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Results: 1 to 20 of 129

1.

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
2.

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
3.

Computational approaches to the topology, stability and dynamics of metabolic networks.

Steuer R.

Phytochemistry. 2007 Aug-Sep;68(16-18):2139-51. Epub 2007 Jun 14.

PMID:
17574639
[PubMed - indexed for MEDLINE]
4.

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
5.

An optimization model for metabolic pathways.

Planes FJ, Beasley JE.

Bioinformatics. 2009 Oct 15;25(20):2723-9. doi: 10.1093/bioinformatics/btp441. Epub 2009 Jul 20.

PMID:
19620100
[PubMed - indexed for MEDLINE]
Free Article
6.

A critical examination of stoichiometric and path-finding approaches to metabolic pathways.

Planes FJ, Beasley JE.

Brief Bioinform. 2008 Sep;9(5):422-36. doi: 10.1093/bib/bbn018. Epub 2008 Apr 24. Review.

PMID:
18436574
[PubMed - indexed for MEDLINE]
Free Article
7.

Signatures of arithmetic simplicity in metabolic network architecture.

Riehl WJ, Krapivsky PL, Redner S, Segrè D.

PLoS Comput Biol. 2010 Apr 1;6(4):e1000725. doi: 10.1371/journal.pcbi.1000725.

PMID:
20369010
[PubMed - indexed for MEDLINE]
Free PMC Article
8.

Predicting functional associations from metabolism using bi-partite network algorithms.

Veeramani B, Bader JS.

BMC Syst Biol. 2010 Jul 14;4:95. doi: 10.1186/1752-0509-4-95.

PMID:
20630077
[PubMed - indexed for MEDLINE]
Free PMC Article
9.

When metabolism meets topology: Reconciling metabolite and reaction networks.

Montañez R, Medina MA, Solé RV, Rodríguez-Caso C.

Bioessays. 2010 Mar;32(3):246-56. doi: 10.1002/bies.200900145.

PMID:
20127701
[PubMed - indexed for MEDLINE]
10.

Modular decomposition of metabolic systems via null-space analysis.

Poolman MG, Sebu C, Pidcock MK, Fell DA.

J Theor Biol. 2007 Dec 21;249(4):691-705. Epub 2007 Aug 19.

PMID:
17949756
[PubMed - indexed for MEDLINE]
11.

Algebraic properties of automata associated to Petri nets and applications to computation in biological systems.

Egri-Nagy A, Nehaniv CL.

Biosystems. 2008 Oct-Nov;94(1-2):135-44. doi: 10.1016/j.biosystems.2008.05.019. Epub 2008 Jun 20.

PMID:
18611428
[PubMed - indexed for MEDLINE]
12.

An extended bioreaction database that significantly improves reconstruction and analysis of genome-scale metabolic networks.

Stelzer M, Sun J, Kamphans T, Fekete SP, Zeng AP.

Integr Biol (Camb). 2011 Nov;3(11):1071-86. doi: 10.1039/c1ib00008j. Epub 2011 Sep 27.

PMID:
21952610
[PubMed - indexed for MEDLINE]
13.
14.

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
15.

Spontaneous reaction silencing in metabolic optimization.

Nishikawa T, Gulbahce N, Motter AE.

PLoS Comput Biol. 2008 Dec;4(12):e1000236. doi: 10.1371/journal.pcbi.1000236. Epub 2008 Dec 5.

PMID:
19057639
[PubMed - indexed for MEDLINE]
Free PMC Article
16.

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
17.

Computing the shortest elementary flux modes in genome-scale metabolic networks.

de Figueiredo LF, Podhorski A, Rubio A, Kaleta C, Beasley JE, Schuster S, Planes FJ.

Bioinformatics. 2009 Dec 1;25(23):3158-65. doi: 10.1093/bioinformatics/btp564. Epub 2009 Sep 30.

PMID:
19793869
[PubMed - indexed for MEDLINE]
Free Article
18.

Leveraging modeling approaches: reaction networks and rules.

Blinov ML, Moraru II.

Adv Exp Med Biol. 2012;736:517-30. doi: 10.1007/978-1-4419-7210-1_30.

PMID:
22161349
[PubMed - indexed for MEDLINE]
Free PMC Article
19.

Exploring metabolic pathways in genome-scale networks via generating flux modes.

Rezola A, de Figueiredo LF, Brock M, Pey J, Podhorski A, Wittmann C, Schuster S, Bockmayr A, Planes FJ.

Bioinformatics. 2011 Feb 15;27(4):534-40. doi: 10.1093/bioinformatics/btq681. Epub 2010 Dec 10.

PMID:
21149278
[PubMed - indexed for MEDLINE]
Free Article
20.

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]

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