The yeast Saccharomyces cerevisiae is one of the oldest and most frequently used
microorganisms in biotechnology with successful applications in the production of both bulk …

Describing the determinants of robustness of biological systems has become one of the
central questions in systems biology. Despite the increasing research efforts, it has proven …

The metabolism of organisms can be studied with comprehensive stoichiometric models of
their metabolic networks. Flux balance analysis (FBA) calculates optimal metabolic …

Background Flux coupling analysis (FCA) has become a useful tool in the constraint-based
analysis of genome-scale metabolic networks. FCA allows detecting dependencies between …

The survival and proliferation of cells and organisms require a highly coordinated allocation
of cellular resources to ensure the efficient synthesis of cellular components. In particular …

Metabolic modelling has entered a mature phase with dozens of methods and software
implementations available to the practitioner and the theoretician. It is not easy for a …

Bioinformatics tools have facilitated the reconstruction and analysis of cellular metabolism of
various organisms based on information encoded in their genomes. Characterization of …

Motivation: The reconstruction of metabolic networks at the genome scale has allowed the
analysis of metabolic pathways at an unprecedented level of complexity. Elementary flux …

Background Modeling molecules as undirected graphs and chemical reactions as graph
rewriting operations is a natural and convenient approach to modeling chemistry. Graph …

The topology of metabolic networks is recognisably modular with modules weakly
connected apart from sharing a pool of currency metabolites. Here, we defined modules as …