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Supervisors' Foreword; List of PublicationsParts of this thesis have been published in:Güell O, Sagués F, Serrano MÁ (2012) Predicting effects of structural stress in a genome-reduced model bacterial metabolism. Sci Rep 2:621Güell O, Sagués F, Basler G, Nikoloski Z, Serrano MÁ (2012) Assessing the significance of knockout cascades in metabolic networks. J Comp Int Sci 3(1-2):45-53Güell O, Sagués F, Serrano MÁ (2012) Essential plasticity and redundancy of metabolism unveiled by synthetic lethality analysis. PLoS Comput; Acknowledgements; Contents; Abbreviations; Organisms; Methods; Concepts
PathwaysUnits; 1 Cellular Metabolism at the Systems Level; 1.1 A Brief Introduction to Cellular Metabolism; 1.1.1 Key Compounds; 1.1.2 Biochemical Reactions; 1.1.3 Biochemical Pathways; 1.1.4 Classical Studies of Metabolism; 1.2 Genome-Scale Models; 1.2.1 Reconstructing Metabolism; 1.2.2 The Systems-Level Approach; 1.3 Aims and Objectives; 1.4 Outline; References; 2 Methods and Data; 2.1 Structural Properties of Metabolic Networks as Complex Networks; 2.1.1 Basic Representation Frameworks; 2.1.2 Degree Distribution; 2.1.3 Average Path Length; 2.1.4 Communities at the Mesoscale
2.1.5 Large-Scale Connected Components2.1.6 Other Structural Properties of Complex Networks; 2.1.7 Null Model Networks and Randomization Methods; 2.2 Flux Balance Analysis; 2.2.1 Formulation of the Biomass Reaction; 2.2.2 Simulation of Different Environments; 2.2.3 Activity and Essentialify of Genes and Reactions; 2.2.4 Flux Variability Analysis; 2.3 Model Organisms; 2.3.1 Escherichia coli; 2.3.2 Mycoplasma Pneumoniae; 2.3.3 Staphylococcus aureus; References; 3 Structural Knockout Cascades in Metabolic Networks; 3.1 Cascading Failure Algorithm; 3.2 Impact of Reaction Failures
3.2.1 Impact of Individual Reactions Failures3.2.2 Non-linear Effects Triggered by Pairs of Reactions Cascades; 3.3 Impact of Gene Knockouts in Metabolic Structure; 3.3.1 Metabolic Effects of Individual Mutations; 3.3.2 Metabolic Effects of Knocking Out Gene Co-expression Clusters; 3.4 Robustness Versus Regulation in Metabolic Networks; 3.5 Conclusions; 3.6 Summary; References; 4 Effects of Reaction Knockouts on Steady States of Metabolism; 4.1 Activity and Essentiality of Single Reactions of E. coli Across Media; 4.1.1 Quantifying Activity and Essentiality
4.1.2 Characterization of the Reactions4.2 SL Pairs and Plasticity and Redundancy of Metabolism; 4.2.1 Classification of SL Pairs; 4.2.2 Classification of SL Reactions Pairs into Plasticity and Redundancy; 4.2.3 Pathways Entanglement; 4.2.4 Sensitivity to Differences on Environmental Conditions; 4.3 Conclusions; 4.4 Summary; References; 5 Detection of Evolution and Adaptation Fingerprints in Metabolic Networks; 5.1 Identification of the Disparity Backbones of Metabolic Networks; 5.2 Evolutionary Signatures in the Backbones of Metabolites
PathwaysUnits; 1 Cellular Metabolism at the Systems Level; 1.1 A Brief Introduction to Cellular Metabolism; 1.1.1 Key Compounds; 1.1.2 Biochemical Reactions; 1.1.3 Biochemical Pathways; 1.1.4 Classical Studies of Metabolism; 1.2 Genome-Scale Models; 1.2.1 Reconstructing Metabolism; 1.2.2 The Systems-Level Approach; 1.3 Aims and Objectives; 1.4 Outline; References; 2 Methods and Data; 2.1 Structural Properties of Metabolic Networks as Complex Networks; 2.1.1 Basic Representation Frameworks; 2.1.2 Degree Distribution; 2.1.3 Average Path Length; 2.1.4 Communities at the Mesoscale
2.1.5 Large-Scale Connected Components2.1.6 Other Structural Properties of Complex Networks; 2.1.7 Null Model Networks and Randomization Methods; 2.2 Flux Balance Analysis; 2.2.1 Formulation of the Biomass Reaction; 2.2.2 Simulation of Different Environments; 2.2.3 Activity and Essentialify of Genes and Reactions; 2.2.4 Flux Variability Analysis; 2.3 Model Organisms; 2.3.1 Escherichia coli; 2.3.2 Mycoplasma Pneumoniae; 2.3.3 Staphylococcus aureus; References; 3 Structural Knockout Cascades in Metabolic Networks; 3.1 Cascading Failure Algorithm; 3.2 Impact of Reaction Failures
3.2.1 Impact of Individual Reactions Failures3.2.2 Non-linear Effects Triggered by Pairs of Reactions Cascades; 3.3 Impact of Gene Knockouts in Metabolic Structure; 3.3.1 Metabolic Effects of Individual Mutations; 3.3.2 Metabolic Effects of Knocking Out Gene Co-expression Clusters; 3.4 Robustness Versus Regulation in Metabolic Networks; 3.5 Conclusions; 3.6 Summary; References; 4 Effects of Reaction Knockouts on Steady States of Metabolism; 4.1 Activity and Essentiality of Single Reactions of E. coli Across Media; 4.1.1 Quantifying Activity and Essentiality
4.1.2 Characterization of the Reactions4.2 SL Pairs and Plasticity and Redundancy of Metabolism; 4.2.1 Classification of SL Pairs; 4.2.2 Classification of SL Reactions Pairs into Plasticity and Redundancy; 4.2.3 Pathways Entanglement; 4.2.4 Sensitivity to Differences on Environmental Conditions; 4.3 Conclusions; 4.4 Summary; References; 5 Detection of Evolution and Adaptation Fingerprints in Metabolic Networks; 5.1 Identification of the Disparity Backbones of Metabolic Networks; 5.2 Evolutionary Signatures in the Backbones of Metabolites