A simplified metabolic network reconstruction to promote understanding and development of flux balance analysis tools.

Animals Humans Metabolic Flux Analysis Metabolic Networks and Pathways / physiology Models, Biological
Computational modeling Flux balance analysis Metabolic engineering Metabolic networks Systems biology

Journal

Computers in biology and medicine
ISSN: 1879-0534
Titre abrégé: Comput Biol Med
Pays: United States
ID NLM: 1250250

Informations de publication

Date de publication:
02 2019
Historique:
received: 26 09 2018
revised: 11 12 2018
accepted: 13 12 2018
pubmed: 26 12 2018
medline: 26 3 2020
entrez: 26 12 2018
Statut: ppublish

Résumé

GEnome-scale Network REconstructions (GENREs) mathematically describe metabolic reactions of an organism or a specific cell type. GENREs can be used with a number of constraint-based reconstruction and analysis (COBRA) methods to make computational predictions on how a system changes in different environments. We created a simplified GENRE (referred to as iSIM) that captures central energy metabolism with nine metabolic reactions to illustrate the use of and promote the understanding of GENREs and constraint-based methods. We demonstrate the simulation of single and double gene deletions, flux variability analysis (FVA), and test a number of metabolic tasks with the GENRE. Code to perform these analyses is provided in Python, R, and MATLAB. Finally, with iSIM as a guide, we demonstrate how inaccuracies in GENREs can limit their use in the interrogation of energy metabolism.

Identifiants

DOI: 10.1016/j.compbiomed.2018.12.010 PMID: 30584952
pubmed: 30584952
pii: S0010-4825(18)30408-6
doi: 10.1016/j.compbiomed.2018.12.010
pii:
doi:

Types de publication

Journal Article Research Support, U.S. Gov't, Non-P.H.S.

Langues

eng

Sous-ensembles de citation

IM

Pagination

64-71

Informations de copyright

Copyright © 2018. Published by Elsevier Ltd.

Auteurs

Kristopher D Rawls (KD)

Department of Biomedical Engineering, University of Virginia, Charlottesville, VA, 22908, USA.

Bonnie V Dougherty (BV)

Department of Biomedical Engineering, University of Virginia, Charlottesville, VA, 22908, USA.

Edik M Blais (EM)

Department of Biomedical Engineering, University of Virginia, Charlottesville, VA, 22908, USA.

Ethan Stancliffe (E)

Department of Biomedical Engineering, University of Virginia, Charlottesville, VA, 22908, USA.

Glynis L Kolling (GL)

Department of Biomedical Engineering, University of Virginia, Charlottesville, VA, 22908, USA; Department of Medicine, Division of Infectious Diseases and International Health, University of Virginia, Charlottesville, VA, 22908, USA.

Kalyan Vinnakota (K)

Department of Defense Biotechnology High Performance Computing Software Applications Institute, Telemedicine and Advanced Technology Research Center, U.S. Army Medical Research and Materiel Command, Fort Detrick, Maryland, USA.

Venkat R Pannala (VR)

Department of Defense Biotechnology High Performance Computing Software Applications Institute, Telemedicine and Advanced Technology Research Center, U.S. Army Medical Research and Materiel Command, Fort Detrick, Maryland, USA.

Anders Wallqvist (A)

Department of Defense Biotechnology High Performance Computing Software Applications Institute, Telemedicine and Advanced Technology Research Center, U.S. Army Medical Research and Materiel Command, Fort Detrick, Maryland, USA.

Jason A Papin (JA)

Department of Biomedical Engineering, University of Virginia, Charlottesville, VA, 22908, USA. Electronic address: papin@virginia.edu.

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Classifications MeSH

questionsmedicales.fr › Eucaryotes › Animaux › A simplified metabolic network reconstruction...
questionsmedicales.fr › Eucaryotes › Animaux › Chordés › Vertébrés › Mammifères › Eutheria › Primates › Haplorhini › Catarrhini › Hominidae › Humains › A simplified metabolic network reconstruction...
questionsmedicales.fr › Techniques d'investigation › Techniques cytologiques › Analyse des flux métaboliques › A simplified metabolic network reconstruction...
questionsmedicales.fr › Métabolisme › Voies et réseaux métaboliques › A simplified metabolic network reconstruction...
questionsmedicales.fr › Techniques d'investigation › Modèles théoriques › Modèles biologiques › A simplified metabolic network reconstruction...