CV

Education

• Ph.D in Version Control Theory, GitHub University, 2018 (expected)
• M.S. in Jekyll, GitHub University, 2014
• B.S. in GitHub, GitHub University, 2012

Work experience

• Spring 2024: Academic Pages Collaborator
  • Github University
  • Duties includes: Updates and improvements to template
  • Supervisor: The Users
• Fall 2015: Research Assistant
  • Github University
  • Duties included: Merging pull requests
  • Supervisor: Professor Hub
• Summer 2015: Research Assistant
  • Github University
  • Duties included: Tagging issues
  • Supervisor: Professor Git

Skills

• Skill 1
• Skill 2
  • Sub-skill 2.1
  • Sub-skill 2.2
  • Sub-skill 2.3
• Skill 3

Publications

PoseX: AI Defeats Physics Approaches on Protein-Ligand Cross Docking

Jiang, Yize, Xinze Li, Yuanyuan Zhang, Jin Han, Youjun Xu, Ayush Pandit, Zaixi Zhang et al. "PoseX: AI Defeats Physics Approaches on Protein-Ligand Cross Docking." arXiv preprint arXiv:2505.01700 (2025).

Biomedical foundation model: A survey

Liu, Xiangrui, Yuanyuan Zhang, Yingzhou Lu, Changchang Yin, Xiaoling Hu, Xiaoou Liu, Lulu Chen et al. "Biomedical foundation model: A survey." arXiv preprint arXiv:2503.02104 (2025).

CryoNeRF: reconstruction of homogeneous and heterogeneous cryo-EM structures using neural radiance field

Qu, Huaizhi, Xiao Wang, Yuanyuan Zhang, Sheng Wang, William Stafford Noble, and Tianlong Chen. "CryoNeRF: reconstruction of homogeneous and heterogeneous cryo-EM structures using neural radiance field." bioRxiv (2025): 2025-01.

A generalizable Hi-C foundation model for chromatin architecture, single-cell and multi-omics analysis across species

Xiao Wang, Yuanyuan Zhang, Suhita Ray, Anupama Jha, Tangqi Fang, Shengqi Hang, Sergei Doulatov, William Stafford Noble, & Sheng Wang. A generalizable Hi-C foundation model for chromatin architecture, single-cell and multi-omics analysis across species. bioRxiv, 2024.

Retrieval-reasoning large language model-based synthetic clinical trial generation

Xu, Zerui, Fang Wu, Yuanyuan Zhang, and Yue Zhao. "Retrieval-reasoning large language model-based synthetic clinical trial generation." arXiv preprint arXiv:2410.12476 (2024).

Distance-AF: Modifying Predicted Protein Structure Models by Alphafold2 with User-Specified Distance Constraints

Zhang, Y., Zhang, Z., Kagaya, Y., Terashi, G., Zhao, B., Xiong, Y., & Kihara, D. (2023). Distance-AF: Modifying Predicted Protein Structure Models by Alphafold2 with User-Specified Distance Constraints. bioRxiv, 2023-12.

Impact of AlphaFold on structure prediction of protein complexes: the CASP15‐CAPRI experiment

Lensink, M. F., ..., Zhang, Y,... & Wodak, S. J. (2023). Impact of AlphaFold on structure prediction of protein complexes: the CASP15‐CAPRI experiment. Proteins: Structure, Function, and Bioinformatics, 91(12), 1658-1683.

Computerized adaptive English ability assessment based on deep learning

Wang, X., Zhang, Y., Yu, S., Liu, X., & Wang, F. Y. (2018). Computerized adaptive English ability assessment based on deep learning. In Image and Video Technology: PSIVT 2017 International Workshops, Wuhan, China, November 20-24, 2017, Revised Selected Papers 8 (pp. 158-171). Springer International Publishing.

E-learning recommendation framework based on deep learning

Wang, X., Zhang, Y., Yu, S., Liu, X., Yuan, Y., & Wang, F. Y. (2017, October). E-learning recommendation framework based on deep learning. In 2017 IEEE international conference on systems, man, and cybernetics (SMC) (pp. 455-460). IEEE.

Talks

Distance-AF: Flexible protein structure prediction with distance constraints using AlphaFold2

April 04, 2024

Poster and Oral at D.E. Shaw Research Fellowship, New York

Distance-AF: Flexible protein structure prediction with distance constraints using AlphaFold2

May 17, 2023

Poster at Purdue Biomolecular Galaxy, West Lafayette, IN

Teaching

CS25100-Data Structures And Algorithms

CS50023-Data Engineering I

CS49000-DSC:Data Science Capstone

CS38003-Python Programming

Service and leadership

• Currently signed in to 43 different slack teams