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Titlebook: Computational Methods in Systems Biology; International Confer Corrado Priami Conference proceedings 2006 Springer-Verlag Berlin Heidelberg

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Modeling Evolutionary Dynamics of HIV Infection,ions from R5 to X4 strains which reflect HIV late infection dynamics. Our model investigates the action of Tumor Necrosis Factor in AIDS progression and makes suggestions on better design of HAART therapy.
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Regulatory Network Reconstruction Using Stochastic Logical Networks,numerical simulation of known regulatory networks. We compare the reconstructed networks with the ones reconstructed from the same data using Dynamic Bayesian Networks and show that in these cases our method provides the same or better results. The supplemental materials to this article are available from the website .
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Randomization and Feedback Properties of Directed Graphs Inspired by Gene Networks,al and analytical calculations. Our results are the following. First, the leaf-removal behavior for large system size enables to distinguish between different regimes of feedback. We show their relations and the connection with the onset of complexity in the graph. Second, the influence of the diagonal structure on this behavior can be relevant.
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Operationalization of Constructsnumerical simulation of known regulatory networks. We compare the reconstructed networks with the ones reconstructed from the same data using Dynamic Bayesian Networks and show that in these cases our method provides the same or better results. The supplemental materials to this article are available from the website .
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https://doi.org/10.1007/978-1-4302-1605-6 modular yet faithful manner based on the mathematically well-founded formalism of differential inclusions. We then propose a compositional algorithm to efficiently analyze reachability properties of the model. A case study shows the potential of this approach.
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