Literature DB >> 15613397

Expa: a program for calculating extreme pathways in biochemical reaction networks.

Steven L Bell1, Bernhard Ø Palsson.   

Abstract

UNLABELLED: The set of extreme pathways, a generating set for all possible steady-state flux maps in a biochemical reaction network, can be computed from the stoichiometric matrix, an incidence-like matrix reflecting the network topology. Here, we describe the implementation of a well-known algorithm to compute these pathways and give a summary of the features of the available software. AVAILABILITY: The C-code, along with a Windows executable and sample network reaction files, are available at http://systemsbiology.ucsd.edu CONTACT: palsson@ucsd.edu.

Mesh:

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Year:  2004        PMID: 15613397     DOI: 10.1093/bioinformatics/bti228

Source DB:  PubMed          Journal:  Bioinformatics        ISSN: 1367-4803            Impact factor:   6.937


  23 in total

1.  Deep epistasis in human metabolism.

Authors:  Marcin Imielinski; Calin Belta
Journal:  Chaos       Date:  2010-06       Impact factor: 3.642

2.  Enumerating metabolic pathways for the production of heterologous target chemicals in chassis organisms.

Authors:  Pablo Carbonell; Davide Fichera; Shashi B Pandit; Jean-Loup Faulon
Journal:  BMC Syst Biol       Date:  2012-02-06

3.  Analysis of metabolic subnetworks by flux cone projection.

Authors:  Sayed-Amir Marashi; Laszlo David; Alexander Bockmayr
Journal:  Algorithms Mol Biol       Date:  2012-05-29       Impact factor: 1.405

4.  On algebraic properties of extreme pathways in metabolic networks.

Authors:  Dimitrije Jevremovic; Cong T Trinh; Friedrich Srienc; Daniel Boley
Journal:  J Comput Biol       Date:  2010-02       Impact factor: 1.479

Review 5.  Recent advances in elementary flux modes and yield space analysis as useful tools in metabolic network studies.

Authors:  Predrag Horvat; Martin Koller; Gerhart Braunegg
Journal:  World J Microbiol Biotechnol       Date:  2015-06-12       Impact factor: 3.312

6.  FASIMU: flexible software for flux-balance computation series in large metabolic networks.

Authors:  Andreas Hoppe; Sabrina Hoffmann; Andreas Gerasch; Christoph Gille; Hermann-Georg Holzhütter
Journal:  BMC Bioinformatics       Date:  2011-01-22       Impact factor: 3.169

Review 7.  Which metabolic pathways generate and characterize the flux space? A comparison among elementary modes, extreme pathways and minimal generators.

Authors:  Francisco Llaneras; Jesús Picó
Journal:  J Biomed Biotechnol       Date:  2010-05-11

Review 8.  Elementary mode analysis: a useful metabolic pathway analysis tool for characterizing cellular metabolism.

Authors:  Cong T Trinh; Aaron Wlaschin; Friedrich Srienc
Journal:  Appl Microbiol Biotechnol       Date:  2008-11-15       Impact factor: 4.813

9.  Systematic analysis of conservation relations in Escherichia coli genome-scale metabolic network reveals novel growth media.

Authors:  Marcin Imielinski; Calin Belta; Harvey Rubin; Adam Halász
Journal:  Biophys J       Date:  2006-02-03       Impact factor: 4.033

10.  Optimal flux spaces of genome-scale stoichiometric models are determined by a few subnetworks.

Authors:  Steven M Kelk; Brett G Olivier; Leen Stougie; Frank J Bruggeman
Journal:  Sci Rep       Date:  2012-08-15       Impact factor: 4.379

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