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Predicting genes for orphan metabolic activities using phylogenetic profiles
Lifeng Chen, Dennis Vitkup
Genome Biol. 2006; 7(2): R17. Published online 2006 February 15. doi: 10.1186/gb-2006-7-2-r17
PMCID:
PMC1431735
Abstract Full Text PDF–633K Supplementary Material
 Is Cited by the Following 15 Articles in this Archive:
The human metabolic reconstruction Recon 1 directs hypotheses of novel human metabolic functions
Ottar Rolfsson, Bernhard Ø Palsson, Ines Thiele
BMC Syst Biol. 2011; 5: 155. Published online 2011 October 1. doi: 10.1186/1752-0509-5-155
PMCID:
PMC3224382
Abstract Full Text PDF–4.8M Supplementary Material
Prioritizing orphan proteins for further study using phylogenomics and gene expression profiles in Streptomyces coelicolor
Mohammad Tauqeer Alam, Eriko Takano, Rainer Breitling
BMC Res Notes. 2011; 4: 325. Published online 2011 September 7. doi: 10.1186/1756-0500-4-325
PMCID:
PMC3224560
Abstract Full Text PDF–3.8M Supplementary Material
Reconstruction and Validation of RefRec: A Global Model for the Yeast Molecular Interaction Network
Tommi Aho, Henrikki Almusa, Jukka Matilainen, Antti Larjo, Pekka Ruusuvuori, Kaisa-Leena Aho, Thomas Wilhelm, Harri Lähdesmäki, Andreas Beyer, Manu Harju, Sharif Chowdhury, Kalle Leinonen, Christophe Roos, Olli Yli-Harja
PLoS One. 2010; 5(5): e10662. Published online 2010 May 14. doi: 10.1371/journal.pone.0010662
PMCID:
PMC2871048
Abstract Full Text PDF–839K Supplementary Material
Eating at the Table of Another: Metabolomics of Host/Parasite Interactions
Björn F.C. Kafsack, Manuel Llinás
Cell Host Microbe. Author manuscript; available in PMC 2011 February 18.
Published in final edited form as: Cell Host Microbe. 2010 February 18; 7(2): 90–99. doi: 10.1016/j.chom.2010.01.008
PMCID:
PMC2825149
Abstract Full Text PDF–735K
FUNGIpath: a tool to assess fungal metabolic pathways predicted by orthology
Sandrine Grossetête, Bernard Labedan, Olivier Lespinet
BMC Genomics. 2010; 11: 81. Published online 2010 February 1. doi: 10.1186/1471-2164-11-81
PMCID:
PMC2829015
Abstract Full Text PDF–1.6M Supplementary Material
Automatic policing of biochemical annotations using genomic correlations
Tzu-Lin Hsiao, Olga Revelles, Lifeng Chen, Uwe Sauer, Dennis Vitkup
Nat Chem Biol. Author manuscript; available in PMC 2010 September 8.
Published in final edited form as: Nat Chem Biol. 2010 January; 6(1): 34–40. Published online 2009 November 22. doi: 10.1038/nchembio.266
PMCID:
PMC2935526
Abstract Full Text PDF–802K Supplementary Material
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
GrowMatch: An Automated Method for Reconciling In Silico/In Vivo Growth Predictions
Vinay Satish Kumar, Costas D. Maranas
PLoS Comput Biol. 2009 March; 5(3): e1000308. Published online 2009 March 13. doi: 10.1371/journal.pcbi.1000308
PMCID:
PMC2645679
Abstract Full Text PDF–486K Supplementary Material
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
Inferring modules of functionally interacting proteins using the Bond Energy Algorithm
Ryosuke LA Watanabe, Enrique Morett, Edgar E Vallejo
BMC Bioinformatics. 2008; 9: 285. Published online 2008 June 17. doi: 10.1186/1471-2105-9-285
PMCID:
PMC2474619
Abstract Full Text PDF–418K Supplementary Material
The Growing Scope of Applications of Genome-scale Metabolic Reconstructions: the case of E. coli
Adam M. Feist, Bernhard Ø. Palsson
Nat Biotechnol. Author manuscript; available in PMC 2011 June 6.
Published in final edited form as: Nat Biotechnol. 2008 June; 26(6): 659–667. doi: 10.1038/nbt1401
PMCID:
PMC3108568
Abstract Full Text PDF–1.2M Supplementary Material
Rapid acid treatment of Escherichia coli: transcriptomic response and recovery
Geetha Kannan, Jessica C Wilks, Devon M Fitzgerald, Brian D Jones, Sandra S BonDurant, Joan L Slonczewski
BMC Microbiol. 2008; 8: 37. Published online 2008 February 26. doi: 10.1186/1471-2180-8-37
PMCID:
PMC2270276
Abstract Full Text PDF–523K Supplementary Material
Computational Prediction and Experimental Verification of the Gene Encoding the NAD+/NADP+-Dependent Succinate Semialdehyde Dehydrogenase in Escherichia coli
Tobias Fuhrer, Lifeng Chen, Uwe Sauer, Dennis Vitkup
J Bacteriol. 2007 November; 189(22): 8073–8078. Published online 2007 September 14. doi: 10.1128/JB.01027-07
PMCID:
PMC2168661
Abstract Full Text PDF–360K Supplementary Material
Optimization based automated curation of metabolic reconstructions
Vinay Satish Kumar, Madhukar S Dasika, Costas D Maranas
BMC Bioinformatics. 2007; 8: 212. Published online 2007 June 20. doi: 10.1186/1471-2105-8-212
PMCID:
PMC1933441
Abstract Full Text PDF–659K Supplementary Material
A metabolic network in the evolutionary context: Multiscale structure and modularity
Victor Spirin, Mikhail S. Gelfand, Andrey A. Mironov, Leonid A. Mirny
Proc Natl Acad Sci U S A. 2006 June 6; 103(23): 8774–8779. Published online 2006 May 26. doi: 10.1073/pnas.0510258103
PMCID:
PMC1482654
Abstract Full Text PDF–712K Supplementary Material
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