Associate, Department of Computer Science at Duke University and Duke University School of Medicine, Oct. 2011 - Aug. 2012.\r
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Education Background\r
Ph.D., Computer Science, Duke University (2011)\r
B.S., M.S., Zhejiang University\r
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Awards\r
国家杰出青年科学基金，2021.\r
Wuwenjun AI Science and Technology Award, Natural Science track, Third Prize, 2019 (吴文俊人工智能自然科学奖三等奖).\r
International Conference on Intelligent Biology and Medicine (ICIBM), Best Paper Award, 2019.\r
Finalist Lane Fellows in Computational Biology, Carnegie Mellon University (CMU), 2012.\r
Best Paper Award, International Conference on Parallel and Distributed Computing Applications and Technologies (PDCAT), 2005.\r
2015年全国挑战杯优秀指导教师奖。

研究领域

"Computational Biology

近期论文

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.\r
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Shuya Li#, Tingzhong Tian#, Ziting Zhang, Ziheng Zou, Dan Zhao* and Jianyang Zeng*.PocketAnchor: Learning Structure-based Pocket Representations for Protein-Ligand Interaction Prediction.Cell Systems. 2023. Minor revision.\r
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Chang Liu#, Cuinan Yu#, Yipin Lei#, Kangbo Lyu, Tingzhong Tian, Qianhao Li, Dan Zhao*, Fengfeng Zhou*, Jianyang Zeng*.Improving target-disease association prediction through a graph neural network with credibility information.Pacific Symposium on Biocomputing. 2023.\r
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Siqin Zhang, Kuo Yang, Zhenhong Liu, Xinxing Lai, Zhen Yang, Jianyang Zeng, Shao Li*.DrugAI: a multi-view deep learning model for predicting drug–target activating/inhibiting mechanisms.Briefings in Bioinformatics. 2022.\r
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Han Li, Xinyi Zhao, Shuya Li, Fangping Wan, Dan Zhao*, Jianyang Zeng*.Improving molecular property prediction through a task similarity enhanced transfer learning strategy.iScience. 2022.\r
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Hantao Shu, Fan Ding, Jingtian Zhou, Yexiang Xue, Dan Zhao, Jianyang Zeng*, Jianzhu Ma*.Boosting single-cell gene regulatory network reconstruction via bulk-cell transcriptomic data.Briefings in Bioinformatics. 2022.\r
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Xiaolong Feng#, Xiaofan Zhang#, Shuangying Jiang, Yuanwei Tang, Chao Cheng, Parthasarathy Abinand Krishna, Xiaoting Wang, Junbiao Dai, Jianyang Zeng*, Tian Xia*, Dan Zhao*.A DNA-based non-infectious replicon system to study SARS-CoV-2 RNA synthesis.Computational and Structural Biotechnology Journal. 2022.\r
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Eugene F Douglass Jr.#, Robert J Allaway#, Bence Szalai#, Wenyu Wang, Tingzhong Tian, Adrià Fernández-Torras, Ron Realubit, Charles Karan, Shuyu Zheng, Alberto Pessia, Ziaurrehman Tanoli, Mohieddin Jafari, Fangping Wan, Shuya Li, Yuanpeng Xiong, Miquel Duran-Frigola, Martino Bertoni, Pau Badia-i-Mompel, Lídia Mateo, Oriol Guitart-Pla, Verena Chung, Jing Tang, Jianyang Zeng, Patrick Aloy, Julio Saez- Rodriguez*, Justin Guinney*, Daniela S Gerhard*, Andrea Califano*, Challenge Consor- tium.A Community Challenge for Pancancer Drug Mechanism of Action Inference from Perturbational Profile Data.Cell Reports Medicine. 2022.\r
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Wuai Zhou, Kuo Yang, Jianyang Zeng, Xinxing Lai, Xin Wang, Chaofan Ji, Yan Li, Peng Zhang, Shao Li*.FordNet: recommending traditional Chinese medicine formula via deep neural network integrating phenotype and molecule.Pharmacological Research. 2021.\r
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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.\r
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Zhaofeng Ye, Fengling Chen, Jiangyang Zeng, Juntao Gao*, Michael Q. Zhang*.ScaffComb: A Phenotype-Based Framework for Drug Combination Virtual Screening in Large-Scale Chemical Datasets.Advanced Science. 2021.\r
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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.\r
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Peiyuan Feng, Jianyang Zeng*, Jianzhu Ma*.Predicting MHC-peptide binding affinity by differential boundary tree.ISMB 2021.?Bioinformatics. 2021.\r
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Anna Cichonska, Balaguru Ravikumar, Robert J Allaway, Sungjoon Park, Fangping Wan, Olexandr Isayev, Shuya Li, Michael J Mason, Andrew Lamb, Minji Jeon, Sunkyu Kim, Mariya Popova, Jianyang Zeng, Kristen Dang, Gregory Koytiger, Jaewoo Kang, Carrow I Wells, Timothy M Willson, Tudor I Oprea, Avner Schlessinger, David H Drewry, Gustavo A Stolovitzky, Krister Wennerberg, Justin Guinney*, Tero Aittokallio*.Crowdsourced mapping of unexplored target space of kinase inhibitors.Nature communications. 2021.\r
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Peiyuan Feng#, An Xiao#, Meng Fang, Fangping Wan, Shuya Li, Peng Lang, Dan Zhao*, and Jianyang Zeng*.A novel machine learning based framework for modeling transcription elongation.Proceedings of the National Academy of Sciences (PNAS). 2021.\r
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Tingzhong Tian, Shuya Li, Peng Lang, Dan Zhao*, Jianyang Zeng*.Full-length ribosome density prediction by a multi-input and multi-output model.PLOS Computational Biology. 2021.\r
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Dan Zhao#, Weifan Xu#, Xiaofan Zhang#, Xiaoting Wang, Enming Yuan, Yuanpeng Xiong, Shenyang Wu, Shuya Li, Nian Wu, Tingzhong Tian, Xiaolong Feng, Hantao Shu, Peng Lang, Xiaokun Shen, Haitao Li, Pilong Li,* and Jianyang Zeng*.Understanding the phase separation characteristics of nucleocapsid protein provides a new therapeutic opportunity against SARS-CoV-2.Protein & Cell. 2021. (Impact Factor: 10.164).\r
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Yuanpeng Xiong#, Xuan He#, Dan Zhao, Tingzhong Tian, Lixiang Hong, Tao Jiang*, and Jianyang Zeng*.Modelling Multi-species RNA Modification through Multi-task Curriculum Learning.Nucleic Acids Research. 2021.\r
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Yiyue Ge#, Tingzhong Tian#, Suling Huang#, Fangping Wan#, Jingxin Li#, Shuya Li, Xiaoting Wang, Hui Yang, Lixiang Hong, Nian Wu, Enming Yuan, Yunan Luo, Lili Cheng, Chengliang Hu, Yipin Lei, Hantao Shu, Xiaolong Feng, Ziyuan Jiang, Yunfu Wu, Ying Chi, Xiling Guo, Lunbiao Cui, Liang Xiao, Zeng Li, Chunhao Yang, Zehong Miao, Ligong Chen, Haitao Li, Hainian Zeng, Dan Zhao*, Fengcai Zhu*, Xiaokun Shen*, and Jianyang Zeng*.An integrative drug repositioning framework discovered a potential therapeutic agent targeting COVID-19.Signal Transduction and Targeted Therapy. 2021. (Impact Factor: 13.493).\r
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Hailin Hu# , Xianggen Liu#; , An Xiao, YangYang Li, Chengdong Zhang, Tao Jiang, Dan Zhao, Sen Song*, and Jianyang Zeng*.Riboexp: an interpretable reinforcement learning framework for ribosome density modeling.Briefings in Bioinformatics. 2021. (Impact Factor: 8.99).\r
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Han Li, Xinyi Zhao, Shuya Li, Fangping Wan, Dan Zhao*, and Jianyang Zeng*.MoTSE: an interpretable task similarity estimator for small molecular property prediction tasks.RECOMB. 2021.\r
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Lixiang Hong, Jinjian Lin, Shuya Li, Fangping Wan, Hui Yang, Tao Jiang, Dan Zhao*, and Jianyang Zeng*.A novel machine learning framework for automated biomedical relation extraction from large-scale literature repositories.Nature Machine Intelligence. 2020.\r
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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.\r
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Fangping Wan#, Shuya Li#, Tingzhong Tian, Yipin Lei, Dan Zhao*, Jianyang Zeng*.EXP2SL: a Machine Learning Framework for Cell-Line Specific Synthetic Lethality Prediction.Frontiers in Pharmacology. 2020.\r
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Rong Ma#, Yi Li#, Chenxing Li#, Fangping Wan, Hailin Hu, Wei Xu*, Jianyang Zeng*.Secure multiparty computation for privacy-preserving drug discovery.Bioinformatics. 2020.\r
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Shuya Li#, FangpingWan#, Hantao Shu, Tao Jiang, Dan Zhao*, and Jianyang Zeng*.MONN: a Multi-Objective Neural Network for Predicting Pairwise Non-Covalent Interactions and Binding Affinities between Compounds and Proteins.RECOMB 2020.Also invited to?Cell Systems. 2020.