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The systems biology markup language (SBML): a medium for representation and exchange of biochemical network models
We summarize the Systems Biology Markup Language (SBML) Level 1, a free, open, XML-based format for representing biochemical reaction networks. Expand
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Computational modeling of the dynamics of the MAP kinase cascade activated by surface and internalized EGF receptors
We present a computational model that offers an integrated quantitative, dynamic, and topological representation of intracellular signal networks, based on known components of epidermal growth factorExpand
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Structural and functional analysis of cellular networks with CellNetAnalyzer
We introduce CellNetAnalyzer, a toolbox for MATLAB facilitating, in an interactive and visual manner, a comprehensive structural analysis of metabolic, signalling and regulatory networks. Expand
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Metabolic network structure determines key aspects of functionality and regulation
The relationship between structure, function and regulation in complex cellular networks is a still largely open question. Systems biology aims to explain this relationship by combining experimentalExpand
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A methodology for the structural and functional analysis of signaling and regulatory networks
We propose formalisms and methods, relying on adapted and partially newly introduced approaches, which facilitate a structural analysis of signaling and regulatory networks with focus on functional aspects. Expand
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Bistability Analyses of a Caspase Activation Model for Receptor-induced Apoptosis*
Apoptosis is an important physiological process crucially involved in development and homeostasis of multicellular organisms. Although the major signaling pathways have been unraveled, a detailedExpand
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Robustness properties of circadian clock architectures.
Robustness, a relative insensitivity to perturbations, is a key characteristic of living cells. However, the specific structural characteristics that are responsible for robust performance are notExpand
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A Logical Model Provides Insights into T Cell Receptor Signaling
A large-scale Boolean model for T cell activation is applied to the functional analysis of the complex signaling network governing the activation of T cells via the T cell receptor, the CD4/CD8 co-receptor, and the accessory signaling receptor CD28. Expand
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Minimal cut sets in biochemical reaction networks
We address the analysis of potential failure modes in metabolic networks whose occurrence will render the network structurally incapable of performing certain functions. Expand
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FluxAnalyzer: exploring structure, pathways, and flux distributions in metabolic networks on interactive flux maps
The FluxAnalyzer is a package for MATLAB and facilitates integrated pathway and flux analysis for metabolic networks within a graphical user interface. Expand
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