Afficher la notice abrégée

hal.structure.identifierLaboratoire Bordelais de Recherche en Informatique [LaBRI]
hal.structure.identifierModels and Algorithms for the Genome [ MAGNOME]
dc.contributor.authorSHERMAN, David James
hal.structure.identifierLaboratoire Bordelais de Recherche en Informatique [LaBRI]
hal.structure.identifierModels and Algorithms for the Genome [ MAGNOME]
dc.contributor.authorLOIRA, Nicolás
dc.date.accessioned2024-04-15T09:46:06Z
dc.date.available2024-04-15T09:46:06Z
dc.date.issued2010-09-07
dc.date.conference2010-09-07
dc.identifier.urihttps://oskar-bordeaux.fr/handle/20.500.12278/197979
dc.descriptionJOBIM 2010 Poster
dc.description.abstractEnFor many fungal genomes of biotechnological interest, the combination of large-scale sequencing projects and in-depth experimental studies has made it feasible to undertake metabolic network reconstruction. An excellent representative of this new class of organisms is Yarrowia lipolytica, an oleaginous yeast studied experimentally for its role as a food contaminant and its use in bioremediation and cell factory applications. As one of the hemiascomycetous yeasts completely sequenced in the Génolevures program it enjoys a high quality manual annotation by a network of experts. We have developed a method of semi-automatic reconstruction of metabolic models, based on the prediction of conservation of enzymatic activities between two species. Following our reconstruction protocol, we extrapolated a Y.lipolytica genome-scale metabolic model (called iNL705) from an existing S. cerevisiae model (iIN800). This draft model was curated by a group of experts in Y. lipolytica metabolism, and iteratively improved and validated through comparison with experimental data by flux balance analysis. In order to design better automatic methods, we formalized the steps of expert manual curation as an algebra of edit operations on metabolic models. The cycle of iterative refinements is represented as transformations of the automatically produced draft model, with an evaluation of improvement in accuracy after every step. This study underscores the particular challenges of metabolic model reconstruction for eukaryotes. The experience acquired with our methods and formalizations should prove useful for similar reconstruction efforts.
dc.language.isoen
dc.subject.enOleaginous yeasts
dc.subject.enSystems biology
dc.subject.enMetabolic networks
dc.title.enReconstruction and validation of the genome-scale metabolic model of Yarrowia lipolytica iNL750
dc.typeAutre communication scientifique (congrès sans actes - poster - séminaire...)
dc.subject.halInformatique [cs]/Bio-informatique [q-bio.QM]
dc.subject.halSciences du Vivant [q-bio]/Bio-Informatique, Biologie Systémique [q-bio.QM]
bordeaux.hal.laboratoriesLaboratoire Bordelais de Recherche en Informatique (LaBRI) - UMR 5800*
bordeaux.institutionUniversité de Bordeaux
bordeaux.institutionBordeaux INP
bordeaux.institutionCNRS
bordeaux.conference.titleJournées Ouvertes en Biologie, Informatique et Mathématiques (JOBIM'10)
bordeaux.countryFR
bordeaux.conference.cityMontpellier
bordeaux.peerReviewedoui
hal.identifierhal-00652929
hal.version1
hal.invitednon
hal.proceedingsnon
hal.conference.end2010-09-09
hal.popularnon
hal.audienceNationale
hal.origin.linkhttps://hal.archives-ouvertes.fr//hal-00652929v1
bordeaux.COinSctx_ver=Z39.88-2004&rft_val_fmt=info:ofi/fmt:kev:mtx:journal&rft.date=2010-09-07&rft.au=SHERMAN,%20David%20James&LOIRA,%20Nicol%C3%A1s&rft.genre=conference


Fichier(s) constituant ce document

FichiersTailleFormatVue

Il n'y a pas de fichiers associés à ce document.

Ce document figure dans la(les) collection(s) suivante(s)

Afficher la notice abrégée