Multistability of signal transduction motifs (2008)
Saez-Rodriguez, J., Hammerle-Fickinger, A., Dalal, O., Klamt, S., Gilles, E. D., Conradi, C.
Franke, R., Mueller, M., Wundrack, N., Gilles, E. D., Klamt, S., Kaehne, T., ...
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 tyrosine kinase...
Modeling the electron transport chain of purple non-sulfur bacteria (2008)
Klamt, S., Grammel, H., Straube, R., Ghosh, R., Gilles, E. D.
Purple non-sulfur bacteria (Rhodospirillaceae) have been extensively employed for studying principles of photosynthetic and respiratory electron transport phosphorylation and for investigating the...
Mathematical modeling and analysis of insulin clearance in vivo (2008)
Koschorreck, M., Gilles, E. D.
Background: Analyzing the dynamics of insulin concentration in the blood is necessary for a comprehensive understanding of the effects of insulin in vivo. Insulin removal from the blood has been...
Feuer, R., Ederer, M., Gilles, E. D., Sprenger, G. A., Sawodny, O., Sauter, T.
Die biotechnische Herstellung von Substanzen mit Hilfe von Mikroorganismen ist ein wirtschaftlich wichtiges Einsatzgebiet der Systembiologie. In diesem Artikel wird ein pyruvat-auxotropher...
Saez-Rodriguez, J., Gayer, S., Ginkel, M., Gilles, E. D.
Abstract: Motivation: The modularity of biochemical networks in general, and signaling networks in particular, has been extensively studied over the past few years. It has been proposed to be a...
ALC : automated reduction of rule-based models (2008)
Koschorreck, M., Gilles, E. D.
Background Combinatorial complexity is a challenging problem for the modeling of cellular signal transduction since the association of a few proteins can give rise to an enormous amount of feasible...
Structural and functional analysis of cellular networks with CellNetAnalyzer (2007)
Klamt, S., Saez-Rodriguez, J., Gilles, E. D.
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 with...
Bettenbrock, K., Sauter, T., Jahreis, K., Kremling, A., Lengeler, J. W., Gilles, E. D.
In Escherichia coli K-12, components of the phosphoenolpyruvate-dependent phosphotransferase systems (PTSs) represent a signal transduction system involved in the global control of carbon catabolism...
A logical model provides insights into T cell receptor signaling (2007)
Saez-Rodriguez, J., Simeoni, L., Lindquist, J., Hemenway, R., Bommhardt, U., Arndt, B., ...
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)
Saez-Rodriguez, J., Simeoni, L., Lindquist, J., Hemenway, R., Bommhardt, U., Arndt, B., ...
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...
Analysis of global control of Escherichia coli carbohydrate uptake (2007)
Kremling, A., Bettenbrock, K., Gilles, E. D.
Global control influences the regulation of many individual subsystems by superimposed regulator proteins. A prominent example is the control of carbohydrate uptake systems by the transcription...
Reduced modeling of signal transduction - a modular approach (2007)
Koschorreck, M., Conzelmann, H., Ebert, S., Ederer, M., Gilles, E. D.
Methods for analysis of evolutive adaptation of E. coli (2007)
Feuer, R., Ederer, M., Trachtmann, N., Sauter, T., Gilles, E. D., Sprenger, G., ...
Mathematical models of the metabolism of organisms like Escherichia coli provide a possibility to improve the production of industrial relevant compounds. These models allow predictions of the...
Thermodynamic-Kinetic Modeling and Electrical Engineering (2007)
Thermodynamic-kinetic modeling provides a thermodynamically sound way for formulating dynamic model equations of biochemical reaction systems. State variables of this approach are thermokinetic...
A methodology for the structural and functional analysis of signaling and regulatory networks (2006)
Klamt,S., Saez-Rodriguez,J., Lindquist,J., Simeoni,L., Gilles,E. D.
A quantitative approach to catabolite repression in Escherichia coli (2006)
Bettenbrock, K., Fischer, S., Kremling, A., Jahreis, K., Sauter, T., Gilles, E. D.
A dynamic mathematical model was developed to describe the uptake of various carbohydrates (glucose, lactose, glycerol, sucrose and galactose) in E.coli. For validation a number of isogenic strains...
A methodology for the structural and functional analysis of signaling and regulatory networks (2006)
Klamt, S., Saez-Rodriguez, J., Lindquist, J., Simeoni, L., Gilles, E. D.
Visual set-up of logical models of signaling and regulatory networks with ProMoT (2006)
Saez-Rodriguez, J., Mirschel, S., Hemenway, R., Klamt, S., Gilles, E. D., Ginkel, M.
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 signaling...
Chemical Reaction Network Theory : a tool for systems biology (2006)
Conradi, C., Saez-Rodriguez, J., Gilles, E. D., Raisch, J.
Feinberg's Chemical Reaction Network Theory (CRNT) connects the structure of a biochemical reaction network to qualitative properties of the corresponding system of ordinary differential equations....
Metabolic networks : Biology meets engineering sciences (2005)
Kremling,A., Stelling,J., Bettenbrock,K., Fischer,S., Gilles,E. D.
A hallmark of systems biology is the interdisciplinary approach to the complexity of biological systems, in which mathematical modeling constitutes an important part. Here, we use the example of...
Computer Aided Modeling of Chemical and Biological Systems : Methods, Tools, and Applications (2005)
Mangold,M., Angeles-Palacios,O., Ginkel,M., Kremling,A., Waschler,R., Kienle,A., ...
Computer tools can support and accelerate the development and implementation of first principle models for chemical and biological processes significantly. Several application examples illustrate...
Dissecting the Puzzle of Life : Modularization of Signal Transduction Networks (2005)
Saez-Rodriguez,J., Kremling,A., Gilles,E. D.
Cells have developed complex control networks which allow them to sense and response to changes in their environment. Although they have different underlying biochemical mechanisms, signal...
Using chemical reaction network theory to discard a kinetic mechanism hypothesis (2005)
Conradi,C., Saez-Rodriguez,J., Gilles,E. D., Raisch,J.
Feinberg s Chemical Reaction Network Theory (CRNT) connects the structure of a biochemical reaction network to qualitative properties of the corresponding system of ordinary differential equations....
Mathematical Model of rpoS Regulation in E. coli (2005)
Backfisch,T., Pruteanu,M., Hengge,R., Gilles,E. D.
This contribution presents a mathematical model of rpoS regulation in E. coli. It is well known that many stress signals cause increases in cellular σS (RpoS) level and activate σS-dependent...
Saez-Rodriguez,J., Conzelmann,H., Sauter,T., Kholodenko,B. N., Gilles,E. D.
A rigorous, detailed description of signaling networks gives rise to huge models, while an a priori simplified model relies on assumptions difficult to prove. Therefore, models which are manageable,...
Automatic Track-Keeping of Inland Vessels in Flowing Waterways (2005)
Integrated navigation systems for inland vessels, combining different technologies like radar, satellite navigation (GPS) and electronic charts (ECDIS), have been developed in the Max Planck...
Nutsch,T., Oesterhelt,D., Gilles,E. D., Marwan,W.
By reverse-engineering we have detected eight kinetic phases of the symmetric switch cycle of the Halobacterium salinarum flagellar motor assembly and identified those steps in the switch cycle that...
Computer Aided Modeling of Chemical and Biological Systems : Methods, Tools, and Applications (2005)
Mangold, M., Angeles-Palacios, O., Ginkel, M., Kremling, A., Waschler, R., Kienle, A., ...
Computer tools can support and accelerate the development and implementation of first principle models for chemical and biological processes significantly. Several application examples illustrate...
Dissecting the Puzzle of Life : Modularization of Signal Transduction Networks (2005)
Saez-Rodriguez, J., Kremling, A., Gilles, E. D.
Cells have developed complex control networks which allow them to sense and response to changes in their environment. Although they have different underlying biochemical mechanisms, signal...
Using chemical reaction network theory to discard a kinetic mechanism hypothesis (2005)
Conradi, C., Saez-Rodriguez, J., Gilles, E. D., Raisch, J.
Feinberg s Chemical Reaction Network Theory (CRNT) connects the structure of a biochemical reaction network to qualitative properties of the corresponding system of ordinary differential equations....
Using Chemical Reaction Network Theory to discard a Kinetic Mechanism Hypothesis (2005)
Conradi, C., Saez-Rodriguez, J., Gilles, E. D., Raisch, J.
Feinberg’s Chemical Reaction Network Theory (CRNT) connects the structure of a biochemical reaction network to qualitative properties of the corresponding system of ordinary differential equations....
Mathematical Model of rpoS Regulation in E. coli (2005)
Backfisch, T., Pruteanu, M., Hengge, R., Gilles, E. D.
This contribution presents a mathematical model of rpoS regulation in E. coli. It is well known that many stress signals cause increases in cellular σS (RpoS) level and activate σS-dependent...
Metabolic networks : Biology meets engineering sciences (2005)
Kremling, A., Stelling, J., Bettenbrock, K., Fischer, S., Gilles, E. D.
A hallmark of systems biology is the interdisciplinary approach to the complexity of biological systems, in which mathematical modeling constitutes an important part. Here, we use the example of...
Saez-Rodriguez, J., Conzelmann, H., Sauter, T., Kholodenko, B. N., Gilles, E. D.
A rigorous, detailed description of signaling networks gives rise to huge models, while an a priori simplified model relies on assumptions difficult to prove. Therefore, models which are manageable,...
Automatic Track-Keeping of Inland Vessels in Flowing Waterways (2005)
Integrated navigation systems for inland vessels, combining different technologies like radar, satellite navigation (GPS) and electronic charts (ECDIS), have been developed in the Max Planck...
Nutsch, T., Oesterhelt, D., Gilles, E. D., Marwan, W.
By reverse-engineering we have detected eight kinetic phases of the symmetric switch cycle of the Halobacterium salinarum flagellar motor assembly and identified those steps in the switch cycle that...
Conzelmann, H., Saez-Rodriguez, J., Sauter, T., Bullinger, E.*, Allgower, F., Gilles, E.D.
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...
Conzelmann, H., Saez-Rodriguez, J., Sauter, T., Bullinger, E., Allgower, F., Gilles, E.D.
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...
Nutsch,T., Marwan,W., Oesterhelt,D., Gilles,E. D.
Halobacterium salinarium shows a qualitatively different swimming behavior than E. coli, what demands a different mechanism of flagellar motor switching. In this study we postulate general properties...
Mathematical Modeling of Complex Regulatory Networks (2004)
Cellular regulation comprises overwhelmingly complex interactions between genes and proteins that ultimately will only be rendered understandable by employing formal approaches. Developing...
Robustness properties of circadian clock architectures (2004)
Stelling,J., Gilles,E. D., Doyle III,F. J.
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 not...
Bistability Analyses of a Caspase Activation Model for Receptor-induced Apoptosis (2004)
Eissing,T., Conzelmann,H., Gilles,E. D., Allgöwer,F., Bullinger,E., Scheurich,P.
Apoptosis is an important physiological process crucially involved in development and homeostasis of multicellular organisms. Although the major signaling pathways have been unraveled, a detailed...
Kremling,A., Heermann,R., Centler,F., Jung,K., Gilles,E. D.
A mathematical model for the KdpD/KdpE two-component system is presented and its dynamical behavior is analyzed. KdpD and KdpE regulate expression of the kdpFABC operon encoding the high affinity K+...
Kremling,A., Fischer,S., Gadkar,K., Doyle,F. J., Sauter,T., Bullinger,E., ...
A benchmark problem is described for the reconstruction and analysis of biochemical networks given sampled experimental data. The growth of the organisms is described in a bio-reactor where one...
Schmid,J. W., Mauch,K., Reuss,M., Gilles,E. D., Kremling,A.
The presumably high potential of a holistic design approach for complex biochemical reaction networks is exemplified here for the network of tryptophan biosynthesis from glucose, a system whose...
Workbench zur Modellbildung, Simulation und Analyse zellulärer Systeme (2004)
Kremling,A., Ginkel,M., Klamt,S., Gilles,E. D.
Die aktuelle Forschung in der molekularen Genetik und die Erfolge bei der Analyse von Genexpression und Proteinfunktion führen zu einer bisher unerreichten Fülle von Informationen über biologische...
Conzelmann,H., Saez-Rodriguez,J., Sauter,T., Bullinger,E., Allgöwer,F., Gilles,E. D.
Biological systems and, in particular, cellular signal transduction pathways are characterized by their high complexity. Mathematical models describing these processes might be of great help to gain...
Nonlinear model predictive control of multicomponent distillation columns using wave models (2004)
Grüner,S., Schwarzkopf,S., Disli-Uslu,I., Kienle,A., Gilles,E. D.
Modular Analysis of Signal Transduction Networks (2004)
Saez-Rodriguez,J., Kremling,A., Conzelmann,H., Bettenbrock,K., Gilles,E. D.
This paper introduces compelling problems of biological systems and signaling networks to show how engineering tools can be applied to the analysis of the cellular machinery. The mechanisms that...
Minimal cut sets in biochemical reaction networks (2004)
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...
Time hierarchies in the Escherichia coli carbohydrate uptake and metabolism (2004)
Kremling,A., Fischer,S., Sauter,T., Bettenbrock,K., Gilles,E. D.
The analysis of metabolic pathways with mathematical models contributes to the better understanding of the behavior of metabolic processes. This paper presents the analysis of a mathematical model...
A model library for membrane reactors implemented in the process modelling tool ProMoT (2004)
Mangold,M., Ginkel,M., Gilles,E. D.
A model library for spatially distributed membrane reactor models is presented. The structure of the library is guided by a general modelling concept for the systematic formulation of chemical...
Integral approximation : an approach to reduced models for particulate processes (2004)
Motz,S., Mannal,S., Gilles,E. D.
In this contribution, a model reduction technique for population balance systems describing particulate processes is presented. This technique is based on integral approximation and allows the...
Nutsch, T., Marwan, W., Oesterhelt, D., Gilles, E. D.
Halobacterium salinarium shows a qualitatively different swimming behavior than E. coli, what demands a different mechanism of flagellar motor switching. In this study we postulate general properties...
Mathematical Modeling of Complex Regulatory Networks (2004)
Cellular regulation comprises overwhelmingly complex interactions between genes and proteins that ultimately will only be rendered understandable by employing formal approaches. Developing...
Robustness properties of circadian clock architectures (2004)
Stelling, J., Gilles, E. D., Doyle III, F. J.
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 not...
Bistability Analyses of a Caspase Activation Model for Receptor-induced Apoptosis (2004)
Eissing, T., Conzelmann, H., Gilles, E. D., Allgöwer, F., Bullinger, E., Scheurich, P.
Apoptosis is an important physiological process crucially involved in development and homeostasis of multicellular organisms. Although the major signaling pathways have been unraveled, a detailed...
Kremling, A., Heermann, R., Centler, F., Jung, K., Gilles, E. D.
A mathematical model for the KdpD/KdpE two-component system is presented and its dynamical behavior is analyzed. KdpD and KdpE regulate expression of the kdpFABC operon encoding the high affinity K+...
Kremling, A., Fischer, S., Gadkar, K., Doyle, F. J., Sauter, T., Bullinger, E., ...
A benchmark problem is described for the reconstruction and analysis of biochemical networks given sampled experimental data. The growth of the organisms is described in a bio-reactor where one...
Schmid, J. W., Mauch, K., Reuss, M., Gilles, E. D., Kremling, A.
The presumably high potential of a holistic design approach for complex biochemical reaction networks is exemplified here for the network of tryptophan biosynthesis from glucose, a system whose...