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Metabolic Network Reconstruction and Modeling

Methods and Protocols

  • Book
  • © 2018

Overview

Editors:
  1. Marco Fondi

    1. Department of Biology, University of Florence, Sesto Fiorentino, Florence, Italy

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  • Includes cutting-edge methods and protocols
  • Provides step-by-step detail essential for reproducible results
  • Contains key notes and implementation advice from the experts
  • Includes supplementary material: sn.pub/extras

Part of the book series: Methods in Molecular Biology (MIMB, volume 1716)

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Table of contents (18 protocols)

  1. Front Matter

    Pages i-xi
    Download chapter PDF

  2. Reconstructing High-Quality Large-Scale Metabolic Models with merlin

    • Oscar Dias, Miguel Rocha, Eugénio Campos Ferreira, Isabel Rocha
    Pages 1-36

  3. Analyzing and Designing Cell Factories with OptFlux

    • Paulo Vilaça, Paulo Maia, Hugo Giesteira, Isabel Rocha, Miguel Rocha
    Pages 37-76

  4. The MONGOOSE Rational Arithmetic Toolbox

    • Christopher Le, Leonid Chindelevitch
    Pages 77-99

  5. The FASTCORE Family: For the Fast Reconstruction of Compact Context-Specific Metabolic Networks Models

    • Maria Pires Pacheco, Thomas Sauter
    Pages 101-110

  6. Reconstruction and Analysis of Central Metabolism in Microbes

    • Janaka N. Edirisinghe, José P. Faria, Nomi L. Harris, Benjamin H. Allen, Christopher S. Henry
    Pages 111-129

  7. Using PSAMM for the Curation and Analysis of Genome-Scale Metabolic Models

    • Keith Dufault-Thompson, Jon Lund Steffensen, Ying Zhang
    Pages 131-150

  8. Integration of Comparative Genomics with Genome-Scale Metabolic Modeling to Investigate Strain-Specific Phenotypical Differences

    • Jonathan Monk, Emanuele Bosi
    Pages 151-175

  9. Template-Assisted Metabolic Reconstruction and Assembly of Hybrid Bacterial Models

    • Tiziano Vignolini, Alessio Mengoni, Marco Fondi
    Pages 177-196

  10. Integrated Host-Pathogen Metabolic Reconstructions

    • Anu Raghunathan, Neema Jamshidi
    Pages 197-217

  11. Metabolic Model Reconstruction and Analysis of an Artificial Microbial Ecosystem

    • Chao Ye, Nan Xu, Xiulai Chen, Liming Liu
    Pages 219-238

  12. RNA Sequencing and Analysis in Microorganisms for Metabolic Network Reconstruction

    • Eva Pinatel, Clelia Peano
    Pages 239-265

  13. Differential Proteomics Based on 2D-Difference In-Gel Electrophoresis and Tandem Mass Spectrometry for the Elucidation of Biological Processes in Antibiotic-Producer Bacterial Strains

    • Giuseppe Gallo, Andrea Scaloni
    Pages 267-289

  14. Techniques for Large-Scale Bacterial Genome Manipulation and Characterization of the Mutants with Respect to In Silico Metabolic Reconstructions

    • George C. diCenzo, Turlough M. Finan
    Pages 291-314

  15. Computational Prediction of Synthetic Lethals in Genome-Scale Metabolic Models Using Fast-SL

    • Karthik Raman, Aditya Pratapa, Omkar Mohite, Shankar Balachandran
    Pages 315-336

  16. Coupling Fluxes, Enzymes, and Regulation in Genome-Scale Metabolic Models

    • Paul A. Jensen
    Pages 337-351

  17. Dynamic Flux Balance Analysis Using DFBAlab

    • Jose Alberto Gomez, Paul I. Barton
    Pages 353-370

  18. Designing Optimized Production Hosts by Metabolic Modeling

    • Christian Jungreuthmayer, Matthias P. Gerstl, David A. Peña Navarro, Michael Hanscho, David E. Ruckerbauer, Jürgen Zanghellini
    Pages 371-387

  19. Optimization of Multi-Omic Genome-Scale Models: Methodologies, Hands-on Tutorial, and Perspectives

    • Supreeta Vijayakumar, Max Conway, Pietro Lió, Claudio Angione
    Pages 389-408

  20. Back Matter

    Pages 409-410
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Keywords

About this book

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, MetabolicNetwork 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.


Editors and Affiliations

  • Department of Biology, University of Florence, Sesto Fiorentino, Florence, Italy

    Marco Fondi

About the editor

Marco Fondi
Department of Biology
University of Florence
Via Madonna del Piano 6, I-50019 Sesto Fiorentino, Italy
Email: marco.fondi@unifi.it

Bibliographic Information

  • Book Title: Metabolic Network Reconstruction and Modeling

  • Book Subtitle: Methods and Protocols

  • Editors: Marco Fondi

  • Series Title: Methods in Molecular Biology

  • DOI: https://doi.org/10.1007/978-1-4939-7528-0

  • Publisher: Humana New York, NY

  • eBook Packages: Springer Protocols

  • Copyright Information: Springer Science+Business Media, LLC 2018

  • Hardcover ISBN: 978-1-4939-7527-3Published: 09 December 2017

  • Softcover ISBN: 978-1-4939-8511-1Published: 30 August 2018

  • eBook ISBN: 978-1-4939-7528-0Published: 08 December 2017

  • Series ISSN: 1064-3745

  • Series E-ISSN: 1940-6029

  • Edition Number: 1

  • Number of Pages: XI, 410

  • Number of Illustrations: 11 b/w illustrations, 92 illustrations in colour

  • Topics: Cell Biology

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