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This thesis uses a systems-level approach to study cellular metabolism, unveiling new mechanisms and responses that were impossible to demonstrate with traditional reductionists procedures. The results reported have potential applications in areas like metabolic engineering and disease treatment. They could also be used in determining the accuracy of the gene essentiality of new genome-scale reconstructions. The book applies different methods and techniques within the contexts of systems biology and the field of complex networks analysis to show different features of the robustness of metabolic networks. The specific issues addressed range from pure topological aspects of the networks themselves to the balance of biochemical fluxes.