References of "Bullinger, Eric"
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See detailA systems biology perspective of apoptosis signalling
Bullinger, Eric ULg

Conference (2007)

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See detailAn Observability Based Strategy for Parameter Identification in Systems Biology
Farina, M.; Bullinger, Eric ULg; Findeisen, R. et al

in Proc. of the 2nd Foundations of Systems Biology in Engineering FOSBE 2007, 9–12 September, Stuttgart Germany (2007)

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See detailNonlinear Sensitivity Analysis of Biochemical Reaction Networks, by Bilinear Approximation
Streif, Stefan; Findeisen, Rolf; Bullinger, Eric ULg

in Proc. of the 2nd Foundations of Systems Biology in Engineering FOSBE 2007, 9–12 September, Stuttgart Germany (2007)

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See detailSteady state and (bi-) stability evaluation of simple protease signalling networks
Eissing, Thomas; Waldherr, Steffen; Allgöwer, Frank et al

in Biosystems (2007), 90(3), 591-601

Signal transduction networks are complex, as are their mathematical models. Gaining a deeper understanding requires a system analysis. Important aspects are the number, location and stability of steady ... [more ▼]

Signal transduction networks are complex, as are their mathematical models. Gaining a deeper understanding requires a system analysis. Important aspects are the number, location and stability of steady states. In particular, bistability has been recognised as an important feature to achieve molecular switching. This paper compares different model structures and analysis methods particularly useful for bistability analysis. The biological applications include proteolytic cascades as, for example, encountered in the apoptotic signalling pathway or in the blood clotting system. We compare three model structures containing zero-order, inhibitor and cooperative ultrasensitive reactions, all known to achieve bistability. The combination of phase plane and bifurcation analysis provides an illustrative and comprehensive understanding of how bistability can be achieved and indicates how robust this behaviour is. Experimentally, some so-called "inactive" components were shown to have a residual activity. This has been mostly ignored in mathematical models. Our analysis reveals that bistability is only mildly affected in the case of zero-order or inhibitor ultrasensitivity. However, the case where bistability is achieved by cooperative ultrasensitivity is severely affected by this perturbation. (c) 2007 Elsevier Ireland Ltd. All rights reserved. [less ▲]

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See detailApproximations and their consequences for dynamic modelling of signal transduction pathways
Millat, Thomas; Bullinger, Eric ULg; Rohwer, Johann et al

in Mathematical Biosciences (2007), 207(1), 40-57

Signal transduction is the process by which the cell converts one kind of signal or stimulus into another. This involves a sequence of biochemical reactions, carried out by proteins. The dynamic response ... [more ▼]

Signal transduction is the process by which the cell converts one kind of signal or stimulus into another. This involves a sequence of biochemical reactions, carried out by proteins. The dynamic response of complex cell signalling networks can be modelled and simulated in the framework of chemical kinetics. The mathematical formulation of chemical kinetics results in a system of coupled differential equations. Simplifications can arise through assumptions and approximations. The paper provides a critical discussion of frequently employed approximations in dynamic modelling of signal transduction pathways. We discuss the requirements for conservation laws, steady state approximations, and the neglect of components. We show how these approximations simplify the mathematical treatment of biochemical networks but we also demonstrate differences between the complete system (c) 2006 Elsevier Inc. All rights reserved. [less ▲]

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See detailResponse to bistability in apoptosis: Roles of Bax, Bcl-2, and mitochondrial permeability transition pores
Eissing, Thomas; Waldherr, Steffen; Allgöwer, Frank et al

in Biophysical Journal (2007), 92(9), 3332-3334

Recently, a mathematical model of the mitochondrial apoptotic pathway was proposed. In that study, the robustness of different simplified signaling models with respect to parameter changes was also ... [more ▼]

Recently, a mathematical model of the mitochondrial apoptotic pathway was proposed. In that study, the robustness of different simplified signaling models with respect to parameter changes was also investigated. It was found that bistability achieved via cooperative ultrasensitivity is ‘‘much more robust’’ than other mechanisms such as inhibitor ultrasensitivity. We reinvestigate this interesting finding to reveal that it does not hold in such generality. Our results indicate that mechanisms other than cooperative ultrasensitivity, such as inhibitor ultrasensitivity, can confer a similar robust bistable performance. Thereby, these findings are not restricted to apoptosis signaling, but relevant to bistable signaling in general. In addition, example calculations indicate the potential practical relevance of inhibitor ultrasensitivity for generating robustness in apoptosis signaling. [less ▲]

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See detailResults towards identifiability properties of biochemical reaction networks
Farina, Marcello; Findeisen, Rolf; Bullinger, Eric ULg et al

in Proc. of the 45th IEEE Conference on Decision and Control, San Diego, USA (2006, December)

In this paper we consider the question of parameter identifiability for biochemical reaction networks, as typically encountered in systems biology. Specifically, we are interested in deriving conditions ... [more ▼]

In this paper we consider the question of parameter identifiability for biochemical reaction networks, as typically encountered in systems biology. Specifically, we are interested in deriving conditions on the biochemical reaction network and on the measured outputs that guarantee identifiability of the parameters. Taking the specific system structure of biochemical reaction networks into account, we derive sufficient conditions for local parameter identifiability based on a suitable system expansion which does not any more directly depend on the parameters. Rather, as shown, the problem of identifiability can be recast as the question of observability of the (parameter free) expanded system. The conditions derived are exemplified considering a simple example [less ▲]

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See detailControl Theoretical Challenges in Systems Biology
Bullinger, Eric ULg

Conference (2006, August 29)

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See detailControllability, Observability and Sensitivity Analysis in Biological Systems
Bullinger, Eric ULg

Conference (2006, June 16)

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See detailControl Theoretical Challenges in Systems Biology
Bullinger, Eric ULg

Scientific conference (2006, June 15)

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See detailControl Theoretical Challenges in Systems Biology
Bullinger, Eric ULg

Scientific conference (2006, May 26)

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See detailControl Theoretical Challenges in Systems Biology
Bullinger, Eric ULg

Scientific conference (2006, May 24)

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See detailRelating Cross Gramians and Sensitivity Analysis in Systems Biology
Streif, S.; Findeisen, R.; Bullinger, Eric ULg

in Proceedings of the 17th International Symposium on Mathematical Theory of Networks and Systems (MTNS 2006) (2006)

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See detailSensitivity analysis of programmed cell death and implications for crosstalk phenomena during tumor necrosis factor stimulation
Eissing, Thomas; Waldherr, Steffen; Gondro, Cedric et al

in Proc. of the 2006 IEEE Conference on Control Applications (2006)

Different methods for analyzing the sensitivity of the direct signal transduction pathway of receptor-induced apoptosis to parameter changes are presented. Apoptosis is a form of programmed cell death ... [more ▼]

Different methods for analyzing the sensitivity of the direct signal transduction pathway of receptor-induced apoptosis to parameter changes are presented. Apoptosis is a form of programmed cell death, removing unwanted cells within multicellular organisms to maintain a proper balance between cell reproduction and death. The results indicate the importance of controlling activated caspases by direct inhibition to prevent apoptosis. A misregulation of IAP molecules, one of the main inhibitors, appears to be especially critical. The results indicate how an increased production of this molecule promotes survival and might promote cancer progression, while a reduced degradation might not, thereby providing insight of potential pharmaceutical relevance and also stimulating experimental verification. The different engineering methods applied, nicely complement each other to provide valuable insight into this important process. Because IAPs, among others, are also an important connection to other signaling pathways, the results will enable a more efficient extension of the current model. This is outlined at the example of tumor necrosis factor induced signaling pathways [less ▲]

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See detailFunctional morphology of Tethya species (Porifera): 2. Three-dimensional morphometrics on spicules and skeleton superstructures of T-minuta
Nickel, M.; Bullinger, Eric ULg; Beckmann, F.

in Zoomorphology (2006), 125(4), 225-239

The biomechanics of body contraction in Porifera is almost unknown, although sponge contraction has been observed already in ancient times. Some members of the genus Tethya represent the most contractile ... [more ▼]

The biomechanics of body contraction in Porifera is almost unknown, although sponge contraction has been observed already in ancient times. Some members of the genus Tethya represent the most contractile poriferan species. All of them show a highly ordered skeleton layout. Based on three main spicule types, functional units are assembled, termed skeleton superstructures here. Using synchrotron radiation based x-ray microtomography and quantitative image analysis with specially developed particle and structure recognition algorithms allowed us to perform spatial allocation and 3D-morphometric characterizations of single spicules and skeleton superstructures in T. minuta. We found and analyzed three skeleton superstructures in the investigated specimen: (1) 85 megasclere bundles, (2) a megaster sphere, composed by 16,646 oxyasters and (3) a pinacoderm-tylaster layer composed by micrasters. All three skeleton superstructures represent composite materials of siliceous spicules and extracellular matrix. From structure recognition we developed an abstracted mathematical model of the bundles and the sphere. In addition, we analyzed the megaster network interrelation topology and found a baso-apical linear symmetry axis for the megaster density inside the sphere. Based on our results, we propose a hypothetical biomechanical contraction model for T. minuta and T. wilhelma, in which the skeleton superstructures restrain physical stress generated by contraction in the tissue. While skeletal structures within the genus Tethya have been explained using R. Buckminster Fullers principle of tensegrity by other authors, we prefer material science based biomechanical approaches, to understand skeletal superstructures by referring to their composite material properties. [less ▲]

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See detailSystem Analysis of a Programmed Cell Death Model
Bullinger, Eric ULg

in IEEE Conference on Decision and Control (2005, December)

Apoptosis is a programmed cell death by which the organism removes unwanted cells. Its core reactions can be described by a system of differential equations exhibiting multiple steady-states. In this ... [more ▼]

Apoptosis is a programmed cell death by which the organism removes unwanted cells. Its core reactions can be described by a system of differential equations exhibiting multiple steady-states. In this paper we analyse how this model can include both very slow dynamics for the lag phase before apoptosis (in theory up to several days) while the apoptosis itself is more switch-like with changes occurring within minutes. We both describe how the trajectories evolve during the lag phase and show which of the states have the most impact on the slow dynamics. [less ▲]

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See detailDynamic Modelling, Simulation Analysis---Useful for Understanding Biology?
Bullinger, Eric ULg

Scientific conference (2005, November 11)

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See detailModelling of Cellular Dynamics
Bullinger, Eric ULg

Conference (2005, September 01)

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