• 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

  • 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.