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Faeder Lab


My 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 (complete list)


Toward a comprehensive language for biological systems
J. R. Faeder
BMC Biol., 9, 68, 2011. (link)

RULEBENDER: A Visual Interface for Rule-Based Modeling
W. Xu, A. M. Smith, J. R. Faeder,* and G. E. Marai*
Bioinformatics., 27, 1721-2, 2011. (link) (preprint)
*Corresponding authors

Efficient modeling, simulation and coarse-graining of biological complexity with NFsim
M. W. Sneddon, J. R. Faeder, and T. Emonet
Nature Methods., 8, 177-183, 2011. (link)

Guidelines for visualizing and annotating rule-based models
Chylek LA, Hu B, Blinov ML, Emonet T, Faeder JR, Goldstein B, Gutenkunst RN, Haugh JM, Lipniacki T, Posner RG, Yang J, Hlavacek WS
Mol. Biosyst., 7, 2779-95, 2011. (pdf)


Rules for modeling signal-transduction systems
W. S. Hlavacek, J. R. Faeder, M. L. Blinov, R. G. Posner, M. Hucka, and W. Fontana
Sci. STKE., 2006, re6, 2006. (link)

Rule-Based Modeling of Biochemical Systems with BioNetGen
J. R. Faeder, M. L. Blinov, and W. S. Hlavacek
Methods Mol. Biol., 500, 113-167, 2009. (pdf) (link)

The Complexity of Cell Signaling and the Need for a New Mechanics
W. S. Hlavacek and J. R. Faeder
Sci. Signaling, 2, pe46, 2009. (abstract) (full text)

Applications of Rule-Based Modeling

Aggregation of membrane proteins by cytosolic cross-linkers: Theory and simulation of the LAT-Grb2-Sos1 system
A. Nag, M. I. Monine, J. R. Faeder, and B. Goldstein
Biophys. J., 96, 2604-2623, 2009. (link)

Detailed qualitative dynamic knowledge representation using a BioNetGen model of TLR-4 signaling and preconditioning
G. C. An and J. R. Faeder
Math. Biosci., 217, 53-63, 2009 (link)

A bipolar clamp mechanism for activation of Jak-family protein tyrosine kinases
D. Barua, J. R. Faeder, and J. M. Haugh
PLoS Comput. Biol. 2009, 5, e1000364, 2009. (link)

Analysis and Verification of the HMGB1 Signaling Pathway
H. Gong, P. Zuliani, A. Komuravelli, J. R. Faeder, and E.M. Clarke. BMC Bioinformatics, 11, S10 (13 pages). (link) Best paper award

Methods and Algorithms

Kinetic Monte Carlo Method for Rule-based Modeling of Biochemical Networks
J. Yang, M. I. Monine, James R. Faeder, and W. S. Hlavacek
Phys. Rev. E, 78, 031910, 2008. (pdf)

Compartmental Rule-Based Modeling of Biochemical Systems
L. A. Harris, J. S. Hogg, and J. R. Faeder
Proceedings of the 2009 Winter Simulation Conference. (pdf) (link)