Biography

• Deputy director, Faculty of Science, Peking University (2022-now)

• Principal Investigator, Biomedical Pioneering Innovation Center, Peking University (2013-now)

• Cheung Kong Professor, College of Chemistry and Molecular Engineering, Peking University (2010-now)

• Assistant Professor, Texas A&M University(2004-2010)

• Postdoctoral Research Fellow, Harvard University (2002-2004)

• Postdoctoral Research Fellow, California Institute of Technology (2001- 2002)

• Ph.D., California Institute of Technology (2001)

• M.S., Institute of Chemistry, Chinese Academy of Sciences (1996)

• B.S., Sichuan University (1993)

Research Interests

• Dynamics calculations for solvation effects in chemical and enzymatic reactions

• Developing efficient molecular dynamics simulation software package in conjunction with deep learning

• Machine-learning based protein sequence generation and improvement on protein structure prediction

• Organization principle of 3D chromatin and effects on gene regulation

• Chromatin structure and epigenetic changes in cancer

Teaching

PhysicalChemistry

Awards

• 2023 Beijing Advanced Science and Technology Worker, Beijing Municipal Association of Science and Technology

• 2023 Top 10 Pioneering Cases of Artificial Intelligence, Artificial Intelligence Industry Alliance of China

• 2023 New Cornerstone Investigator, New Cornerstone Science Foundation

• 2023 AI Dean's Summit Best Innovative Collaboration Award, Huawei Cloud Computing Co. Ltd.

• 2022 Beijing Outstanding Undergraduate Thesis Supervisor Award, Beijing Municipal Commission of Education

• 2022 Outstanding Instructor Award for Undergraduate Research Training, Peking University

• 2022 Ascend MVP, Huawei Technologies Co. Ltd.

• 2021Outstanding Instructor Award for Undergraduate Research Training, Peking University

• 2018 China's 10 top scientific advances of 2018, Ministry of Science and Technology, China

• 2016 Pople Medal, Asia-Pacific Association of Theoretical and Computational Chemists

• 2015 SUSTC Chemical Sciences Lectureship, Department of Chemistry, South University of Science and Technology of China

• 2015 Most Popular Course Award, College of Chemistry and Molecular Engineering, Peking University

• 2015 Innovation Award for Young and Mid-Career Scientists, Ministry of Science and Technology, China

• 2014 Promising Scientist Prize of CMOA (Centre de MécaniqueOndulatoireAppliquée), 国际QSCP（Quantum Systems in Chemistry and Physics）组织

• 2014 Distinguished Lecturer Award, Chemical Society of Japan

• 2012 NSFC Outstanding Young Investigator Award

• 2011 Zhongchenyulan Award, College of Chemistry and Molecular Engineering, Peking University

• 2008 Cheung Kong Scholar,The Chinese Ministry of Education

• 2006 Searle Scholar, Kinship Foundation

• 2004 Camille and Henry Dreyfus New Faculty Award, The Camille and Henry Dreyfus Foundation

• 2001 Milton and Francis Clauser Prize for the Best Doctoral Thesis, Caltech

• 2001 Herbert Newby McCoy Award, Caltech

• 1998 Li Ming Scholarship, Caltech

• 1998 Chinese-American Engineers and Scientists Association Scholarship

Selected Publications

1. Huang, Y. P.; Xia, Y. J.; Yang, L. J.; Wei, J. C.; Yang, Y. I.; Gao*, Y. Q., SPONGE: A GPU-Accelerated Molecular Dynamics Package with Enhanced Sampling and AI-Driven Algorithms. Chinese Journal of Chemistry 2022, 40 (1), 160-168.

2. Xue, Y.; Yang, Y.; Tian, H.; Quan, H.; Liu, S. R.; Zhang, L.; Yang, L.; Zhu, H. C.; Wu, H.; Gao*, Y. Q., Computational characterization of domain-segregated 3D chromatin structure and segmented DNA methylation status in carcinogenesis. Molecular Oncology 2022, 16 (3), 699-716.

3. He, Y.; Xue, Y.; Wang, J.; Huang, Y.; Liu, L.; Huang, Y.; Gao*, Y. Q., Diffusion-enhanced characterization of 3D chromatin structure reveals its linkage to gene regulatory networks and the interactome. Genome Research 2023, 33 (8), 1354-1368.

4. Huang, Y. P.; Zhang, H.; Jiang, S. Y.; Yue, D. J.; Lin, X. H.; Zhang, J.; Gao*, Y. Q., DSDP: A Blind Docking Strategy Accelerated by GPUs. Journal of Chemical Information and Modeling 2023, 63 (14), 4355-4363.

5. Wang, J.; Xue, Y.; He, Y.; Quan, H.; Zhang, J.; Gao*, Y. Q., Characterization of network hierarchy reflects cell state specificity in genome organization. Genome Research 2023, 33 (2), 247-260.

6. Zhang, J.; Chen, D. C.; Xia, Y. J.; Huang, Y. P.; Lin, X. H.; Han, X.; Ni, N. X.; Wang, Z. D.; Yu, F.; Yang, L. J.; Yang*, Y. I.; Gao*, Y. Q., Artificial Intelligence Enhanced Molecular Simulations. Journal of Chemical Theory and Computation 2023, 19 (14), 4338-4350.

7. Zhang, J.; Liu, S.; Chen, M.; Chu, H.; Wang, M.; Wang, Z.; Yu, J.; Ni, N.; Yu, F.; Chen, D.; Yang, Y. I.; Xue, B.; Yang, L.; Liu, Y.; Gao*, Y. Q., Unsupervisedly Prompting AlphaFold2 for Accurate Few-Shot Protein Structure Prediction. Journal of Chemical Theory and Computation 2023, 19 (22), 8460-8471.

8. Feng, S. H.; Chen, Z. Y.; Zhang, C. W.; Xie, Y. H.; Ovchinnikov*, S.; Gao*, Y. Q.; Liu*, S. R., Integrated structure prediction of protein-protein docking with experimental restraints using ColabDock (vol 6, pg 924, 2024). Nature Machine Intelligence 2024, 6 (10), 1270-1270.

9. Han, X.; Sun, T. Y.; Yang, Y. I.; Zhang, J.; Qiu, J.; Xiong, Z. P.; Qiao, N.; Wu*, Y. D.; Gao*, Y. Q., Enhanced Sampling Simulations on Transition-Metal-Catalyzed Organic Reactions: Zirconocene-Catalyzed Propylene Polymerization and Sharpless Epoxidation. CCS Chemistry 2024, 6 (4), 964-975.

10. Tian, Y.; Song, Y. Z.; Xia, Y. J.; Hong, J. N.; Huang, Y. P.; Ma, R. Z.; You, S. F.; Guan, D.; Cao, D. Y.; Zhao, M. Z.; Chen, J.; Song, C.; Liu, K. H.; Xu*, L. M.; Gao*, Y. Q.; Wang*, E. G.; Jiang*, Y., Nanoscale one-dimensional close packing of interfacial alkali ions driven by water-mediated attraction. Nature Nanotechnology 2024, 19 (4), 479-484.