Yang Shen

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News

05/2013  Antiandrogen paper highlighted by Nature Reviews Cancer and Science-Business eXchange (Cover Story).

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.

01/2012  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.

Bio

Yang Shen is a research assistant professor at Toyota Technological Institute at Chicago, a philanthropically endowed academic computer science institute with a close affiliation with the University of Chicago Computer Science Department. 

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.