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Titlebook: Computational Methods in Systems Biology; 7th International Co Pierpaolo Degano,Roberto Gorrieri Conference proceedings 2009 Springer-Verla

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Prediction of Protein-Protein Interacting Sites: How to Bridge Molecular Events to Large Scale Prote devoted to the study of protein-protein interactions. Large-scale experiments on whole genomes allowed the identification of interacting protein pairs. However residues involved in the interaction are generally not known and the majority of the interactions still lack a structural characterization
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,, – , for Biologists,The main elements of a biological model are specified by filling in a number of tables. Such tables include descriptions of both static and dynamic aspects of the biological system at hand and can then be automatically mapped to . programs for simulation and analysis by means of the . software platf
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Modelling Biological Clocks with Bio-PEPA: Stochasticity and Robustness for the , Circadian Networkproteins to synchronise rhythms of metabolism, physiology and behaviour to the 24 hour day/night cycle. Because of their experimental tractability and biological significance, circadian clocks have been the subject of a number of computational modelling studies..In this study we focus on the simple
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Quantitative Pathway Logic for Computational Biology,iological processes, such as element concentrations and reactions kinetics. Besides, it supports the modeling of inhibitors, that is, chemicals which may block a given reaction whenever their concentration exceeds a certain threshold. QPL models can be specified and directly simulated using rewritin
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A Prize-Collecting Steiner Tree Approach for Transduction Network Inference,lgorithm to infer transduction networks from heterogeneous data, using both the protein interaction network and expression datasets. We formulate the inference problem as an optimization task, and develop a message-passing, probabilistic and distributed formalism to solve it. We apply our algorithm
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