Complétion combinatoire pour la reconstruction de réseaux métaboliques, et application au modèle des algues brunes Ectocarpus siliculosus

Sylvain Prigent 1
1 Dyliss - Dynamics, Logics and Inference for biological Systems and Sequences
Inria Rennes – Bretagne Atlantique , IRISA-D7 - GESTION DES DONNÉES ET DE LA CONNAISSANCE
Abstract : In this thesis we focused on the development of a comprehensive approach to reconstruct metabolic networks applied to unconventional biological species for which we have little information. Traditionally, this reconstruction is based on three points : the creation of a metabolic draft from a genome, the completion of this draft and the verification of the results. We have been particularly interested in the hard combinatorial optimization problem represented by the gap-filling step. We used Answer Set Programming (or ASP) to solve this combinatorial problem. Changes to an existing method allowed us to improve both the computational time and the quality of modeling. This entire process of metabolic network reconstruction was applied to the model of brown algae, Ectocarpus siliculosus, allowing us to reconstruct the first metabolic network of a brown macro-algae. The reconstruction of this network allowed us to improve our understanding of the metabolism of this species and to improve annotation of its genome.
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Theses
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https://hal.inria.fr/tel-01093287
Contributor : Sylvain Prigent <>
Submitted on : Wednesday, December 10, 2014 - 2:33:31 PM
Last modification on : Friday, November 16, 2018 - 1:38:36 AM
Long-term archiving on: Saturday, April 15, 2017 - 7:13:04 AM

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  • HAL Id : tel-01093287, version 1

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Sylvain Prigent. Complétion combinatoire pour la reconstruction de réseaux métaboliques, et application au modèle des algues brunes Ectocarpus siliculosus. Bio-informatique [q-bio.QM]. Université Rennes 1, 2014. Français. ⟨NNT : 2014REN1S077⟩. ⟨tel-01093287⟩

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