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The Resource A Network-Based Approach to Cell Metabolism : From Structure to Flux Balances

A Network-Based Approach to Cell Metabolism : From Structure to Flux Balances

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A Network-Based Approach to Cell Metabolism : From Structure to Flux Balances
Title
A Network-Based Approach to Cell Metabolism
Title remainder
From Structure to Flux Balances
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eng
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MiAaPQ
Literary form
non fiction
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dictionaries
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Springer Theses Ser
A Network-Based Approach to Cell Metabolism : From Structure to Flux Balances
Label
A Network-Based Approach to Cell Metabolism : From Structure to Flux Balances
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http://libproxy.rpi.edu/login?url=https://ebookcentral.proquest.com/lib/rpi/detail.action?docID=4978965
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Carrier category
online resource
Carrier category code
cr
Carrier MARC source
rdacarrier
Color
multicolored
Content category
text
Content type code
txt
Content type MARC source
rdacontent
Contents
  • 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 -- Pathways -- Units -- 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 Components -- 2.1.6 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 Failures -- 3.2.2 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 Reactions -- 4.2 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 -- 5.3 The Metabolic Backbones of E. Coli Encode Its Short-Term Adaptation Capabilities -- 5.4 Conclusions -- 5.5 Summary -- References -- 6 Assessing FBA Optimal States in the Feasible Flux Phenotypic Space -- 6.1 Optimal Growth Is Eccentric with Respect to the Full FFP Space -- 6.2 The FFP Space Gives a Standard to Calibrate the Deviation of Optimal Phenotypes from Experimental Observations -- 6.3 The High-Biomass Production Region of the FFP Space Displays Aerobic Fermentation in Minimal Medium with Unlimited Oxygen Uptake -- 6.4 Conclusions -- 6.5 Summary -- References -- 7 Conclusions -- References -- Appendix A Kolmogorov--Smirnov Test -- Appendix B Spearman's Rank Correlation Coefficient
  • Appendix C Point-Biserial Correlation Coefficient -- Appendix D Disparity Filter -- Appendix E Hit-And-Run Algorithm -- Appendix F Principal Component Analysis
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1 online resource (162 pages)
Form of item
online
Isbn
9783319640006
Media category
computer
Media MARC source
rdamedia
Media type code
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