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Items: 1 to 20 of 93

1.

BioMet Toolbox: genome-wide analysis of metabolism.

Cvijovic M, Olivares-Hernández R, Agren R, Dahr N, Vongsangnak W, Nookaew I, Patil KR, Nielsen J.

Nucleic Acids Res. 2010 Jul;38(Web Server issue):W144-9. doi: 10.1093/nar/gkq404. Epub 2010 May 18.

2.

BioMet Toolbox 2.0: genome-wide analysis of metabolism and omics data.

Garcia-Albornoz M, Thankaswamy-Kosalai S, Nilsson A, Väremo L, Nookaew I, Nielsen J.

Nucleic Acids Res. 2014 Jul;42(Web Server issue):W175-81. doi: 10.1093/nar/gku371. Epub 2014 May 3.

3.

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.

4.

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.

5.

YANA - a software tool for analyzing flux modes, gene-expression and enzyme activities.

Schwarz R, Musch P, von Kamp A, Engels B, Schirmer H, Schuster S, Dandekar T.

BMC Bioinformatics. 2005 Jun 1;6:135.

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.

Sampling the solution space in genome-scale metabolic networks reveals transcriptional regulation in key enzymes.

Bordel S, Agren R, Nielsen J.

PLoS Comput Biol. 2010 Jul 15;6(7):e1000859. doi: 10.1371/journal.pcbi.1000859.

8.

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.

9.
10.

Metabolic pathway analysis web service (Pathway Hunter Tool at CUBIC).

Rahman SA, Advani P, Schunk R, Schrader R, Schomburg D.

Bioinformatics. 2005 Apr 1;21(7):1189-93. Epub 2004 Nov 30.

PMID:
15572476
11.

NeAT: a toolbox for the analysis of biological networks, clusters, classes and pathways.

Brohée S, Faust K, Lima-Mendez G, Sand O, Janky R, Vanderstocken G, Deville Y, van Helden J.

Nucleic Acids Res. 2008 Jul 1;36(Web Server issue):W444-51. doi: 10.1093/nar/gkn336. Epub 2008 Jun 4.

12.

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.

13.

Using flux balance analysis to guide microbial metabolic engineering.

Curran KA, Crook NC, Alper HS.

Methods Mol Biol. 2012;834:197-216. doi: 10.1007/978-1-61779-483-4_13.

PMID:
22144361
14.

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.

PMID:
22563070
15.

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.

16.

Kiwi: a tool for integration and visualization of network topology and gene-set analysis.

Väremo L, Gatto F, Nielsen J.

BMC Bioinformatics. 2014 Dec 11;15:408. doi: 10.1186/s12859-014-0408-9.

17.

ReMatch: a web-based tool to construct, store and share stoichiometric metabolic models with carbon maps for metabolic flux analysis.

Pitkänen E, Akerlund A, Rantanen A, Jouhten P, Ukkonen E.

J Integr Bioinform. 2008 Aug 25;5(2). doi: 10.2390/biecoll-jib-2008-102.

PMID:
20134058
18.

Flux analysis and metabolomics for systematic metabolic engineering of microorganisms.

Toya Y, Shimizu H.

Biotechnol Adv. 2013 Nov;31(6):818-26. doi: 10.1016/j.biotechadv.2013.05.002. Epub 2013 May 13. Review.

PMID:
23680193
19.

Constraints-based genome-scale metabolic simulation for systems metabolic engineering.

Park JM, Kim TY, Lee SY.

Biotechnol Adv. 2009 Nov-Dec;27(6):979-88. doi: 10.1016/j.biotechadv.2009.05.019. Epub 2009 May 20. Review.

PMID:
19464354
20.

Genome-scale in silico aided metabolic analysis and flux comparisons of Escherichia coli to improve succinate production.

Wang Q, Chen X, Yang Y, Zhao X.

Appl Microbiol Biotechnol. 2006 Dec;73(4):887-94. Epub 2006 Aug 23.

PMID:
16927085

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