Metabolic Network Reconstruction and Modeling

Methods and Protocols

  • Marco Fondi

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

Table of contents

  1. Front Matter
    Pages i-xi
  2. Oscar Dias, Miguel Rocha, Eugénio Campos Ferreira, Isabel Rocha
    Pages 1-36
  3. Paulo Vilaça, Paulo Maia, Hugo Giesteira, Isabel Rocha, Miguel Rocha
    Pages 37-76
  4. Christopher Le, Leonid Chindelevitch
    Pages 77-99
  5. Janaka N. Edirisinghe, José P. Faria, Nomi L. Harris, Benjamin H. Allen, Christopher S. Henry
    Pages 111-129
  6. Keith Dufault-Thompson, Jon Lund Steffensen, Ying Zhang
    Pages 131-150
  7. Tiziano Vignolini, Alessio Mengoni, Marco Fondi
    Pages 177-196
  8. Anu Raghunathan, Neema Jamshidi
    Pages 197-217
  9. Chao Ye, Nan Xu, Xiulai Chen, Liming Liu
    Pages 219-238
  10. Karthik Raman, Aditya Pratapa, Omkar Mohite, Shankar Balachandran
    Pages 315-336
  11. Jose Alberto Gomez, Paul I. Barton
    Pages 353-370
  12. Christian Jungreuthmayer, Matthias P. Gerstl, David A. Peña Navarro, Michael Hanscho, David E. Ruckerbauer, Jürgen Zanghellini
    Pages 371-387
  13. Supreeta Vijayakumar, Max Conway, Pietro Lió, Claudio Angione
    Pages 389-408
  14. Back Matter
    Pages 409-410

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, 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.


metabolic landscape Phenotype Microarray Transcriptomics Proteomics Metabolomics

Editors and affiliations

  • Marco Fondi
    • 1
  1. 1.Department of BiologyUniversity of FlorenceSesto Fiorentino, FlorenceItaly

Bibliographic information

  • DOI
  • Copyright Information Springer Science+Business Media, LLC 2018
  • Publisher Name Humana Press, New York, NY
  • eBook Packages Springer Protocols
  • Print ISBN 978-1-4939-7527-3
  • Online ISBN 978-1-4939-7528-0
  • Series Print ISSN 1064-3745
  • Series Online ISSN 1940-6029
  • Buy this book on publisher's site
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