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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.PMID: 19038030 [PubMed - indexed for MEDLINE]Related articlesFree article

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]Related articlesFree article

Large-scale identification of genetic design strategies using local search.

Lun DS, Rockwell G, Guido NJ, Baym M, Kelner JA, Berger B, Galagan JE, Church GM.

Mol Syst Biol. 2009;5:296. Epub 2009 Aug 18.PMID: 19690565 [PubMed - indexed for MEDLINE]Related articlesFree article

Metabolic flux balance analysis and the in silico analysis of Escherichia coli K-12 gene deletions.

Edwards JS, Palsson BO.

BMC Bioinformatics. 2000;1:1. Epub 2000 Jul 27.PMID: 11001586 [PubMed - indexed for MEDLINE]Related articlesFree article

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 [PubMed - indexed for MEDLINE]Related articles

In silico metabolic pathway analysis and design: succinic acid production by metabolically engineered Escherichia coli as an example.

Lee SY, Hong SH, Moon SY.

Genome Inform. 2002;13:214-23.PMID: 14571390 [PubMed - indexed for MEDLINE]Related articlesFree article

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]Related articlesFree article

Estimating the size of the solution space of metabolic networks.

Braunstein A, Mulet R, Pagnani A.

BMC Bioinformatics. 2008 May 19;9:240.PMID: 18489757 [PubMed - indexed for MEDLINE]Related articlesFree article

Metabolic engineering of Escherichia coli for enhanced production of succinic acid, based on genome comparison and in silico gene knockout simulation.

Lee SJ, Lee DY, Kim TY, Kim BH, Lee J, Lee SY.

Appl Environ Microbiol. 2005 Dec;71(12):7880-7.PMID: 16332763 [PubMed - indexed for MEDLINE]Related articlesFree article

Description and interpretation of adaptive evolution of Escherichia coli K-12 MG1655 by using a genome-scale in silico metabolic model.

Fong SS, Marciniak JY, Palsson BØ.

J Bacteriol. 2003 Nov;185(21):6400-8.PMID: 14563875 [PubMed - indexed for MEDLINE]Related articlesFree article

Algorithms for computing parsimonious evolutionary scenarios for genome evolution, the last universal common ancestor and dominance of horizontal gene transfer in the evolution of prokaryotes.

Mirkin BG, Fenner TI, Galperin MY, Koonin EV.

BMC Evol Biol. 2003 Jan 6;3:2. Epub 2003 Jan 6.PMID: 12515582 [PubMed - indexed for MEDLINE]Related articlesFree article

Origin of co-expression patterns in E. coli and S. cerevisiae emerging from reverse engineering algorithms.

Zampieri M, Soranzo N, Bianchini D, Altafini C.

PLoS One. 2008 Aug 20;3(8):e2981.PMID: 18714358 [PubMed - indexed for MEDLINE]Related articlesFree article

Escherichia coli K-12 undergoes adaptive evolution to achieve in silico predicted optimal growth.

Ibarra RU, Edwards JS, Palsson BO.

Nature. 2002 Nov 14;420(6912):186-9.PMID: 12432395 [PubMed - indexed for MEDLINE]Related articles

Optknock: a bilevel programming framework for identifying gene knockout strategies for microbial strain optimization.

Burgard AP, Pharkya P, Maranas CD.

Biotechnol Bioeng. 2003 Dec 20;84(6):647-57.PMID: 14595777 [PubMed - indexed for MEDLINE]Related articles

Large-scale evaluation of in silico gene deletions in Saccharomyces cerevisiae.

Förster J, Famili I, Palsson BO, Nielsen J.

OMICS. 2003 Summer;7(2):193-202.PMID: 14506848 [PubMed - indexed for MEDLINE]Related articles

Understanding the adaptive growth strategy of Lactobacillus plantarum by in silico optimisation.

Teusink B, Wiersma A, Jacobs L, Notebaart RA, Smid EJ.

PLoS Comput Biol. 2009 Jun;5(6):e1000410. Epub 2009 Jun 12.PMID: 19521528 [PubMed - indexed for MEDLINE]Related articlesFree article

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.PMID: 18218092 [PubMed - indexed for MEDLINE]Related articlesFree article

Including metabolite concentrations into flux balance analysis: thermodynamic realizability as a constraint on flux distributions in metabolic networks.

Hoppe A, Hoffmann S, Holzhütter HG.

BMC Syst Biol. 2007 Jun 1;1:23.PMID: 17543097 [PubMed - indexed for MEDLINE]Related articlesFree article

OptStrain: a computational framework for redesign of microbial production systems.

Pharkya P, Burgard AP, Maranas CD.

Genome Res. 2004 Nov;14(11):2367-76.PMID: 15520298 [PubMed - indexed for MEDLINE]Related articlesFree article

Extraction of elementary rate constants from global network analysis of E. coli central metabolism.

Zhao J, Ridgway D, Broderick G, Kovalenko A, Ellison M.

BMC Syst Biol. 2008 May 7;2:41.PMID: 18462493 [PubMed - indexed for MEDLINE]Related articlesFree article