Edmund M. Clarke, James R. Faeder, Christopher J. Langmead, A. Harris, Sumit Kumar Jha, Axel Legay
Abstract. We present an algorithm, called BioLab, for verifying temporal properties of rule-based models of cellular signalling networks. BioLab models are encoded in the BioNetGen language, and...
Simulation of large-scale rule-based models (2009)
Colvin, Joshua, Monine, Michael I., Faeder, James R., Hlavacek, William S., Von Hoff, Daniel D., Posner, Richard G.
Motivation: Interactions of molecules, such as signaling proteins, with multiple binding sites and/or multiple sites of post-translational covalent modification can be modeled using reaction rules....
GetBonNie for building, analyzing and sharing rule-based models (2009)
Hu, Bin, Matthew Fricke, G., Faeder, James R., Posner, Richard G., Hlavacek, William S.
Summary: GetBonNie is a web-based application for building, analyzing and sharing rule-based models encoded in the BioNetGen language (BNGL). Tools accessible within the GetBonNie environment include...
ABSTRACT Graphical Rule-Based Representation of Signal-Transduction Networks (2008)
The process by which a cell senses and responds to its environment, as in signal transduction, is often mediated by a network of protein-protein interactions, in which proteins combine to form...
Domain-Oriented Reduction of Rule-Based Network Models (2008)
Borisov, Nikolay M., Chistopolsky, Alexander S., Faeder, James R., Kholodenko, Boris N.
The coupling of membrane-bound receptors to transcriptional regulators and other effector functions is mediated by multi-domain proteins that form complex assemblies. The modularity of protein...
Systems biology Carbon fate maps for metabolic reactions (2008)
Fangping Mu, Robert F. Williams, Clifford J. Unkefer, Pat J. Unkefer, James R. Faeder, William S. Hlavacek
Motivation: Stable isotope labeling of small-molecule metabolites (e.g., 13 C-labeling of glucose) is a powerful tool for characterizing pathways and reaction fluxes in a metabolic network. Analysis...
Simulation of systems marked by combinatorial complexity (2008)
Michael Monine, Jin Yang, Ambarish Nag, Byron Goldstein, Richard G. Posner, Joshua Colvin, ...
Signal transduction generally involves multivalent protein-protein interactions that can produce myriad protein complexes and post-translational modifications. By using reaction rules to represent...
Kinetic Monte Carlo Method for Rule-based Modeling of Biochemical Networks (2007)
Yang, Jin, Monine, Michael I., Faeder, James R., Hlavacek, William S.
We present a kinetic Monte Carlo method for simulating chemical transformations specified by reaction rules, which can be viewed as generators of chemical reactions, or equivalently, definitions of...
Structure-based Kinetic Models of Modular Signaling Protein Function: Focus on Shp2 (2007)
Dipak Barua, James R. Faeder, Jason M. Haugh
This un-edited manuscript has been accepted for publication in Biophysical Journal and is freely available on BioFast at
Carbon-fate maps for metabolic reactions (2007)
Mu, Fangping, Williams, Robert F., Unkefer, Clifford J., Unkefer, Pat J., Faeder, James R., Hlavacek, William S.
Motivation: Stable isotope labeling of small-molecule metabolites (e.g. 13C-labeling of glucose) is a powerful tool for characterizing pathways and reaction fluxes in a metabolic network. Analysis of...
Rules for Modeling Signal-Transduction Systems (2006)
William S. Hlavacek, James R. Faeder, Michael L. Blinov, Richard G. Posner, Michael Hucka, Walter Fontana
Formalized rules for protein-protein interactions have recently been introduced to represent the binding and enzymatic activities of proteins in cellular signaling. Rules encode an understanding of...
Rule-based modeling of biochemical networks (2005)
James R. Faeder, Michael L. Blinov, Byron Goldstein, S. Hlavacek
We present a method for generating a biochemical reaction network from a description of the interactions of components of biomolecules. The interactions are specified in the form of reaction rules,...
Combinatorial complexity and dynamical restriction of network flows in signal transduction (2004)
Faeder, James R., Blinov, Michael L., Goldstein, Byron, Hlavacek, William S.
The activities and interactions of proteins that govern the cellular response to a signal generate a multitude of protein phosphorylation states and heterogeneous protein complexes. Here, using a...
transduction based on the interactions (2004)
Michael L. Blinov, James R. Faeder, Byron Goldstein, William S. Hlavacek
M.L. Blinov et al. BioNetGen: software for rule-based modeling of signal
Blinov, Michael L., Faeder, James R., Goldstein, Byron, Hlavacek, William S.
Summary: BioNetGen allows a user to create a computational model that characterizes the dynamics of a signal transduction system and that accounts comprehensively and precisely for specified...
Blinov, Michael L., Faeder, James R., Goldstein, Byron, Hlavacek, William S.
Summary: BioNetGen allows a user to create a computational model that characterizes the dynamics of a signal transduction system, and that accounts comprehensively and precisely for specified...
Blinov, Michael L., Faeder, James R., Goldstein, Byron, Hlavacek, William S.
Summary: BioNetGen allows a user to create a computational model that characterizes the dynamics of a signal transduction system and that accounts comprehensively and precisely for specified...
Thesis (Ph. D.)--University of Colorado, 1998.
q-bio 2007: a watershed moment in modern biology
Edwards, Jeremy S, Faeder, James R, Hlavacek, William S, Jiang, Yi, Nemenman, Ilya, Wall, Michael E
Structure-Based Kinetic Models of Modular Signaling Protein Function: Focus on Shp2
Barua, Dipak, Faeder, James R., Haugh, Jason M.
We present here a computational, rule-based model to study the function of the SH2 domain-containing protein tyrosine phosphatase, Shp2, in intracellular signal transduction. The two SH2 domains of...
Barua, Dipak, Faeder, James R., Haugh, Jason M.
Intracellular signal transduction proteins typically utilize multiple interaction domains for proper targeting, and thus a broad diversity of distinct signaling complexes may be assembled....
A Bipolar Clamp Mechanism for Activation of Jak-Family Protein Tyrosine Kinases
Barua, Dipak, Faeder, James R., Haugh, Jason M.
Most cell surface receptors for growth factors and cytokines dimerize in order to mediate signal transduction. For many such receptors, the Janus kinase (Jak) family of non-receptor protein tyrosine...