Yang Shen

Assistant Professor

Yang Shen

Office: WEB 215I
Phone: 979.862.1694
Fax: 979.845.6259
Email: yshen@tamu.edu

Personal Website
Google Scholar Profile

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


Awards & Honors

  • Maximizing Investigators' Research Award (MIRA) for Early Stage Investigators, National Institute of General Medical Sciences, National Institutes of Health, 2017


  • Ph.D., Systems Engineering, Boston University, 2008
  • B.E., Automation, University of Science and Technology of China, 2002

Selected Publications

Predicting Protein Conformational Changes for Unbound and Homology Docking: Learning from Intrinsic and Induced Flexibility”, H Chen, Y Sun, and Y Shen, Proteins: Structure, Function, and Bioinformatics 85(3), 544-556, 2017

cNMA: A Framework of Encounter Complex-based Normal Mode Analysis to Model Conformational Changes in Protein Interactions”, T Oliwa and Y Shen, Bioinformatics 31(12), i151–i160, 2015

ESR1 Ligand-Binding Domain Mutations in Hormone-Resistant Breast Cancer", W Toy, Y Shen, H Won, B Green, RA Sakr, M Will, Z Li, K Gala, S Fanning et. al.,Nature Genetics 45(12), 1439–1445, 2013

Improved Flexible Refinement of Protein Docking in CAPRI rounds 22–27", Y Shen, Proteins: Structure, Function, and Bioinformatics 81(12), 2129–2136, 2013

Overcoming Mutation-Based Resistance to Antiandrogens with Rational Drug Design", MD Balbas, MJ Evans, DJ Hosfield, J Wongvipat, VK Arora, PA Watson et. al., eLife 2, e00499, 2013

Charge Optimization Theory for Induced-Fit Ligands", Y Shen, MK Gilson, B Tidor, Journal of Chemical Theory and Computation 8(11), 4580-4592, 2012