William Chen

Education

B.A. Physics, Molecular Biology, University of California Berkeley 1998 Ph.D. Biophysics, Harvard University 2006

Research

My background is in theoretical and computational physics of biopolymers and other soft-matter or biological systems.

Recently I've been working on the ErbB receptor project, focusing on computational model development, but collaborating closely with the experimental biologists. On the experimental side, we are characterizing the ErbB system with a battery of dynamic, multiplex protein-based assays. On the computational side, we are developing a mass-action model that encapsulates key events of ErbB signaling. In our studies, we have observed great variation in ErbB-driven signals, and are trying to understand the factors responsible for, and the impact of, diversity in signal timing and intensity across cancer cell lines. This motivates us to understand and dissect the parameter space that corresponds to classes of dynamics in these nonlinear systems. Using techniques from optimization theory and tools such as action principles, I am also considering how one goes about finding specific parameter sets of generalized mass action models that match dynamic data, and whether such parameters are well-identified or constrained. Further, we are hopeful that this understanding will identify measurable signals that are most informative with respect to details of the ErbB system.

I have also been maintaining an interest in new methods to build and analyze large biochemical models. The traditional way of writing out large sets of ODEs by hand is cumbersome and prone to error. New methods based on computer science appear to tackle some of these issues more efficiently.