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Results: 1 to 20 of 192

1.

Impact of stoichiometry representation on simulation of genotype-phenotype relationships in metabolic networks.

Brochado AR, Andrejev S, Maranas CD, Patil KR.

PLoS Comput Biol. 2012;8(11):e1002758. doi: 10.1371/journal.pcbi.1002758. Epub 2012 Nov 1.

PMID:
23133362
[PubMed - indexed for MEDLINE]
Free PMC Article
2.
3.

Evolutionary programming as a platform for in silico metabolic engineering.

Patil KR, Rocha I, Förster J, Nielsen J.

BMC Bioinformatics. 2005 Dec 23;6:308.

PMID:
16375763
[PubMed - indexed for MEDLINE]
Free PMC Article
4.

Path finding methods accounting for stoichiometry in metabolic networks.

Pey J, Prada J, Beasley JE, Planes FJ.

Genome Biol. 2011;12(5):R49. doi: 10.1186/gb-2011-12-5-r49. Epub 2011 May 27.

PMID:
21619601
[PubMed - indexed for MEDLINE]
Free PMC Article
5.

OptFlux: an open-source software platform for in silico metabolic engineering.

Rocha I, Maia P, Evangelista P, Vilaça P, Soares S, Pinto JP, Nielsen J, Patil KR, Ferreira EC, Rocha M.

BMC Syst Biol. 2010 Apr 19;4:45. doi: 10.1186/1752-0509-4-45.

PMID:
20403172
[PubMed - indexed for MEDLINE]
Free PMC Article
6.

Inferring branching pathways in genome-scale metabolic networks.

Pitkänen E, Jouhten P, Rousu J.

BMC Syst Biol. 2009 Oct 29;3:103. doi: 10.1186/1752-0509-3-103.

PMID:
19874610
[PubMed - indexed for MEDLINE]
Free PMC Article
7.

Natural computation meta-heuristics for the in silico optimization of microbial strains.

Rocha M, Maia P, Mendes R, Pinto JP, Ferreira EC, Nielsen J, Patil KR, Rocha I.

BMC Bioinformatics. 2008 Nov 27;9:499. doi: 10.1186/1471-2105-9-499.

PMID:
19038030
[PubMed - indexed for MEDLINE]
Free PMC Article
8.

Towards kinetic modeling of genome-scale metabolic networks without sacrificing stoichiometric, thermodynamic and physiological constraints.

Chakrabarti A, Miskovic L, Soh KC, Hatzimanikatis V.

Biotechnol J. 2013 Sep;8(9):1043-57. doi: 10.1002/biot.201300091. Epub 2013 Aug 20.

PMID:
23868566
[PubMed - indexed for MEDLINE]
9.

Genome-scale model for Clostridium acetobutylicum: Part II. Development of specific proton flux states and numerically determined sub-systems.

Senger RS, Papoutsakis ET.

Biotechnol Bioeng. 2008 Dec 1;101(5):1053-71. doi: 10.1002/bit.22009.

PMID:
18767191
[PubMed - indexed for MEDLINE]
Free PMC Article
10.

Predicting biological system objectives de novo from internal state measurements.

Gianchandani EP, Oberhardt MA, Burgard AP, Maranas CD, Papin JA.

BMC Bioinformatics. 2008 Jan 24;9:43. doi: 10.1186/1471-2105-9-43.

PMID:
18218092
[PubMed - indexed for MEDLINE]
Free PMC Article
11.

Symbolic flux analysis for genome-scale metabolic networks.

Schryer DW, Vendelin M, Peterson P.

BMC Syst Biol. 2011 May 23;5:81. doi: 10.1186/1752-0509-5-81.

PMID:
21605414
[PubMed - indexed for MEDLINE]
Free PMC Article
12.

Estimating the size of the solution space of metabolic networks.

Braunstein A, Mulet R, Pagnani A.

BMC Bioinformatics. 2008 May 19;9:240. doi: 10.1186/1471-2105-9-240.

PMID:
18489757
[PubMed - indexed for MEDLINE]
Free PMC Article
13.

A hybrid model of anaerobic E. coli GJT001: combination of elementary flux modes and cybernetic variables.

Kim JI, Varner JD, Ramkrishna D.

Biotechnol Prog. 2008 Sep-Oct;24(5):993-1006. doi: 10.1002/btpr.73.

PMID:
19194908
[PubMed - indexed for MEDLINE]
14.

Genotype networks, innovation, and robustness in sulfur metabolism.

Matias Rodrigues JF, Wagner A.

BMC Syst Biol. 2011 Mar 7;5:39. doi: 10.1186/1752-0509-5-39.

PMID:
21385333
[PubMed - indexed for MEDLINE]
Free PMC Article
15.

Predictive potential of flux balance analysis of Saccharomyces cerevisiae using as optimization function combinations of cell compartmental objectives.

García Sánchez CE, Vargas García CA, Torres Sáez RG.

PLoS One. 2012;7(8):e43006. doi: 10.1371/journal.pone.0043006. Epub 2012 Aug 9.

PMID:
22912775
[PubMed - indexed for MEDLINE]
Free PMC Article
16.

regEfmtool: speeding up elementary flux mode calculation using transcriptional regulatory rules in the form of three-state logic.

Jungreuthmayer C, Ruckerbauer DE, Zanghellini J.

Biosystems. 2013 Jul;113(1):37-9. doi: 10.1016/j.biosystems.2013.04.002. Epub 2013 May 7.

PMID:
23664840
[PubMed - indexed for MEDLINE]
17.

Genome-scale modeling using flux ratio constraints to enable metabolic engineering of clostridial metabolism in silico.

McAnulty MJ, Yen JY, Freedman BG, Senger RS.

BMC Syst Biol. 2012 May 14;6:42. doi: 10.1186/1752-0509-6-42.

PMID:
22583864
[PubMed - indexed for MEDLINE]
Free PMC Article
18.

Continuous modeling of metabolic networks with gene regulation in yeast and in vivo determination of rate parameters.

Moisset P, Vaisman D, Cintolesi A, Urrutia J, Rapaport I, Andrews BA, Asenjo JA.

Biotechnol Bioeng. 2012 Sep;109(9):2325-39. doi: 10.1002/bit.24503. Epub 2012 Apr 24.

PMID:
22447363
[PubMed - indexed for MEDLINE]
19.

F2C2: a fast tool for the computation of flux coupling in genome-scale metabolic networks.

Larhlimi A, David L, Selbig J, Bockmayr A.

BMC Bioinformatics. 2012 Apr 23;13:57. doi: 10.1186/1471-2105-13-57.

PMID:
22524245
[PubMed - indexed for MEDLINE]
Free PMC Article
20.

Properties of metabolic networks: structure versus function.

Mahadevan R, Palsson BO.

Biophys J. 2005 Jan;88(1):L07-9. Epub 2004 Dec 1. Erratum in: Biophys J. 2006 Jan 15;90(2):708.

PMID:
15574705
[PubMed - indexed for MEDLINE]
Free PMC Article
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