• Publications
  • Influence
The systems biology markup language (SBML): a medium for representation and exchange of biochemical network models
TLDR
This work summarizes the Systems Biology Markup Language (SBML) Level 1, a free, open, XML-based format for representing biochemical reaction networks, a software-independent language for describing models common to research in many areas of computational biology. Expand
Computational modeling of the dynamics of the MAP kinase cascade activated by surface and internalized EGF receptors
TLDR
The model provides insight into signal–response relationships between the binding of EGF to its receptor at the cell surface and the activation of downstream proteins in the signaling cascade, showing that EGF-induced responses are remarkably stable over a 100-fold range of ligand concentration. Expand
Structural and functional analysis of cellular networks with CellNetAnalyzer
TLDR
CellNetAnalyzer is introduced, a toolbox for MATLAB facilitating, in an interactive and visual manner, a comprehensive structural analysis of metabolic, signalling and regulatory networks and provides a large toolbox with various, partially unique, functions and algorithms for functional network analysis. Expand
Metabolic network structure determines key aspects of functionality and regulation
TLDR
A theoretical method for simultaneously predicting key aspects of network functionality, robustness and gene regulation from network structure alone is devised by determining and analysing the non-decomposable pathways able to operate coherently at steady state (elementary flux modes). Expand
A methodology for the structural and functional analysis of signaling and regulatory networks
TLDR
This work proposes 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, and proposes a formalism based on logical interaction hypergraphs, which facilitates a logical steady state analysis (LSSA). Expand
Bistability Analyses of a Caspase Activation Model for Receptor-induced Apoptosis*
TLDR
The current knowledge of the molecular mechanisms of the death-receptor-activated caspase cascade is translated into a mathematical model and a reduction down to the apoptotic core machinery enables the application of analytical mathematical methods to evaluate the system behavior within a wide range of parameters. Expand
Minimal cut sets in biochemical reaction networks
TLDR
This work addresses the analysis of potential failure modes in metabolic networks whose occurrence will render the network structurally incapable of performing certain functions, and introduces the concept of minimal cut sets for biochemical networks. Expand
A Logical Model Provides Insights into T Cell Receptor Signaling
TLDR
A methodology relying on a logical formalism 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-receptors, and the accessory signaling receptor CD28, and it proves to be a promising in silico tool. Expand
Robustness properties of circadian clock architectures.
TLDR
This analysis focuses on the genetic oscillator responsible for generating circadian rhythms in Drosophila as a prototypic dynamical cellular system and shows that the tradeoff between robustness and fragility is largely determined by the regulatory structure. Expand
Correlation between Growth Rates, EIIACrr Phosphorylation, and Intracellular Cyclic AMP Levels in Escherichia coli K-12
TLDR
The relation between cellular growth rates and the key parameters of catabolite repression were increasingly uncoupled from the growth rate, which perhaps indicates an increasing role executed by other global control systems, in particular the stringent-relaxed response system. Expand
...
1
2
3
4
5
...