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马剑竹副研究员/副教授

马剑竹,现任清华大学智能产业研究院副研究员/副教授,博导,海外优青项目入选者。2016年于芝加哥丰田工业研究院获得博士学位,随后在加州大学圣地亚哥分校医学院担任项目科学家。2020年开始担任美国普度大学计算机系Walther助理教授,兼任普渡大学生物化学系助理教授,2021年担任北京大学人工智能研究院副教授,北京大学公共卫生学院副教授,主要研究领域为人工智能、系统生物学、生物制药和智慧医疗。曾获得生物计算学国际顶级会议RECOMB的最佳论文奖,国际计算生物学会议ISMB的Warren DeLano奖,国际RNA和蛋白质折叠大会的最佳海报奖,论文曾被Nature Methods,Nature Machine Intelligence评为封面论文。


个人主页:

https://majianzhu.com/


邮箱地址:

majianzhu@air.tsinghua.edu.cn


教育经历:

2010-2016 丰田工业大学芝加哥分校 博士

2007-2010 北京大学信息科学技术学院计算机系 硕士

2003-2007 北京大学信息科学技术学院计算机系 学士


工作经历:

2022-至今 清华大学智能产业研究院副教授

2021-2022 北京大学人工智能研究院 副教授

2021-2022 北京大学医学部公共卫生学院 副教授

2020-2021 美国普渡大学计算机系 助理教授

2020-2021 美国普渡大学生化系 助理教授


研究领域:

人工智能、系统生物学、生物制药、智慧医疗



Nature Science Cell及子刊生物论文:


1. Single-cell multiomics analysis reveals regulatory programs in clear cell renal cell carcinoma

Qi Xie, Zhilin Long, Chengfang Sun, Min Tang, Yin Wang, Jiayan Ma, Jichuan Yu, Jingchao Wei, Jianzhu Ma , Bohan Wang, and Jiaming Wen,Cell Discovery 2022


2. A multi-scale map of cell structure fusing protein images and interactions

Yue Qin, Edward L. Huttlin, Casper F. Winsnes, Maya L. Gosztyla, Ludivine Wacheul, Marcus R. Kelly, Steven M. Blue, Fan Zheng, Michael Chen, Leah V. Schaffer, Katherine Licon, Anna Bäckström, Laura Pontano Vaites, John J. Lee, Wei Ouyang, Sophie N. Liu, Tian Zhang, Erica Silva, Jisoo Park, Adriana Pitea, Jason F. Kreisberg, Steven P. Gygi, Jianzhu Ma, J. Wade Harper, Gene W. Yeo, Denis L. J. Lafontaine, Emma Lundberg,Trey Ideker,Nature 2021


3. SARS-CoV-2 exacerbates proinflammatory responses in myeloid cells through ACE2-independent interactions via C-type lectin receptors and TTYH2

Qiao Lu, Jia Liu, Shuai Zhao, Maria Florencia Gomez Castro, Maudry Laurent-Rolle, Jianbo Dong, Xiaojuan Ran, Payal Damani-Yokota, Hongzheng Tang, Triantafyllia Karakousi, Juhee Son, Maria E. Kaczmarek, Ze Zhang, Stephen T. Yeung, Broc T. McCune, Rita E. Chen, Fei Tang, Xianwen Ren, Xufeng Chen, Jack C.C. Hsu, Marianna Teplova, Betty Huang, Haijing Deng, Zhilin Long, Tenny Mudianto, Shumin Jin, Peng Lin, Jasper Du, Ruochen Zang, Tina Tianjiao Su, Alberto Herrera, Ming Zhou, Renhong Yan, Jia Cui, James Zhu, Qiang Zhou, Tao Wang, Jianzhu Ma, Sergei B. Koralov, Zemin Zhang, Iannis Aifantis, Leopoldo N. Segal, Michael S. Diamond, Kamal M. Khanna, Kenneth A. Stapleford, Peter Cresswel, Yue Liu, Siyuan Ding, Qi Xie, Jun Wang,Immunity 2021 (Impact Factor=22)


4. Modeling Gene Regulatory Networks Using Neural Network Architectures

Hantao Shu, Jingtian Zhou, Qiuyu Lian, Han Li, Dan Zhao, Jianyang Zeng, Jianzhu Ma,Nature Computational Science 2021


5. Predicting drug response and synergy using a deep learning model of a cancer cell

Brent Kuenzi, Jisoo Park, Samson H. Fong, Kyle Salinas Sanchez, Jason F. Kreisberg, Jianzhu Ma, Trey Ideker,Cancer Cell 2020


6. A conserved epigenetic progression aligns dog and human age

Tina Wang, Jianzhu Ma, Andrew N. Hogan, Samson Fong, Katherine Licon, Brian Tsui, Jason F. Kreisberg, Peter D. Adams, Anne-Ruxandra Carvunis, Danika L. Bannasch, Elaine A. Ostrander and Trey Ideker,Cell Systems 2020


7. Learning predictive models of drug response that translate across biological contexts

Jianzhu Ma, Samson Fong, Yunan Luo, Christopher Bakkenist, John Paul Shen, Soufiane Mourragui, Lodewyk Wessels, Marc Hafner, Roded Sharan, Jian Peng, Trey Ideker

Nature Cancer 2020


8. DDOT: A Swiss-Army Knife for Investigating Data-Driven Biological Ontologies

Michael Ku Yu, Jianzhu Ma, Keiichiro Ono, Fan Zheng, Samson H. Fong, Aaron Gary, Jing Chen, Barry Demchak, Dexter Pratt, Trey Ideker

Cell Systems 2019 co-first author


9. Visible Machine Learning for Biomedicine

Michael Ku Yu, Jianzhu Ma, Jasmin Fisher, Jason F. Kreisberg, Benjamin J. Raphael, Trey Ideker

Cell 2018 co-first author


10. Typing tumors using pathways selected by somatic evolution

Sheng Wang, Jianzhu Ma, Wei Zhang, John Shen, Justin Huang, Jian Peng, Trey Ideker

Nature Communications 2018 co-first author


11. Using deep learning to model the hierarchical structure and function of a cell

Jianzhu Ma, Michael Ku Yu, Samson Fong, Keiichiro Ono, Eric Sage, Barry Demchak, Roded Sharan, Trey Ideker

Nature Methods 2018


近期人工智能会议及期刊论文:


1. Antigen-Specific Antibody Design and Optimization with Diffusion-Based Generative Models

Shitong Luo, Yufeng Su, Xingang Peng, Sheng Wang, Jian Peng, Jianzhu Ma,NeurlPS 2022


2. Efficient Meta Reinforcement Learning for Preference-based Fast Adaptation

Zhizhou Ren, Anji Liu, Yitao Liang, Jian Peng, Jianzhu Ma,NeurlPS 2022


3. MobilePrune: Neural Network Compression via ℓ0 Sparse Group Lasso on the Mobile System

Yubo Shao, Kaikai Zhao, Zhiwen Cao, Zhehao Peng, Xingang Peng, Pan Li, Yijie Wang, Jianzhu Ma,Sensor 2022


4. Multiwave COVID-19 Prediction from Social Awareness using Web Search and Mobility Data

Jiawei Xue, Takahiro Yabe, Kota Tsubouchi, Jianzhu Ma , Satish V. Ukkusuri,KDD 2022 corresponding author Oral presentation


5. Proximal Exploration for Model-guided Biological Sequence Design

Zhizhou Ren, Jiahan Li, Fan Ding, Yuan Zhou, Jianzhu Ma , Jian Peng,ICML 2022 Short presentation


6. Pocket2Mol: Efficient Molecular Sampling Based on 3D Protein Pockets

Xingang Peng, Shitong Luo, Jiaqi Guan, Qi Xie, Jian Peng, Jianzhu Ma,ICML 2022 Short presentation


7. 3DLinker: An E(3) Equivariant Variational Autoencoder for Molecular Linker Design

Yinan Huang, Xingang Peng, Jianzhu Ma , Muhan Zhang,ICML 2022 corresponding author Long presentation


8. Equivariant Point Set Analysis via Learning Orientations for Message Passing

Shitong Luo, Jiahan Li, Jiaqi Guan, Yufeng Su, Chaoran Cheng, Jian Peng, Jianzhu Ma,CVPR 2022 Oral presentation

9. Physics-Guided and Physics-Explainable Recurrent Neural Network for Time Dynamics in Optical Resonances,Yingheng Tang, Jichao Fan, Xinwei Li, Jianzhu Ma , Minghao Qi, Cunxi Yu, Weilu Gao,Nature Computational Science 2022


10. Neural Energy Minimization for Molecular Conformation Optimization

Jiaqi Guan, Wei Qian, Qiang Liu, Wei-ying Ma, Jianzhu Ma, Jian Peng,ICLR 2022


11. Neural Predicting Higher-order Patterns in Temporal Networks

Yuyun Liu, Jianzhu Ma, Pan Li,WWW 2022


12. Quantifying spatial homogeneity of urban road networks via graph neural networks

Jiawei Xue, Nan Jiang, Senwei Liang, Qiyuan Pang, Takahiro Yabe, Satish Ukkusuri, Jianzhu Ma,Nature Machine intelligence 2022 cover paper


13. A 3D Generative Model for Structure-Based Drug Design

Shitong Luo, Jiaqi Guan, Jianzhu Ma, Jian Peng,NeurlPS 2021


14. Fast Projection onto the Capped Simplex withApplications to Sparse Regression in Bioinformatics Andersen Ang, Jianzhu Ma, Nianjun Liu, Kun Huang, Yijie Wang,NeurlPS 2021


15. XOR-CD: Linearly Convergent Constrained Structure Generation

Fan Ding, Jianzhu Ma, Jinbo Xu, Yexiang Xue,ICML 2021 oral presentation


16. AirSign: Smartphone Authentication by Signing in the Air

Yubo Shao, Tinghan Yang, He Wang, Jianzhu Ma,Sensor 2021


17. PALM: Probabilistic Area Loss Minimization for Protein Sequence Alignment

Fan Ding, Nan Jiang, Jianzhu Ma, Jian Peng, Jinbo Xu, Yexiang Xue,UAI 2021


18. Breaking the Limit of Graph Neural Networks by Improving the Assortativity of Graphs with Local Mixing Patterns

Susheel Suresh, Vinith Budde, Jennifer Neville, Pan Li, Jianzhu Ma,KDD 2021


19. Causality in machine learning: When causal inference meets deep neural networks

Yunan Luo, Jian Peng, Jianzhu Ma,Nature Machine intelligence 2020


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