Wittmann, Dominik M, Krumsiek, Jan, Saez-Rodriguez, Julio, Lauffenburger, Douglas A, Klamt, Steffen, Theis, Fabian J
Abstract Background The understanding of regulatory and signaling networks has long been a core objective in Systems Biology. Knowledge about these networks is mainly of qualitative nature, which...
Computing paths and cycles in biological interaction graphs (2009)
Klamt, Steffen, Von Kamp, Axel
Abstract Background Interaction graphs (signed directed graphs) provide an important qualitative modeling approach for Systems Biology. They enable the analysis of causal relationships in cellular...
Franke, Raimo, Müller, Melanie, Wundrack, Nicole, Gilles, Ernst-Dieter, Klamt, Steffen, Kähne, Thilo, ...
Abstract Background The hepatocyte growth factor (HGF) stimulates mitogenesis, motogenesis, and morphogenesis in a wide range of tissues, including epithelial cells, on binding to the receptor...
Computing knock out strategies in metabolic networks (2007)
Haus, Utz-Uwe, Klamt, Steffen, Stephen, Tamon
Given a metabolic network in terms of its metabolites and reactions, our goal is to efficiently compute the minimal knock out sets of reactions required to block a given behaviour. We describe an...
A Logical Model Provides Insights into T Cell Receptor Signaling (2007)
Julio Saez-Rodriguez, Luca Simeoni, Jonathan A. Lindquist, Rebecca Hemenway, Ursula Bommhardt, Boerge Arndt, ...
Cellular decisions are determined by complex molecular interaction networks. Large-scale signaling networks are currently being reconstructed, but the kinetic parameters and quantitative data that...
A Logical Model Provides Insights into T-cell Receptor Signaling (2007)
Julio Saez-Rodriguez, Luca Simeoni, Jonathan A. Lindquist, Rebecca Hemenway, Ursula Bommhardt, Boerge Arndt, ...
Cellular decisions are determined by complex molecular interaction networks. Large-scale signaling networks are currently being reconstructed but the kinetic parameters and quantitative data that...
GSMN-TB: a web-based genome-scale network model of Mycobacterium tuberculosismetabolism (2007)
Beste, Dany JV, Hooper, Tracy, Stewart, Graham, Bonde, Bhushan, Avignone-Rossa, Claudio, Bushell, Michael E, ...
Abstract Background An impediment to the rational development of novel drugs against tuberculosis (TB) is a general paucity of knowledge concerning the metabolism of Mycobacterium tuberculosis ,...
Structural and functional analysis of cellular networks with CellNetAnalyzer (2007)
Klamt, Steffen, Saez-Rodriguez, Julio, Gilles, Ernst D
Abstract Background Mathematical modelling of cellular networks is an integral part of Systems Biology and requires appropriate software tools. An important class of methods in Systems Biology deals...
Visual setup of logical models of signaling and regulatory networks with ProMoT (2006)
Saez-Rodriguez, Julio, Mirschel, Sebastian, Hemenway, Rebecca, Klamt, Steffen, Gilles, Ernst, Ginkel, Martin
Abstract Background The analysis of biochemical networks using a logical (Boolean) description is an important approach in Systems Biology. Recently, new methods have been proposed to analyze large...
A methodology for the structural and functional analysis of signaling and regulatory networks (2006)
Klamt, Steffen, Saez-Rodriguez, Julio, Lindquist, Jonathan A, Simeoni, Luca, Gilles, Ernst D
Abstract Background Structural analysis of cellular interaction networks contributes to a deeper understanding of network-wide interdependencies, causal relationships, and basic functional...
Zugl.: Stuttgart, Universiẗat, Diss., 2005.
BMC Bioinformatics BioMed Central Methodology article (2005)
Steffen Klamt, Julio Saez-rodriguez, Jonathan A Lindquist, Luca Simeoni, Jonathan A Lindquist, ...
A methodology for the structural and functional analysis of signaling and regulatory networks
Computation of elementary modes: a unifying framework and the new binary approach (2004)
Gagneur, Julien, Klamt, Steffen
Abstract Background Metabolic pathway analysis has been recognized as a central approach to the structural analysis of metabolic networks. The concept of elementary (flux) modes provides a rigorous...
Computation of elementary modes: a unifying framework and the
Minimal cut sets in biochemical reaction networks (2004)
Klamt, Steffen, Gilles, Ernst Dieter
Motivation: Structural studies of metabolic networks yield deeper insight into topology, functionality and capabilities of the metabolisms of different organisms. Here, we address the analysis of...
Klamt, Steffen, Stelling, Jörg, Ginkel, Martin, Gilles, Ernst Dieter
Motivation: The analysis of structure, pathways and flux distributions in metabolic networks has become an important approach for understanding the functionality of metabolic systems. The need of a...
A methodology for the structural and functional analysis of signaling and regulatory networks
Klamt, Steffen, Saez-Rodriguez, Julio, Lindquist, Jonathan A, Simeoni, Luca, Gilles, Ernst D
Visual setup of logical models of signaling and regulatory networks with ProMoT
Saez-Rodriguez, Julio, Mirschel, Sebastian, Hemenway, Rebecca, Klamt, Steffen, Gilles, Ernst Dieter, Ginkel, Martin
A methodology for the structural and functional analysis of signaling and regulatory networks
Klamt, Steffen, Saez-Rodriguez, Julio, Lindquist, Jonathan A, Simeoni, Luca, Gilles, Ernst D
Visual setup of logical models of signaling and regulatory networks with ProMoT
Saez-Rodriguez, Julio, Mirschel, Sebastian, Hemenway, Rebecca, Klamt, Steffen, Gilles, Ernst Dieter, Ginkel, Martin
GSMN-TB: a web-based genome-scale network model of Mycobacterium tuberculosis metabolism
Beste, Dany JV, Hooper, Tracy, Stewart, Graham, Bonde, Bhushan, Avignone-Rossa, Claudio, Bushell, Michael E, ...
GSMN-TB, a genome-scale metabolic model of M. tuberculosis, was constructed and validated using experimental data.
A Logical Model Provides Insights into T Cell Receptor Signaling
Saez-Rodriguez, Julio, Simeoni, Luca, Lindquist, Jonathan A, Hemenway, Rebecca, Bommhardt, Ursula, Arndt, Boerge, ...
Cellular decisions are determined by complex molecular interaction networks. Large-scale signaling networks are currently being reconstructed, but the kinetic parameters and quantitative data that...
Modeling the electron transport chain of purple non-sulfur bacteria
Klamt, Steffen, Grammel, Hartmut, Straube, Ronny, Ghosh, Robin, Gilles, Ernst Dieter
Purple non-sulfur bacteria (Rhodospirillaceae) have been extensively employed for studying principles of photosynthetic and respiratory electron transport phosphorylation and for investigating the...
Franke, Raimo, Müller, Melanie, Wundrack, Nicole, Gilles, Ernst-Dieter, Klamt, Steffen, Kähne, Thilo, ...
The Logic of EGFR/ErbB Signaling: Theoretical Properties and Analysis of High-Throughput Data
Samaga, Regina, Saez-Rodriguez, Julio, Alexopoulos, Leonidas G., Sorger, Peter K., Klamt, Steffen
The epidermal growth factor receptor (EGFR) signaling pathway is probably the best-studied receptor system in mammalian cells, and it also has become a popular example for employing mathematical...