Genome-Scale Modeling

  • Pablo Carbonell
Part of the Learning Materials in Biosciences book series (LMB)


Before designing a new metabolic pathway, we need to learn how to model the cell behavior, how to relate its genome to its phenotype and how to simulate multiple growth conditions. In this chapter, we will have a look at some of the genome-scale models that the systems biology community has developed in the past few decades and will assess how these models can assist us in order to understand the cell, model the metabolic network and pathways and even predict the evolution of cell cultures. We will learn how to simulate the equilibrium state of the metabolite fluxes in the cell and how to evaluate cell capabilities depending on their context.


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Further Reading

  1. The following provides a comprehensive review on reconstruction of metabolic networks as well as links to an up-to-date list of metabolic models with their properties (see its Supplementary Table S1):Google Scholar
  2. Feist, A.M., Herrgård, M.J., Thiele, I., Reed, J.L., Palsson, B. Ø.: Reconstruction of biochemical networks in microorganisms. Nat. Rev. Microbiol. 7(2), 129 (2009)CrossRefGoogle Scholar
  3. An excellent and comprehensive introduction to the field of constraint-based analysis:Google Scholar
  4. Palsson, B.Ø.: Systems Biology. Cambridge University Press, Cambridge (2015)CrossRefGoogle Scholar
  5. Other more specialized sources on metabolic network analysis are the following:Google Scholar
  6. Maranas, C.D., Zomorrodi, A.R.: Optimization Methods in Metabolic Networks. Wiley-Blackwell, New Jersey (2016)CrossRefGoogle Scholar
  7. Smolke, C.D. (ed.): The Metabolic Pathway Engineering Handbook. Tools and Applications. CRC Press/Taylor & Francis, Boca Raton (2010)Google Scholar

Copyright information

© Springer Nature Switzerland AG 2019

Authors and Affiliations

  • Pablo Carbonell
    • 1
  1. 1.Manchester Institute of BiotechnologyUniversity of ManchesterManchesterUK

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