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A list of all the posts and pages found on the site. For you robots out there is an XML version available for digesting as well.
Pages
Posts
Future Blog Post
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Blog Post number 4
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This is a sample blog post. Lorem ipsum I can’t remember the rest of lorem ipsum and don’t have an internet connection right now. Testing testing testing this blog post. Blog posts are cool.
Blog Post number 3
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Blog Post number 1
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portfolio
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publications
E-learning recommendation framework based on deep learning
Published in 2017 IEEE international conference on systems, man, and cybernetics (SMC), 2017
Recommended citation: 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. https://ieeexplore.ieee.org/abstract/document/8122647?casa_token=zEmxWnuthkwAAAAA:bR9DtfG1-FLTIMfaEe5RJahJw7qUgB2G8dB0Y_1jWFxZJUOuXXbg6gZXRsAAyhVNg2Im7luSBQ
Computerized adaptive English ability assessment based on deep learning
Published in Image and Video Technology: PSIVT 2017 International Workshops, 2017
Recommended citation: 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. https://link.springer.com/chapter/10.1007/978-3-319-92753-4_13
Impact of AlphaFold on structure prediction of protein complexes: the CASP15‐CAPRI experiment
Published in Proteins: Structure, Function, and Bioinformatics, 2023
Recommended citation: 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. https://onlinelibrary.wiley.com/doi/full/10.1002/prot.26609
Distance-AF: Modifying Predicted Protein Structure Models by Alphafold2 with User-Specified Distance Constraints
Published in BioRxiv, 2023
Recommended citation: 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. https://www.biorxiv.org/content/10.1101/2023.12.01.569498v1
Retrieval-reasoning large language model-based synthetic clinical trial generation
Published in Arxiv, 2024
Recommended citation: 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). https://arxiv.org/pdf/2410.12476?
A generalizable Hi-C foundation model for chromatin architecture, single-cell and multi-omics analysis across species
Published in BioRxiv, 2024
Recommended citation: 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. https://www.biorxiv.org/content/10.1101/2024.12.16.628821v1.full
CryoNeRF: reconstruction of homogeneous and heterogeneous cryo-EM structures using neural radiance field
Published in BioRxiv, 2025
Recommended citation: 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. https://www.biorxiv.org/content/10.1101/2025.01.10.632460v1.full.pdf
Biomedical foundation model: A survey
Published in Arxiv, 2025
Recommended citation: 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). https://arxiv.org/pdf/2503.02104
PoseX: AI Defeats Physics Approaches on Protein-Ligand Cross Docking
Published in Arxiv, 2025
Recommended citation: 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). https://arxiv.org/pdf/2505.01700
talks
Distance-AF: Flexible protein structure prediction with distance constraints using AlphaFold2
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Distance-AF: Flexible protein structure prediction with distance constraints using AlphaFold2
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teaching
CS38003-Python Programming
Undergraduate course, Department of Computer Science, Purdue University, 2021
CS49000-DSC:Data Science Capstone
Undergraduate course, Department of Computer Science, Purdue University, 2021
CS50023-Data Engineering I
Graduate course, Department of Computer Science, Purdue University, 2022
CS25100-Data Structures And Algorithms
Undergraduate course, Department of Computer Science, Purdue University, 2023