Hybrid modeling and robustness analysis of cell cycle regulatory circuitry

Caulobacter is a model system for studying bacterial cell cycle. A regulatory circuitry made of cascading regulatory proteins senses and regulates various cell functions, forming nested feedback control loops. By integrating the continuous regulator models with the discrete cell function models, a scalable hybrid control model was constructed that accurately simulates cell cycle regulation under various conditions for different mutant phenotypes. A novel adaptation of a formal verification tool from asynchronous circuit design further identified potential timing hazards in the regulatory circuitry. Ensuing experiments in-vivo revealed novel robustness mechanisms that were not expressed under normal lab conditions.
Xiling Shen is a PhD student in the Electrical Engineering Department at Stanford University. His current research interest focuses on modeling and analyzing biological regulatory networks using engineering concepts and tools.

Xiling Shen received his BS and MS degree from the Electrical Engineering Department of Stanford University in 2001. He worked at Barcelona Design Inc., a semiconductor startup for two years, specializing in analog circuit design and optimization, before joining Professor Mark Horowtiz' research group in the Electrical Engineering Department at Stanford in 2003. In the first two years of his PhD, Xiling Shen collaborated with Professor Joseph Kahn to use adaptive spatial equalization to compensate modal dispersion in multimode fibers. Starting from 2005, Xiling Shen has been collaborating with Professor Harley McAdams, Professor Lucy Shapiro, and Professor David Dill to model and analyze the robustness of the Caulobacter cell cycle regulation.