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Items: 1 to 20 of 42

1.

A protocol for generating a high-quality genome-scale metabolic reconstruction.

Thiele I, Palsson BØ.

Nat Protoc. 2010 Jan;5(1):93-121. doi: 10.1038/nprot.2009.203. Epub 2010 Jan 7.

2.

Applications of genome-scale metabolic reconstructions.

Oberhardt MA, Palsson BØ, Papin JA.

Mol Syst Biol. 2009;5:320. doi: 10.1038/msb.2009.77. Epub 2009 Nov 3. Review.

3.

Whole-genome resequencing of Escherichia coli K-12 MG1655 undergoing short-term laboratory evolution in lactate minimal media reveals flexible selection of adaptive mutations.

Conrad TM, Joyce AR, Applebee MK, Barrett CL, Xie B, Gao Y, Palsson BØ.

Genome Biol. 2009;10(10):R118. doi: 10.1186/gb-2009-10-10-r118. Epub 2009 Oct 22.

4.

Three-dimensional structural view of the central metabolic network of Thermotoga maritima.

Zhang Y, Thiele I, Weekes D, Li Z, Jaroszewski L, Ginalski K, Deacon AM, Wooley J, Lesley SA, Wilson IA, Palsson B, Osterman A, Godzik A.

Science. 2009 Sep 18;325(5947):1544-9. doi: 10.1126/science.1174671.

5.

Metabolic reconfiguration precedes transcriptional regulation in the antioxidant response.

Ralser M, Wamelink MM, Latkolik S, Jansen EE, Lehrach H, Jakobs C.

Nat Biotechnol. 2009 Jul;27(7):604-5. doi: 10.1038/nbt0709-604. No abstract available.

PMID:
19587661
6.

Understanding the Warburg effect: the metabolic requirements of cell proliferation.

Vander Heiden MG, Cantley LC, Thompson CB.

Science. 2009 May 22;324(5930):1029-33. doi: 10.1126/science.1160809. Review.

7.

Gene expression profiling and the use of genome-scale in silico models of Escherichia coli for analysis: providing context for content.

Lewis NE, Cho BK, Knight EM, Palsson BO.

J Bacteriol. 2009 Jun;191(11):3437-44. doi: 10.1128/JB.00034-09. Epub 2009 Apr 10. Review. No abstract available.

8.

Genome-scale reconstruction of Escherichia coli's transcriptional and translational machinery: a knowledge base, its mathematical formulation, and its functional characterization.

Thiele I, Jamshidi N, Fleming RM, Palsson BØ.

PLoS Comput Biol. 2009 Mar;5(3):e1000312. doi: 10.1371/journal.pcbi.1000312. Epub 2009 Mar 13.

9.

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.

10.

Reconstruction of biochemical networks in microorganisms.

Feist AM, Herrgård MJ, Thiele I, Reed JL, Palsson BØ.

Nat Rev Microbiol. 2009 Feb;7(2):129-43. doi: 10.1038/nrmicro1949. Epub 2008 Dec 31. Review.

11.

Genome-scale models of bacterial metabolism: reconstruction and applications.

Durot M, Bourguignon PY, Schachter V.

FEMS Microbiol Rev. 2009 Jan;33(1):164-90. doi: 10.1111/j.1574-6976.2008.00146.x. Epub 2008 Dec 3. Review.

12.

Global and site-specific quantitative phosphoproteomics: principles and applications.

Macek B, Mann M, Olsen JV.

Annu Rev Pharmacol Toxicol. 2009;49:199-221. doi: 10.1146/annurev.pharmtox.011008.145606. Review.

PMID:
18834307
13.

Towards systems metabolic engineering of microorganisms for amino acid production.

Park JH, Lee SY.

Curr Opin Biotechnol. 2008 Oct;19(5):454-60. doi: 10.1016/j.copbio.2008.08.007. Epub 2008 Sep 6. Review.

PMID:
18760356
14.

Network-based prediction of human tissue-specific metabolism.

Shlomi T, Cabili MN, Herrgård MJ, Palsson BØ, Ruppin E.

Nat Biotechnol. 2008 Sep;26(9):1003-10. doi: 10.1038/nbt.1487.

PMID:
18711341
15.

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.

16.

Formulating genome-scale kinetic models in the post-genome era.

Jamshidi N, Palsson BØ.

Mol Syst Biol. 2008;4:171. doi: 10.1038/msb.2008.8. Epub 2008 Mar 4.

17.

New surveyor tools for charting microbial metabolic maps.

Breitling R, Vitkup D, Barrett MP.

Nat Rev Microbiol. 2008 Feb;6(2):156-61. Review.

PMID:
18026122
18.

Insights from site-specific phosphoproteomics in bacteria.

Soufi B, Jers C, Hansen ME, Petranovic D, Mijakovic I.

Biochim Biophys Acta. 2008 Jan;1784(1):186-92. Epub 2007 Aug 15. Review.

PMID:
17881301
19.
20.

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.

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