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Poster communications

Metabolic Model Generalization

Anna Zhukova 1, 2
1 MAGNOME - Models and Algorithms for the Genome
Inria Bordeaux - Sud-Ouest, UB - Université de Bordeaux, CNRS - Centre National de la Recherche Scientifique : UMR5800
Abstract : Genome-scale metabolic models for new organisms include thousands of reactions that are generated automatically: by inferring them from databases of reactions and pathways, existing models for similar organisms, etc. This process includes several iterations of the draft model analysis, error detection, and improvement; starting from more general issues and going deeper into details. Especially in the first iterations model evaluation by a human expert is important. But genome-scale models are targeted for computer simulation and analysis, and are too detailed and complicated to be easily understood by a human. For example, in the beta-oxidation of fatty acids pathway, a reaction missing for a particular fatty-acyl-CoA type (e.g. decanoyl-CoA) is a more specific issue than missing a whole enoyl-CoA hydratase step (which could happen if the corresponding enzyme is not found). But the abundance of reactions in the model (e.g. those corresponding to other beta-oxidation steps and presented for each of the different types of fatty-acyls-CoA) may hide this fact from the human. That is why we developed a method for knowledge-based scaling of metabolic models, providing a higher-level view of a model, keeping its essential structure and omitting the details.
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https://hal.inria.fr/hal-00859442
Contributor : David James Sherman <>
Submitted on : Sunday, September 8, 2013 - 10:04:34 AM
Last modification on : Thursday, February 11, 2021 - 2:54:03 PM
Long-term archiving on: : Monday, December 9, 2013 - 4:22:52 AM

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Anna Zhukova. Metabolic Model Generalization. International Course in Yeast Systems Biology, Jun 2013, Gothenburg, Sweden. ⟨hal-00859442⟩

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