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Experimental and computational assessment of conditionally essential genes in Escherichia coli.

Joyce AR, Reed JL, White A, Edwards R, Osterman A, Baba T, Mori H, Lesely SA, Palsson BØ, Agarwalla S.

J Bacteriol. 2006 Dec;188(23):8259-71. Epub 2006 Sep 29.


A complete collection of single-gene deletion mutants of Acinetobacter baylyi ADP1.

de Berardinis V, Vallenet D, Castelli V, Besnard M, Pinet A, Cruaud C, Samair S, Lechaplais C, Gyapay G, Richez C, Durot M, Kreimeyer A, Le Fèvre F, Schächter V, Pezo V, Döring V, Scarpelli C, Médigue C, Cohen GN, Marlière P, Salanoubat M, Weissenbach J.

Mol Syst Biol. 2008;4:174. doi: 10.1038/msb.2008.10. Epub 2008 Mar 4.


Genome-scale analysis to the impact of gene deletion on the metabolism of E. coli: constraint-based simulation approach.

Xu Z, Sun X, Yu S.

BMC Bioinformatics. 2009 Jan 30;10 Suppl 1:S62. doi: 10.1186/1471-2105-10-S1-S62.


In silico deletion of PtsG gene in Escherichia coli genome-scale model predicts increased succinate production from glycerol.

Mienda BS, Shamsir MS.

J Biomol Struct Dyn. 2015;33(11):2380-9. doi: 10.1080/07391102.2015.1036461. Epub 2015 Jun 8.


The Genome-Wide Interaction Network of Nutrient Stress Genes in Escherichia coli.

Côté JP, French S, Gehrke SS, MacNair CR, Mangat CS, Bharat A, Brown ED.

MBio. 2016 Nov 22;7(6). pii: e01714-16. doi: 10.1128/mBio.01714-16. Erratum in: MBio. 2016 Dec 20;7(6):.


Isozymes of S-adenosylmethionine synthetase are encoded by tandemly duplicated genes in Escherichia coli.

Satishchandran C, Taylor JC, Markham GD.

Mol Microbiol. 1993 Aug;9(4):835-46.


An expanded genome-scale model of Escherichia coli K-12 (iJR904 GSM/GPR).

Reed JL, Vo TD, Schilling CH, Palsson BO.

Genome Biol. 2003;4(9):R54. Epub 2003 Aug 28.


Integrating high-throughput and computational data elucidates bacterial networks.

Covert MW, Knight EM, Reed JL, Herrgard MJ, Palsson BO.

Nature. 2004 May 6;429(6987):92-6.


Towards the identification of essential genes using targeted genome sequencing and comparative analysis.

Gustafson AM, Snitkin ES, Parker SC, DeLisi C, Kasif S.

BMC Genomics. 2006 Oct 19;7:265.


Nucleotide biosynthesis is critical for growth of bacteria in human blood.

Samant S, Lee H, Ghassemi M, Chen J, Cook JL, Mankin AS, Neyfakh AA.

PLoS Pathog. 2008 Feb 8;4(2):e37. doi: 10.1371/journal.ppat.0040037.


Bacillus subtilis and Escherichia coli essential genes and minimal cell factories after one decade of genome engineering.

Juhas M, Reuß DR, Zhu B, Commichau FM.

Microbiology. 2014 Nov;160(Pt 11):2341-51. doi: 10.1099/mic.0.079376-0. Epub 2014 Aug 4. Review.


Mapping bacterial functional networks and pathways in Escherichia Coli using synthetic genetic arrays.

Gagarinova A, Babu M, Greenblatt J, Emili A.

J Vis Exp. 2012 Nov 12;(69). pii: 4056. doi: 10.3791/4056.


SecG function and phospholipid metabolism in Escherichia coli.

Flower AM.

J Bacteriol. 2001 Mar;183(6):2006-12.


GrowMatch: an automated method for reconciling in silico/in vivo growth predictions.

Kumar VS, Maranas CD.

PLoS Comput Biol. 2009 Mar;5(3):e1000308. doi: 10.1371/journal.pcbi.1000308. Epub 2009 Mar 13.


Genome-scale identification of conditionally essential genes in E. coli by DNA microarrays.

Tong X, Campbell JW, Balázsi G, Kay KA, Wanner BL, Gerdes SY, Oltvai ZN.

Biochem Biophys Res Commun. 2004 Sep 10;322(1):347-54.


Transcriptional regulation in constraints-based metabolic models of Escherichia coli.

Covert MW, Palsson BØ.

J Biol Chem. 2002 Aug 2;277(31):28058-64. Epub 2002 May 10.


A kinetic model of Escherichia coli core metabolism satisfying multiple sets of mutant flux data.

Khodayari A, Zomorrodi AR, Liao JC, Maranas CD.

Metab Eng. 2014 Sep;25:50-62. doi: 10.1016/j.ymben.2014.05.014. Epub 2014 Jun 10.


The global transcriptional regulatory network for metabolism in Escherichia coli exhibits few dominant functional states.

Barrett CL, Herring CD, Reed JL, Palsson BO.

Proc Natl Acad Sci U S A. 2005 Dec 27;102(52):19103-8. Epub 2005 Dec 15.

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