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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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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