Metabolic network reconstruction and modeling : methods and protocols

Author(s)

    • Fondi, Marco

Bibliographic Information

Metabolic network reconstruction and modeling : methods and protocols

edited by Marco Fondi

(Methods in molecular biology / John M. Walker, series editor, 1716)(Springer protocols)

Humana Press, c2018

Available at  / 2 libraries

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Note

Includes bibliographical references and index

Description and Table of Contents

Description

This volume looks at the latest methodologies used to study cellular metabolism with in silico approaches. The chapters in this book are divided into 3 parts: part I discusses tools and methods used for metabolic reconstructions and basic constraint-based metabolic modeling (CBMM); Part II explores protocols for the generation of experimental data for metabolic reconstruction and modeling, including transcriptomics, proteomics, and mutant generations; and Part III cover advanced techniques for quantitative modeling of cellular metabolism, including dynamic Flux Balance Analysis and multi-objective optimization. Written in the highly successful Methods in Molecular Biology series format, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and tips on troubleshooting and avoiding known pitfalls. Cutting-edge and thorough, Metabolic Network Reconstruction and Modeling: Methods and Protocols is a valuable resource for qualified investigators studying cellular metabolism, and novice researchers who want to start working with CBMM.

Table of Contents

Preface...Table of Contents...Contributing Authors... 1. Reconstructing High-Quality Large-Scale Metabolic Models with merlinOscar Dias, Miguel Rocha, Eugenio Campos Ferreira, and Isabel Rocha 2. Analyzing and Designing Cell Factories with OptFluxPaulo Vilaca, Paulo Maia, Hugo Giesteira, Isabel Rocha, and Miguel Rocha 3. The MONGOOSE Rational Arithmetic ToolboxChristopher Le and Leonid Chindelevitch 4. The FASTCORE Family: For the Fast Reconstruction of Compact Context-Specific Metabolic Networks ModelsMaria Pires Pacheco and Thomas Sauter 5. Reconstruction and Analysis of Central Metabolism in MicrobesJanaka N. Edirisinghe, Jose P. Faria, Nomi L. Harris, Benjamin H. Allen, and Christopher S. Henry 6. Using PSAMM for the Curation and Analysis of Genome-Scale Metabolic ModelsKeith Dufault-Thompson, Jon Lund Steffensen, and Ying Zhang 7. Integration of Comparative Genomics with Genome-Scale Metabolic Modeling to Investigate Strain-Specific Phenotypical DifferencesJonathan Monk and Emanuele Bosi 8. Temple-Assisted Metabolic Reconstruction and Assembly of Hybrid Bacterial ModelsTiziano Vignolini, Alessia Mengoni, and Marco Fondi 9. Integrated Host-Pathogen Metabolic ReconstructionAnu Raghunathan and Neema Jamshidi 10. Metabloic Model Reconstruction and Analysis of an Artificial Microbial EcosystemChao Ye, Nan Xu, Xiulai Chen, and Liming Liu 11. RNA Sequencing and Analysis in Microorganisms for Metabolic Network ReconstructionEva Pinatel and Clelia Peano 12. Differential Proteomics Based on 2D-Difference In-Gel Electrophoresis and Tandem Mass Spectrometry for the Elucidation of Biological Processes in Antibiotic-Producer Bacterial StrainsGiuseppe Gallo and Andrea Scaloni 13. Techniques for Large-Scale Bacterial Genome Manipulation and Characterization of the Mutants with respect to In Silico Metabolic ReconstructionsGeorge C. diCenzo and Turlough M. Finan 14. Computational Prediction of Synthetic Lethals in Genome-Scale Metabolic Models using Fast-SLKarthik Raman, Aditya Pratapa, Omkar Mohite, and Shankar Balachandran 15. Coupling Fluxes, Enzymes, and Regulation in Genome-Scale Metabolic ModelsPaul A. Jensen 16. Dynamic Flux Balance Analysis using DFBAlabJose Alberto Gomez and Paul I. Barton 17. Designing Optimized Production Hosts by Metabolic ModelingChristian Jungreuthmayer, Matthias P. Gerstl, David A. Pena Navarro, Michael Hanscho, David E. Ruckerbauer, and Jurgen Zanghellini 18. Optimization of Multi-Omic Genome-Scale Models: Methodologies, Hands-On Tutorial and PerspectivesSupreeta Vijayakumar, Max Conway, Pietro Lio, and Claudio Angione

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Details

  • NCID
    BB25937589
  • ISBN
    • 9781493975273
  • LCCN
    2017959614
  • Country Code
    us
  • Title Language Code
    eng
  • Text Language Code
    eng
  • Place of Publication
    New York
  • Pages/Volumes
    xi, 410 p.
  • Size
    27 cm
  • Parent Bibliography ID
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