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CMSB
2009
Springer
9 years 3 months ago
On the Use of Stochastic Petri Nets in the Analysis of Signal Transduction Pathways for Angiogenesis Process
In this paper we consider the modeling of a selected portion of signal transduction events involved in the angiogenesis process. The detailed model of this process contains a large...
Lucia Napione, Daniele Manini, Francesca Cordero, ...
CMSB
2009
Springer
9 years 3 months ago
Control Strategies for the Regulation of the Eukaryotic Heat Shock Response
Abstract. Elevated temperatures cause proteins in living cells to misfold. They start forming larger and larger aggregates that can eventually lead to the cell's death. The he...
Elena Czeizler, Eugen Czeizler, Ralph-Johan Back, ...
CMSB
2009
Springer
9 years 3 months ago
On Coupling Models Using Model-Checking: Effects of Irinotecan Injections on the Mammalian Cell Cycle
Abstract. In systems biology, the number of models of cellular processes increases rapidly, but re-using models in different contexts or for different questions remains a challengi...
Elisabetta De Maria, François Fages, Sylvai...
CMSB
2009
Springer
9 years 6 months ago
Equivalence and Discretisation in Bio-PEPA
Bio-PEPA is a process algebra for modelling biological systems. An important aspect of Bio-PEPA is the ability it provides to discretise concentrations resulting in a smaller, more...
Vashti Galpin, Jane Hillston
CMSB
2009
Springer
9 years 6 months ago
The Equivalence between Biology and Computation
A major challenge in computational systems biology is the articulation of a biological process in a form which can be understood by the biologist yet is amenable to computational e...
John K. Heath
CMSB
2009
Springer
9 years 6 months ago
A Prize-Collecting Steiner Tree Approach for Transduction Network Inference
Marc Bailly-Bechet, Alfredo Braunstein, Riccardo Z...
CMSB
2009
Springer
9 years 6 months ago
Approximation of Event Probabilities in Noisy Cellular Processes
Molecular noise, which arises from the randomness of the discrete events in the cell, significantly influences fundamental biological processes. Discrete-state continuous-time st...
Frédéric Didier, Thomas A. Henzinger...
CMSB
2009
Springer
9 years 6 months ago
Computing Reachable States for Nonlinear Biological Models
Abstract. In this paper we describe reachability computation for continuous and hybrid systems and its potential contribution to the process of building and debugging biological mo...
Thao Dang, Colas Le Guernic, Oded Maler
CMSB
2009
Springer
9 years 6 months ago
Probabilistic Approximations of Signaling Pathway Dynamics
Systems of ordinary differential equations (ODEs) are often used to model the dynamics of complex biological pathways. We construct a discrete state model as a probabilistic appro...
Bing Liu, P. S. Thiagarajan, David Hsu
CMSB
2009
Springer
9 years 6 months ago
Dynamic Compartments in the Imperative pi-Calculus
Dynamic compartments with mutable configurations and variable volumes are of basic interest for the stochastic modeling of biochemistry in cells. We propose a new language to expr...
Mathias John, Cédric Lhoussaine, Joachim Ni...
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