My main motivation is to unravel molecular mechanisms and to modulate emergent behavior of biomolecular networks with the development and application of computational tools (including molecular modeling, network simulation, optimization, machine learning, graph theory, and systems and control theory). To that end, I aim at an iterative process that models and experiments can feed each other.
- Massachusetts Institute of Technology - (Cambridge, Massachusetts, United States), Postdoctoral Training 2011
- Ph.D. in Systems Engineering, Boston University - (Boston, Massachusetts, United States) 2008
- B.E. in Engineering, University of Science and Technology of China - (Hefei, China) 2002
- Shen, Y., Radhakrishnan, M. L., & Tidor, B. (2015). Molecular mechanisms and design principles for promiscuous inhibitors to avoid drug resistance: lessons learned from HIV-1 protease inhibition.. Proteins: Structure, Function and Bioinformatics. 83(2), 351-372.
- Lensink, M. F., Moal, I. H., Bates, P. A., Kastritis, P. L., Melquiond, A., Karaca, E., ... Wodak, S. J. (2014). Blind prediction of interfacial water positions in CAPRI. Proteins: Structure, Function and Bioinformatics. 82(4), 620-632.
- Toy, W., Shen, Y., Won, H., Green, B., Sakr, R. A., Will, M., ... Chandarlapaty, S. (2013). ESR1 ligand-binding domain mutations in hormone-resistant breast cancer. NATURE GENETICS. 45(12), 1439-1445.
- Shen, Y. (2013). Improved flexible refinement of protein docking in CAPRI rounds 22-27. Proteins: Structure, Function and Bioinformatics. 81(12), 2129-2136.
- Shen, Y., Altman, M. D., Ali, A., Nalam, M., Cao, H., Rana, T. M., Schiffer, C. A., & Tidor, B. (2013). Testing the Substrate-Envelope Hypothesis with Designed Pairs of Compounds. ACS Chemical Biology. 8(11), 2433-2441.