Lab Overview
Our lab is interested in developing mathematical models of biological regulatory processes that integrate specific knowledge about protein-protein interactions. Together with collaborators at Los Alamos National Laboratory, we have developed a simulation framework called BioNetGen that allows rule-based specification of biochemical reaction networks and provides both deterministic and stochastic modeling capabilities. Current research includes the development of specific models of signal transduction and the development of new stochastic simulation algorithms that will greatly broaden the scope of models that can be developed. Other research areas include model reduction, parameter estimation and uncertainty analysis, and automated model construction from databases of protein interactions.
Selected Publications
Reviews
- B. Goldstein, J. R. Faeder, and W. S. Hlavacek. “Mathematical and computational models of immune-receptor signalling.” Nat. Rev. Immunol., 4, 445-456, 2004. (pdf)
- W. S. Hlavacek, et al. “Rules for modeling signal-transduction systems.” Sci. STKE., 2006, re6, 2006. (pdf)
Applications of Rule-Based Modeling
- J. R. Faeder, et al. “Combinatorial complexity and dynamical restriction of network flows in signal transduction.” IEE Syst. Biol., 2, 5-15, 2005. (pdf)
- D. Barua, J. R. Faeder, and J. M. Haugh. “Structure-based Kinetic Models of Modular Signaling Protein Function: Focus on Shp2.” Biophys. J., 92, 2290-2300, 2007. (pdf)
- Mu, F., et al. “Carbon fate maps for metabolic reactions.” Bioinformatics, 23, 3193-3199, 2007. (pdf)
- D. Barua, J. R. Faeder, J. M. Haugh, “Computational models of tandem Src homology 2 domain interactions and application to phosphoinositide 3-kinase.” J. Biol. Chem., in press. (pdf) (supplement-pdf) new
Methods for Rule-Based Modeling
- J. Yang, M. I. Monine, James R. Faeder, and W. S. Hlavacek. “Kinetic Monte Carlo Method for Rule-based Modeling of Biochemical Networks.” arxiv:0712.3773. new