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

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Metabolic Network Reconstruction and Modeling

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

Abstract

Genome-scale metabolic reconstructions are powerful resources that allow translation biological knowledge and genomic information to phenotypical predictions using a number of constraint-based methods. This approach has been applied in recent years to gain deep insights into the cellular phenotype role of the genes at a systems-level, driving the design of targeted experiments and paving the way for knowledge-based synthetic biology.

The identification of genetic determinants underlying the variability at the phenotypical level is crucial to understand the evolutionary trajectories of a bacterial species. Recently, genome-scale metabolic models of different strains have been assembled to highlight the intra-species diversity at the metabolic level. The strain-specific metabolic capabilities and auxotrophies can be used to identify factors related to the lifestyle diversity of a bacterial species.

In this chapter, we present the computational steps to perform genome-scale metabolic modeling in the context of comparative genomics, and the different challenges related to this task.

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Author information

Authors and Affiliations

  1. Department of Bioengineering, University of California, La Jolla, CA, USA

    Jonathan Monk

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

    Emanuele Bosi

Authors
  1. Jonathan Monk
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  2. Emanuele Bosi
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Correspondence to Emanuele Bosi .

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Editors and Affiliations

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

    Marco Fondi

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Monk, J., Bosi, E. (2018). Integration of Comparative Genomics with Genome-Scale Metabolic Modeling to Investigate Strain-Specific Phenotypical Differences. In: Fondi, M. (eds) Metabolic Network Reconstruction and Modeling. Methods in Molecular Biology, vol 1716. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-7528-0_7

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  • DOI: https://doi.org/10.1007/978-1-4939-7528-0_7

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  • Publisher Name: Humana Press, New York, NY

  • Print ISBN: 978-1-4939-7527-3

  • Online ISBN: 978-1-4939-7528-0

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