• Assistant Professor
Yang Shen

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

Awards & Honors

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

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