Mitsos, Alexander, Melas, Ioannis N., Siminelakis, Paraskeuas, Chairakaki, Aikaterini D., Saez-Rodriguez, Julio, Alexopoulos, Leonidas G.
Understanding the mechanisms of cell function and drug action is a major endeavor in the pharmaceutical industry. Drug effects are governed by the intrinsic properties of the drug (i.e., selectivity...
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...
Signal Transduction Networks (2008)
Signal Transduction, Mitberichter Prof, Julio Saez-rodriguez, Jeremy Huard, Martin Ginkel, ...
Foundation (DFG) and the German Ministery of Education and Research (BMBF). First and foremost I would like to thank Professor Ernst Dieter Gilles for his excellent supervision. He always found the...
Flexible informatics for linking experimental data to mathematical models via DataRail (2008)
Saez-Rodriguez, Julio, Goldsipe, Arthur, Muhlich, Jeremy, Alexopoulos, Leonidas G., Millard, Bjorn, Lauffenburger, Douglas A., ...
Motivation: Linking experimental data to mathematical models in biology is impeded by the lack of suitable software to manage and transform data. Model calibration would be facilitated and models...
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...
Modular analysis of signal transduction networks (2007)
Julio Saez-Rodriguez, Saez-Rodriguez, Julio
Two characteristic properties of biochemical (in particular signaling) networks are their complexity and their inherent modularity. The main idea of this work is to take advantage of the latter to...
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...
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...
Conzelmann, Holger, Saez-Rodriguez, Julio, Sauter, Thomas, Kholodenko, Boris N, Gilles, Ernst D
Abstract Background: Receptors and scaffold proteins possess a number of distinct domains and bind multiple partners. A common problem in modeling signaling systems arises from a combinatorial...
Conzelmann, Holger, Saez-Rodriguez, Julio, Sauter, Thomas, Kholodenko, Boris N., Gilles, Ernst D.
Background:Receptors and scaffold proteins possess a number of distinct domains and bind multiple partners. A common problem in modeling signaling systems arises from a combinatorial explosion of...
Rebecca Hemenway, Julio Saez-rodriguez, Sebastian Mirschel, Martin Ginkel
2.1 How do I install ProMoT?...................... 3 2.2 How can I start ProMoT?....................... 4
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
Conzelmann, Holger, Saez-Rodriguez, Julio, Sauter, Thomas, Bullinger, Eric, Allgöwer, Frank, Gilles, Ernst Dieter
Biological systems and, in particular, cellular signal transduction pathways are characterised by their high complexity. Mathematical models describing these processes might be of great help to gain...
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
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...
Fuzzy Logic Analysis of Kinase Pathway Crosstalk in TNF/EGF/Insulin-Induced Signaling
Aldridge, Bree B., Saez-Rodriguez, Julio, Muhlich, Jeremy L., Sorger, Peter K., Lauffenburger, Douglas A.
When modeling cell signaling networks, a balance must be struck between mechanistic detail and ease of interpretation. In this paper we apply a fuzzy logic framework to the analysis of a large,...
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...