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Jianzhu MAAssociate Professor

MA Jianzhu is currently an Associate Researcher/Associate Professor at the Institute for AI Industry Research, Tsinghua University, doctoral supervisor, and is selected for Overseas Excellent Young Scientists. Prof. MA received his PhD from the Toyota Technological Institute at Chicago in 2016 and worked as a project scientist at the School of Medicine, University of California, San Dieg. He was a Walther Assistant Professor in the Department of Computer Science and the Department of Biochemistry at Purdue University in 2020, and an Associate Professor in the Institute for Artificial Intelligence at Peking University and an Associate Professor in the School of Public Health at Peking University in 2021. His main research areas are artificial intelligence, systems biology, biopharmaceuticals, and smart medicine.
Prof. MA has received the Best Paper Award from RECOMB, a top international conference on biocomputing, the Warren DeLano Award from ISMB, and the Best Poster Award from the International Conference on RNA and Protein Folding. His papers have been recognized as cover papers by Nature Methods and Nature Machine Intelligence.





Education experience

2010-2016 PhD, Toyota Technological Institute at Chicago

2007-2010 Master's Degree, Department of Computer Science, School of Information Science and Technology, Peking University

2003-2007 Bachelor's degree, Department of Computer Science, School of Information Science and Technology, Peking University

Working Experience

2022-present Associate Professor, Institute for AI Industry Research, Tsinghua University
2021-2022 Associate Professor, Institute for Artificial Intelligence, Peking University
2021-2022 Associate Professor, School of Public Health, Peking University
2020-2021 Assistant Professor, Department of Computer Science, Purdue University
2020-2021 Assistant Professor, Department of Biochemistry, Purdue University

Research areas

Artificial Intelligence, Systems Biology, Biopharmaceuticals, Smart Healthcare

Nature Science Cell and Subjournal Biology Papers:

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

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

Recent Artificial Intelligence Conference and Journal Papers:

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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