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Items: 1 to 20 of 48

1.

Constraint-based analysis of metabolic capacity of Salmonella typhimurium during host-pathogen interaction.

Raghunathan A, Reed J, Shin S, Palsson B, Daefler S.

BMC Syst Biol. 2009 Apr 8;3:38. doi: 10.1186/1752-0509-3-38.

2.

Flux balance analysis of biological systems: applications and challenges.

Raman K, Chandra N.

Brief Bioinform. 2009 Jul;10(4):435-49. doi: 10.1093/bib/bbp011. Epub 2009 Mar 15.

PMID:
19287049
3.

Elementary mode analysis: a useful metabolic pathway analysis tool for characterizing cellular metabolism.

Trinh CT, Wlaschin A, Srienc F.

Appl Microbiol Biotechnol. 2009 Jan;81(5):813-26. doi: 10.1007/s00253-008-1770-1. Epub 2008 Nov 15. Review.

4.

Modes and cuts in metabolic networks: complexity and algorithms.

Acuña V, Chierichetti F, Lacroix V, Marchetti-Spaccamela A, Sagot MF, Stougie L.

Biosystems. 2009 Jan;95(1):51-60. doi: 10.1016/j.biosystems.2008.06.015. Epub 2008 Aug 3. Review.

PMID:
18722501
5.

Large-scale computation of elementary flux modes with bit pattern trees.

Terzer M, Stelling J.

Bioinformatics. 2008 Oct 1;24(19):2229-35. doi: 10.1093/bioinformatics/btn401. Epub 2008 Aug 1.

PMID:
18676417
6.

Integrating metabolic, transcriptional regulatory and signal transduction models in Escherichia coli.

Covert MW, Xiao N, Chen TJ, Karr JR.

Bioinformatics. 2008 Sep 15;24(18):2044-50. doi: 10.1093/bioinformatics/btn352. Epub 2008 Jul 10.

PMID:
18621757
7.

The growing scope of applications of genome-scale metabolic reconstructions using Escherichia coli.

Feist AM, Palsson BØ.

Nat Biotechnol. 2008 Jun;26(6):659-67. doi: 10.1038/nbt1401. Review.

8.

Highway or byway: the metabolic role of the GABA shunt in plants.

Fait A, Fromm H, Walter D, Galili G, Fernie AR.

Trends Plant Sci. 2008 Jan;13(1):14-9. Epub 2007 Dec 21. Review.

PMID:
18155636
9.

Structural robustness of metabolic networks with respect to multiple knockouts.

Behre J, Wilhelm T, von Kamp A, Ruppin E, Schuster S.

J Theor Biol. 2008 Jun 7;252(3):433-41. Epub 2007 Oct 9.

PMID:
18023456
10.

Response of fluxome and metabolome to temperature-induced recombinant protein synthesis in Escherichia coli.

Wittmann C, Weber J, Betiku E, Krömer J, Böhm D, Rinas U.

J Biotechnol. 2007 Dec 1;132(4):375-84. Epub 2007 Jul 10.

PMID:
17689798
11.

A genome-scale metabolic reconstruction for Escherichia coli K-12 MG1655 that accounts for 1260 ORFs and thermodynamic information.

Feist AM, Henry CS, Reed JL, Krummenacker M, Joyce AR, Karp PD, Broadbelt LJ, Hatzimanikatis V, Palsson BØ.

Mol Syst Biol. 2007;3:121. Epub 2007 Jun 26.

12.

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.

14.

A genome-scale computational study of the interplay between transcriptional regulation and metabolism.

Shlomi T, Eisenberg Y, Sharan R, Ruppin E.

Mol Syst Biol. 2007;3:101. Epub 2007 Apr 17.

15.

Fluxome analysis using GC-MS.

Wittmann C.

Microb Cell Fact. 2007 Feb 7;6:6.

16.

Global reconstruction of the human metabolic network based on genomic and bibliomic data.

Duarte NC, Becker SA, Jamshidi N, Thiele I, Mo ML, Vo TD, Srivas R, Palsson BØ.

Proc Natl Acad Sci U S A. 2007 Feb 6;104(6):1777-82. Epub 2007 Jan 31.

17.

Algorithmic approaches for computing elementary modes in large biochemical reaction networks.

Klamt S, Gagneur J, von Kamp A.

Syst Biol (Stevenage). 2005 Dec;152(4):249-55.

PMID:
16986267
18.

Modeling methanogenesis with a genome-scale metabolic reconstruction of Methanosarcina barkeri.

Feist AM, Scholten JC, Palsson BØ, Brockman FJ, Ideker T.

Mol Syst Biol. 2006;2:2006.0004. Epub 2006 Jan 31.

19.

Metatool 5.0: fast and flexible elementary modes analysis.

von Kamp A, Schuster S.

Bioinformatics. 2006 Aug 1;22(15):1930-1. Epub 2006 May 26.

PMID:
16731697
20.

Metabolic pathway analysis for rational design of L-methionine production by Escherichia coli and Corynebacterium glutamicum.

Krömer JO, Wittmann C, Schröder H, Heinzle E.

Metab Eng. 2006 Jul;8(4):353-69. Epub 2006 Apr 18.

PMID:
16621639

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