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Results: 1 to 20 of 93

1.

FOCAL: an experimental design tool for systematizing metabolic discoveries and model development.

Tervo CJ, Reed JL.

Genome Biol. 2012 Dec 13;13(12):R116. doi: 10.1186/gb-2012-13-12-r116.

PMID:
23236964
[PubMed - in process]
Free PMC Article
2.

An automated phenotype-driven approach (GeneForce) for refining metabolic and regulatory models.

Barua D, Kim J, Reed JL.

PLoS Comput Biol. 2010 Oct 28;6(10):e1000970. doi: 10.1371/journal.pcbi.1000970.

PMID:
21060853
[PubMed - indexed for MEDLINE]
Free PMC Article
3.

Systematic assignment of thermodynamic constraints in metabolic network models.

Kümmel A, Panke S, Heinemann M.

BMC Bioinformatics. 2006 Nov 23;7:512.

PMID:
17123434
[PubMed - indexed for MEDLINE]
Free PMC Article
4.

Identification of genome-scale metabolic network models using experimentally measured flux profiles.

Herrgård MJ, Fong SS, Palsson BØ.

PLoS Comput Biol. 2006 Jul 7;2(7):e72. Epub 2006 May 10.

PMID:
16839195
[PubMed - indexed for MEDLINE]
Free PMC Article
5.

A detailed genome-wide reconstruction of mouse metabolism based on human Recon 1.

Sigurdsson MI, Jamshidi N, Steingrimsson E, Thiele I, Palsson BØ.

BMC Syst Biol. 2010 Oct 19;4:140. doi: 10.1186/1752-0509-4-140.

PMID:
20959003
[PubMed - indexed for MEDLINE]
Free PMC Article
6.

Development of constraint-based system-level models of microbial metabolism.

Navid A.

Methods Mol Biol. 2012;881:531-49. doi: 10.1007/978-1-61779-827-6_18.

PMID:
22639225
[PubMed - indexed for MEDLINE]
7.

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.

PMID:
18840283
[PubMed - indexed for MEDLINE]
Free PMC Article
8.

Genome-scale reconstruction of metabolic network in Bacillus subtilis based on high-throughput phenotyping and gene essentiality data.

Oh YK, Palsson BO, Park SM, Schilling CH, Mahadevan R.

J Biol Chem. 2007 Sep 28;282(39):28791-9. Epub 2007 Jun 15.

PMID:
17573341
[PubMed - indexed for MEDLINE]
Free Article
9.

Yeast 5 - an expanded reconstruction of the Saccharomyces cerevisiae metabolic network.

Heavner BD, Smallbone K, Barker B, Mendes P, Walker LP.

BMC Syst Biol. 2012 Jun 4;6:55. doi: 10.1186/1752-0509-6-55.

PMID:
22663945
[PubMed - indexed for MEDLINE]
Free PMC Article
10.

Predicting gene essentiality using genome-scale in silico models.

Joyce AR, Palsson BØ.

Methods Mol Biol. 2008;416:433-57. doi: 10.1007/978-1-59745-321-9_30.

PMID:
18392986
[PubMed - indexed for MEDLINE]
11.

BioMog: a computational framework for the de novo generation or modification of essential biomass components.

Tervo CJ, Reed JL.

PLoS One. 2013 Dec 5;8(12):e81322. doi: 10.1371/journal.pone.0081322. eCollection 2013.

PMID:
24339916
[PubMed - in process]
Free PMC Article
12.

iAK692: a genome-scale metabolic model of Spirulina platensis C1.

Klanchui A, Khannapho C, Phodee A, Cheevadhanarak S, Meechai A.

BMC Syst Biol. 2012 Jun 15;6:71. doi: 10.1186/1752-0509-6-71.

PMID:
22703714
[PubMed - indexed for MEDLINE]
Free PMC Article
13.

optGpSampler: an improved tool for uniformly sampling the solution-space of genome-scale metabolic networks.

Megchelenbrink W, Huynen M, Marchiori E.

PLoS One. 2014 Feb 14;9(2):e86587. doi: 10.1371/journal.pone.0086587. eCollection 2014.

PMID:
24551039
[PubMed - in process]
Free PMC Article
14.

Optimization based automated curation of metabolic reconstructions.

Satish Kumar V, Dasika MS, Maranas CD.

BMC Bioinformatics. 2007 Jun 20;8:212.

PMID:
17584497
[PubMed - indexed for MEDLINE]
Free PMC Article
15.

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.

PMID:
22666308
[PubMed - indexed for MEDLINE]
Free PMC Article
16.

Toward the automated generation of genome-scale metabolic networks in the SEED.

DeJongh M, Formsma K, Boillot P, Gould J, Rycenga M, Best A.

BMC Bioinformatics. 2007 Apr 26;8:139.

PMID:
17462086
[PubMed - indexed for MEDLINE]
Free PMC Article
17.

Exploring the metabolic network of the epidemic pathogen Burkholderia cenocepacia J2315 via genome-scale reconstruction.

Fang K, Zhao H, Sun C, Lam CM, Chang S, Zhang K, Panda G, Godinho M, Martins dos Santos VA, Wang J.

BMC Syst Biol. 2011 May 25;5:83. doi: 10.1186/1752-0509-5-83.

PMID:
21609491
[PubMed - indexed for MEDLINE]
Free PMC Article
18.

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
19.

Genome-scale metabolic analysis of Clostridium thermocellum for bioethanol production.

Roberts SB, Gowen CM, Brooks JP, Fong SS.

BMC Syst Biol. 2010 Mar 22;4:31. doi: 10.1186/1752-0509-4-31.

PMID:
20307315
[PubMed - indexed for MEDLINE]
Free PMC Article
20.

High-throughput generation, optimization and analysis of genome-scale metabolic models.

Henry CS, DeJongh M, Best AA, Frybarger PM, Linsay B, Stevens RL.

Nat Biotechnol. 2010 Sep;28(9):977-82. doi: 10.1038/nbt.1672. Epub 2010 Aug 29.

PMID:
20802497
[PubMed - indexed for MEDLINE]

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