04/2013 Selected talk at the 5th CAPRI Evaluation Meeting, entitled "Improved flexible refinement of protein docking in CAPRI rounds 22–27".
04/2013 Invited talk at the 245th ACS, entitled "Designing and unraveling promiscuous inhibitors against drug-resistant target mutations".
04/2013 "Overcoming Mutation-Based Resistance to Antiandrogens with Rational Drug Design" published on eLife. (Editor's Choice, eLife Insight)
02/2013 Awarded 2M CPU hours in total (2012-13) at Argonne Leadership Computing Facility.
11/2012 "Charge Optimization Theory for Induced-Fit Ligands" published on JCTC.
06/2012 Visiting assistant professor at MIT.
Best performance in CAPRI Round 26 (1st out of 42 worldwide teams).
01/2012 Started the appointment of research assistant professor at TTI-C.
07/2011 Produced one fair and two medium predictions
for three protein–protein targets and ranked No. 2 among 37 worldwide
teams in CAPRI Round 23.
03/2011 Oral presentation at the 241st
American Chemical Society (ACS) National Meeting.
Yang Shen is a
research assistant professor at Toyota Technological
Chicago, a philanthropically endowed academic computer science
institute with a close affiliation with the University of Chicago Computer Science
He received his B.E. in Automatic Control from the University of Science and Technology of China in 2002 and his Ph.D. in Systems Engineering from Boston University in 2008. His thesis work with Sandor Vajda, Yannis Paschalidis, and Pirooz Vakili involves algorithm development for protein docking, small-molecule mapping, and metabolic engineering. In 2008–2011 he had been a postdoctoral associate with Bruce Tidor in the Department of Biological Engineering and the Computer Science & Artificial Intelligence Laboratory (CSAIL) at Massachusetts Institute of Technology where he remains a research affiliate.
His research interests are in modeling, simulating, and engineering of biomolecular networks, with the goal of probing molecular mechanisms and modulating emergent behavior. Specific topics include protein docking, protein engineering, drug design, systems and synthetic biology, and bioinformatics. Central to these ends are the development and application of computational methods in molecular modeling, network simulation, optimization, machine learning, graph theory, and system and control theory.