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Observing metabolic functions at the genome scale
Jean-Marc Schwartz, Claire Gaugain, Jose C Nacher, Antoine de Daruvar, Minoru Kanehisa
Genome Biol. 2007; 8(6): R123. Published online 2007 June 26. doi: 10.1186/gb-2007-8-6-r123
PMCID:
PMC2394767
Abstract Full Text PDF–1.3M Supplementary Material
 Is Cited by the Following 9 Articles in this Archive:
Predicting the Physiological Role of Circadian Metabolic Regulation in the Green Alga Chlamydomonas reinhardtii
Sascha Schäuble, Ines Heiland, Olga Voytsekh, Maria Mittag, Stefan Schuster
PLoS One. 2011; 6(8): e23026. Published online 2011 August 22. doi: 10.1371/journal.pone.0023026
PMCID:
PMC3161734
Abstract Full Text PDF–845K Supplementary Material
Optimal regulatory strategies for metabolic pathways in Escherichia coli depending on protein costs
Frank Wessely, Martin Bartl, Reinhard Guthke, Pu Li, Stefan Schuster, Christoph Kaleta
Mol Syst Biol. 2011; 7: 515. Published online 2011 July 19. doi: 10.1038/msb.2011.46
PMCID:
PMC3159982
Abstract Full Text PDF–565K Supplementary Material
PathExpress update: the enzyme neighbourhood method of associating gene-expression data with metabolic pathways
Nicolas Goffard, Tancred Frickey, Georg Weiller
Nucleic Acids Res. 2009 July 1; 37(Web Server issue): W335–W339. Published online 2009 July 1. doi: 10.1093/nar/gkp432
PMCID:
PMC2703986
Abstract Full Text PDF–330K
Gene Expression Profiling and the Use of Genome-Scale In Silico Models of Escherichia coli for Analysis: Providing Context for Content
Nathan E. Lewis, Byung-Kwan Cho, Eric M. Knight, Bernhard O. Palsson
J Bacteriol. 2009 June; 191(11): 3437–3444. Published online 2009 April 10. doi: 10.1128/JB.00034-09
PMCID:
PMC2681886
Full Text PDF–684K
Genome-scale models of bacterial metabolism: reconstruction and applications
Maxime Durot, Pierre-Yves Bourguignon, Vincent Schachter
FEMS Microbiol Rev. 2009 January; 33(1): 164–190. Published online 2008 December. doi: 10.1111/j.1574-6976.2008.00146.x
PMCID:
PMC2704943
Abstract Full Text PDF–520K
Elementary Mode Analysis: A Useful Metabolic Pathway Analysis Tool for Characterizing Cellular Metabolism
Cong T. Trinh, Aaron Wlaschin, Friedrich Srienc
Appl Microbiol Biotechnol. Author manuscript; available in PMC 2010 July 23.
Published in final edited form as: Appl Microbiol Biotechnol. 2009 January; 81(5): 813–826. Published online 2008 November 15. doi: 10.1007/s00253-008-1770-1
PMCID:
PMC2909134
Abstract Full Text PDF–2.6M
Gene set analyses for interpreting microarray experiments on prokaryotic organisms
Nathan L Tintle, Aaron A Best, Matthew DeJongh, Dirk Van Bruggen, Fred Heffron, Steffen Porwollik, Ronald C Taylor
BMC Bioinformatics. 2008; 9: 469. Published online 2008 November 5. doi: 10.1186/1471-2105-9-469
PMCID:
PMC2587482
Abstract Full Text PDF–356K Supplementary Material
'Systems toxicology' approach identifies coordinated metabolic responses to copper in a terrestrial non-model invertebrate, the earthworm Lumbricus rubellus
Jacob G Bundy, Jasmin K Sidhu, Faisal Rana, David J Spurgeon, Claus Svendsen, Jodie F Wren, Stephen R Stürzenbaum, A John Morgan, Peter Kille
BMC Biol. 2008; 6: 25. Published online 2008 June 3. doi: 10.1186/1741-7007-6-25
PMCID:
PMC2424032
Abstract Full Text PDF–1.9M Supplementary Material
Context-Specific Metabolic Networks Are Consistent with Experiments
Scott A. Becker, Bernhard O. Palsson
PLoS Comput Biol. 2008 May; 4(5): e1000082. Published online 2008 May 16. doi: 10.1371/journal.pcbi.1000082
PMCID:
PMC2366062
Abstract Full Text PDF–509K
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