Dataset Information

Pitkanen2014 - Metabolic reconstruction of Debaryomyces hansenii using CoReCo

ABSTRACT: Pitkanen2014 - Metabolic reconstruction of Debaryomyces hansenii using CoReCo This model was reconstructed with the CoReCo method (Comparative ReConstruction of genome-scale metabolic networks) from protein sequence and phylogeny data. This model is described in the article: Comparative Genome-Scale Reconstruction of Gapless Metabolic Networks for Present and Ancestral Species Esa Pitkänen, Paula Jouhten, Jian Hou, Muhammad Fahad Syed, Peter Blomberg, Jana Kludas, Merja Oja, Liisa Holm, Merja Penttilä, Juho Rousu, Mikko Arvas PLoS Comput Biol. 2014 Feb 6;10(2):e1003465 Abstract: We introduce a novel computational approach, CoReCo, for comparative metabolic reconstruction and provide genome-scale metabolic network models for 49 important fungal species. Leveraging on the exponential growth in sequenced genome availability, our method reconstructs genome-scale gapless metabolic networks simultaneously for a large number of species by integrating sequence data in a probabilistic framework. High reconstruction accuracy is demonstrated by comparisons to the well-curated Saccharomyces cerevisiae consensus model and large-scale knock-out experiments. Our comparative approach is particularly useful in scenarios where the quality of available sequence data is lacking, and when reconstructing evolutionary distant species. Moreover, the reconstructed networks are fully carbon mapped, allowing their use in 13C flux analysis. We demonstrate the functionality and usability of the reconstructed fungal models with computational steady-state biomass production experiment, as these fungi include some of the most important production organisms in industrial biotechnology. In contrast to many existing reconstruction techniques, only minimal manual effort is required before the reconstructed models are usable in flux balance experiments. CoReCo is available at http://esaskar.github.io/CoReCo/. This model is hosted on BioModels Database and identified by: MODEL1302010023 . To cite BioModels Database, please use: BioModels Database: An enhanced, curated and annotated resource for published quantitative kinetic models . To the extent possible under law, all copyright and related or neighbouring rights to this encoded model have been dedicated to the public domain worldwide. Please refer to CC0 Public Domain Dedication for more information.

SUBMITTER: Esa Pitkänen

PROVIDER: MODEL1302010023 | BioModels | 2014-03-02

REPOSITORIES: BioModels

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	MODEL1302010023?filename=MODEL1302010023-biopax2.owl	Owl
	MODEL1302010023?filename=MODEL1302010023-biopax3.owl	Owl
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Publications

Comparative genome-scale reconstruction of gapless metabolic networks for present and ancestral species.

Pitkänen Esa E Jouhten Paula P Hou Jian J Syed Muhammad Fahad MF Blomberg Peter P Kludas Jana J Oja Merja M Holm Liisa L Penttilä Merja M Rousu Juho J Arvas Mikko M

PLoS computational biology 20140206 2

We introduce a novel computational approach, CoReCo, for comparative metabolic reconstruction and provide genome-scale metabolic network models for 49 important fungal species. Leveraging on the exponential growth in sequenced genome availability, our method reconstructs genome-scale gapless metabolic networks simultaneously for a large number of species by integrating sequence data in a probabilistic framework. High reconstruction accuracy is demonstrated by comparisons to the well-curated Sacc ...[more]

PMID: 24516375

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