Genome-scale models of microbial cells: evaluating the consequences of constraints

Nature Reviews. Microbiology
Nathan D PriceBernhard Ø Palsson

Abstract

Microbial cells operate under governing constraints that limit their range of possible functions. With the availability of annotated genome sequences, it has become possible to reconstruct genome-scale biochemical reaction networks for microorganisms. The imposition of governing constraints on a reconstructed biochemical network leads to the definition of achievable cellular functions. In recent years, a substantial and growing toolbox of computational analysis methods has been developed to study the characteristics and capabilities of microorganisms using a constraint-based reconstruction and analysis (COBRA) approach. This approach provides a biochemically and genetically consistent framework for the generation of hypotheses and the testing of functions of microbial cells.

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Aug 3, 2013·Proceedings of the National Academy of Sciences of the United States of America·Piyush LabhsetwarZaida Luthey-Schulten
Aug 31, 2007·FEMS Yeast Research·Jens Nielsen, Michael C Jewett
Nov 30, 2014·Genome Biology and Evolution·Djordje BajićJuan F Poyatos
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Feb 27, 2010·Journal of Biotechnology·Kwee-Yan Teh, Andrew E Lutz
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Mar 4, 2017·Interdisciplinary Sciences, Computational Life Sciences·Jorge FerreiraMiguel Rocha
Jul 11, 2007·Expert Review of Molecular Diagnostics·Douglas B Kell
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Sep 4, 2014·Microbiology and Molecular Biology Reviews : MMBR·Joana C XavierIsabel Rocha
Sep 27, 2018·FEMS Microbiology Letters·Ilyas KabimoldayevDonghyuk Kim
May 21, 2016·Nature Communications·Balázs SzappanosBalázs Papp
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Jun 22, 2006·Molecular Systems Biology·Steve Van Dien, Christophe H Schilling
Jul 6, 2006·Molecular Systems Biology·Neema Jamshidi, Bernhard Ø Palsson
Oct 7, 2006·Nature·Barbara Di VenturaLuis Serrano
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Jul 13, 2007·Molecular Systems Biology·Jens Nielsen
Nov 21, 2007·Nature Reviews. Microbiology·Rainer BreitlingMichael P Barrett
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Feb 5, 2008·Biotechnology Journal·Tae Yong KimSang Yup Lee
Nov 23, 2007·Journal of Cellular and Molecular Medicine·Nathan D PriceQiang Tian
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Sep 17, 2009·Molecular BioSystems·Josselin NoirelPhillip C Wright
Nov 6, 2009·Molecular Systems Biology·Douwe MolenaarBas Teusink
Mar 1, 2019·PLoS Computational Biology·Chiara DamianiGiancarlo Mauri
Jan 19, 2006·Nature Reviews. Genetics·Jennifer L ReedBernhard Ø Palsson
Feb 24, 2006·Nature Reviews. Molecular Cell Biology·Andrew R Joyce, Bernhard Ø Palsson
Dec 17, 2005·Nature Reviews. Microbiology·Bas Teusink, Eddy J Smid
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Mar 25, 2014·Nature Reviews. Microbiology·Victor ChubukovUwe Sauer
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Jun 14, 2016·Scientific Reports·Rui JiangAlexander Golberg
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Jun 16, 2012·Molecular BioSystems·Swagatika SahooInes Thiele
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Sep 28, 2017·Biotechnology for Biofuels·Areejit SamalN Louise Glass
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Jun 25, 2020·Proteomics·Sanjeev DahalLaurence Yang
Oct 23, 2016·BMC Systems Biology·Sayed-Rzgar Hosseini, Andreas Wagner
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Jan 31, 2019·Metabolites·Partho Sen, Matej Orešič
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Mar 29, 2018·Biochemical Society Transactions·Martin H Rau, Ahmad A Zeidan
Nov 30, 2019·Scientific Reports·Rotem KatzirEytan Ruppin
Oct 27, 2017·FEMS Microbiology Reviews·Kristina Klobucar, Eric D Brown
Nov 27, 2018·Royal Society Open Science·Mauricio Moreno-ZambranoMarc-Thorsten Hütt
Sep 13, 2019·Bioinformatics·Reza MiraskarshahiLeonid Chindelevitch
Oct 7, 2020·Nature Communications·Amin Espah BorujeniChristopher A Voigt
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Dec 2, 2004·The Journal of Biological Chemistry·Ines ThieleBernhard Ø Palsson
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