Pitkanen2014 - Metabolic reconstruction of Coccidioides immitis using CoReCo

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Pitkanen2014 - Metabolic reconstruction of Coccidioides immitis 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:

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/.

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.

Format
SBML (L2V4)
Related Publication
  • Comparative genome-scale reconstruction of gapless metabolic networks for present and ancestral species.
  • Pitkänen E, Jouhten P, Hou J, Syed MF, Blomberg P, Kludas J, Oja M, Holm L, Penttilä M, Rousu J, Arvas M
  • PLoS computational biology , 2/ 2014 , Volume 10 , pages: e1003465
  • Department of Computer Science, University of Helsinki, Helsinki, Finland ; Department of Medical Genetics, Genome-Scale Biology Research Program, University of Helsinki, Helsinki, Finland.
  • 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/.
Contributors
Esa Pitkänen

Metadata information

is
BioModels Database MODEL1302010007
isVersionOf
isDescribedBy
Curation status
Non-curated
  • Model originally submitted by : Esa Pitkänen
  • Submitted: 01-Feb-2013 17:30:09
  • Last Modified: 02-Mar-2014 17:20:01
Revisions
  • Version: 2 public model Download this version
    • Submitted on: 02-Mar-2014 17:20:01
    • Submitted by: Esa Pitkänen
    • With comment: Current version of Pitkanen2014 - Metabolic reconstruction of Coccidioides immitis using CoReCo
  • Version: 1 public model Download this version
    • Submitted on: 01-Feb-2013 17:30:09
    • Submitted by: Esa Pitkänen
    • With comment: Original import of Pitkanen2013 - Metabolic reconstruction of Coccidioides immitis using CoReCo