- Associate Professor, Electrical & Computer Engineering
- Joint Faculty in: Computer Engineering
- Phone: 979-862-1694
- FAX: 979-845-6259
- 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
Selected Publications
- Y Cao, T Chen, Z Wang and Y Shen, "Learning to Optimize in Swarms", Advances in Neural Information Processing Systems (NeurIPS) 32: 15018-15028, 2019.
- Y Cao, Y Sun, M Karimi, H Chen, O Moronfoye and Y Shen, "Predicting Pathogenicity of Missense Variants with Weakly Supervised Regression", Human Mutation 40(9): 1579-1592, 2019.
- M Karimi, D Wu, Z Wang and Y Shen, "DeepAffinity: Interpretable Deep Learning of Compound-Protein Affinity through Unified Recurrent and Convolutional Neural Networks", Bioinformatics 35(18): 3329-3338, 2019.
- M Karimi and Y Shen, "iCFN: An Efficient Exact Algorithm for Multistate Protein Design", Bioinformatics 34(18): i811-i820, 2018.
- H Chen, Y Sun and Y Shen, "Predicting Protein Conformational Changes for Unbound and Homology Docking: Learning from Intrinsic and Induced Flexibility”, Proteins: Structure, Function, and Bioinformatics 85(3), 544-556, 2017.
- T Oliwa and Y Shen, "cNMA: A Framework of Encounter Complex-based Normal Mode Analysis to Model Conformational Changes in Protein Interactions”, Bioinformatics 31(12), i151–i160, 2015.
- W Toy, Y Shen, H Won, B Green, RA Sakr et. al., "ESR1 Ligand-Binding Domain Mutations in Hormone-Resistant Breast Cancer", Nature Genetics 45(12), 1439–1445, 2013.
- Y Shen, "Improved Flexible Refinement of Protein Docking in CAPRI rounds 22–27", Proteins: Structure, Function, and Bioinformatics 81(12), 2129–2136, 2013.
- MD Balbas, MJ Evans, DJ Hosfield, J Wongvipat, VK Arora et. al., "Overcoming Mutation-Based Resistance to Antiandrogens with Rational Drug Design", eLife 2, e00499, 2013.
- Y Shen, MK Gilson and B Tidor, "Charge Optimization Theory for Induced-Fit Ligands", Journal of Chemical Theory and Computation 8(11), 4580-4592, 2012.