- Associate Professor, Electrical & Computer Engineering
- Affiliated Faculty, Computer Science and Engineering
- Phone: 979-862-1694
- Email: yshen@tamu.edu
- Office: WEB 215I
- Website: Personal Website
Educational Background
- Ph.D., Systems Engineering, Boston University – 2008
- B.E., Automation, University of Science and Technology of China – 2002
Research Interests
-
Algorithms for modeling biological molecules, systems, and data.
- Algorithms:
- Optimization and machine learning
- Systems and control
- Applications:
- Protein docking and protein & drug design
- Systems and synthetic biology
- Omics
- Algorithms:
Awards & Honors
- Maximizing Investigators' Research Award (MIRA) for Early Stage Investigators, National Institute of General Medical Sciences, National Institutes of Health, 2017
- Faculty Early Career Development (CAREER) Award, National Science Foundation, 2020
Selected Publications
- Y You and Y Shen (2022). "Cross-Modality and Self-Supervised Protein Embedding for Compound-Protein Affinity and Contact Prediction", Bioinformatics 38(Supplement_2): ii68-ii74.
- M Karimi, S Zhu, Y Cao, and Y Shen (2020). "De Novo Protein Design for Novel Folds using Guided Conditional Wasserstein Generative Adversarial Networks", Journal of Chemical Information and Modeling 60(12): 5667-5681.
- Y Cao and Y Shen (2020). "Bayesian Active Learning for Optimization and Uncertainty Quantification in Protein Docking", Journal of Chemical Theory and Computation 16(8): 5334-5347.
- Y You, T Chen, Z Wang and Y Shen (2019). "When Does Self-Supervision Help Graph Convolutional Networks?." International Conference on Machine Learning (ICML), pp. 10871-10880.
- Y Cao, T Chen, Z Wang and Y Shen (2019). "Learning to Optimize in Swarms", Advances in Neural Information Processing Systems (NeurIPS) 32: 15018-15028.
- M Karimi, D Wu, Z Wang and Y Shen (2019). "DeepAffinity: Interpretable Deep Learning of Compound-Protein Affinity through Unified Recurrent and Convolutional Neural Networks", Bioinformatics 35(18): 3329-3338.
- M Karimi and Y Shen (2018). "iCFN: An Efficient Exact Algorithm for Multistate Protein Design", Bioinformatics 34(18): i811-i820.