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Items: 1 to 20 of 462

1.

Acorn: a grid computing system for constraint based modeling and visualization of the genome scale metabolic reaction networks via a web interface.

Sroka J, Bieniasz-Krzywiec L, Gwóźdź S, Leniowski D, Lącki J, Markowski M, Avignone-Rossa C, Bushell ME, McFadden J, Kierzek AM.

BMC Bioinformatics. 2011 May 24;12:196. doi: 10.1186/1471-2105-12-196.

2.

SurreyFBA: a command line tool and graphics user interface for constraint-based modeling of genome-scale metabolic reaction networks.

Gevorgyan A, Bushell ME, Avignone-Rossa C, Kierzek AM.

Bioinformatics. 2011 Feb 1;27(3):433-4. doi: 10.1093/bioinformatics/btq679. Epub 2010 Dec 9.

3.

Identification of functional differences in metabolic networks using comparative genomics and constraint-based models.

Hamilton JJ, Reed JL.

PLoS One. 2012;7(4):e34670. doi: 10.1371/journal.pone.0034670. Epub 2012 Apr 16.

4.

MicrobesFlux: a web platform for drafting metabolic models from the KEGG database.

Feng X, Xu Y, Chen Y, Tang YJ.

BMC Syst Biol. 2012 Aug 2;6:94.

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.

6.

Quantitative prediction of cellular metabolism with constraint-based models: the COBRA Toolbox.

Becker SA, Feist AM, Mo ML, Hannum G, Palsson BØ, Herrgard MJ.

Nat Protoc. 2007;2(3):727-38.

PMID:
17406635
7.

Sybil--efficient constraint-based modelling in R.

Gelius-Dietrich G, Desouki AA, Fritzemeier CJ, Lercher MJ.

BMC Syst Biol. 2013 Nov 13;7:125. doi: 10.1186/1752-0509-7-125.

8.

MEMOSys: Bioinformatics platform for genome-scale metabolic models.

Pabinger S, Rader R, Agren R, Nielsen J, Trajanoski Z.

BMC Syst Biol. 2011 Jan 31;5:20. doi: 10.1186/1752-0509-5-20.

9.

GEMSiRV: a software platform for GEnome-scale metabolic model simulation, reconstruction and visualization.

Liao YC, Tsai MH, Chen FC, Hsiung CA.

Bioinformatics. 2012 Jul 1;28(13):1752-8. doi: 10.1093/bioinformatics/bts267. Epub 2012 May 4.

10.

BioPP: a tool for web-publication of biological networks.

Viswanathan GA, Nudelman G, Patil S, Sealfon SC.

BMC Bioinformatics. 2007 May 22;8:168.

11.

KEGGconverter: a tool for the in-silico modelling of metabolic networks of the KEGG Pathways database.

Moutselos K, Kanaris I, Chatziioannou A, Maglogiannis I, Kolisis FN.

BMC Bioinformatics. 2009 Oct 8;10:324. doi: 10.1186/1471-2105-10-324.

12.

Iterative reconstruction of a global metabolic model of Acinetobacter baylyi ADP1 using high-throughput growth phenotype and gene essentiality data.

Durot M, Le Fèvre F, de Berardinis V, Kreimeyer A, Vallenet D, Combe C, Smidtas S, Salanoubat M, Weissenbach J, Schachter V.

BMC Syst Biol. 2008 Oct 7;2:85. doi: 10.1186/1752-0509-2-85.

13.

A practical guide to genome-scale metabolic models and their analysis.

Santos F, Boele J, Teusink B.

Methods Enzymol. 2011;500:509-32. doi: 10.1016/B978-0-12-385118-5.00024-4.

PMID:
21943912
14.

BiGG: a Biochemical Genetic and Genomic knowledgebase of large scale metabolic reconstructions.

Schellenberger J, Park JO, Conrad TM, Palsson BØ.

BMC Bioinformatics. 2010 Apr 29;11:213. doi: 10.1186/1471-2105-11-213.

15.
16.

Web-based metabolic network visualization with a zooming user interface.

Latendresse M, Karp PD.

BMC Bioinformatics. 2011 May 19;12:176. doi: 10.1186/1471-2105-12-176.

17.

CARMEN - Comparative Analysis and in silico Reconstruction of organism-specific MEtabolic Networks.

Schneider J, Vorhölter FJ, Trost E, Blom J, Musa YR, Neuweger H, Niehaus K, Schatschneider S, Tauch A, Goesmann A.

Genet Mol Res. 2010 Aug 24;9(3):1660-72. doi: 10.4238/vol9-3gmr901.

18.
19.

Genome Projector: zoomable genome map with multiple views.

Arakawa K, Tamaki S, Kono N, Kido N, Ikegami K, Ogawa R, Tomita M.

BMC Bioinformatics. 2009 Jan 23;10:31. doi: 10.1186/1471-2105-10-31.

20.

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.

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