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1.

AraGEM, a genome-scale reconstruction of the primary metabolic network in Arabidopsis.

de Oliveira Dal'Molin CG, Quek LE, Palfreyman RW, Brumbley SM, Nielsen LK.

Plant Physiol. 2010 Feb;152(2):579-89. doi: 10.1104/pp.109.148817. Epub 2009 Dec 31.

2.

AlgaGEM--a genome-scale metabolic reconstruction of algae based on the Chlamydomonas reinhardtii genome.

Dal'Molin CG, Quek LE, Palfreyman RW, Nielsen LK.

BMC Genomics. 2011 Dec 22;12 Suppl 4:S5. doi: 10.1186/1471-2164-12-S4-S5. Epub 2011 Dec 22.

3.

Zea mays iRS1563: a comprehensive genome-scale metabolic reconstruction of maize metabolism.

Saha R, Suthers PF, Maranas CD.

PLoS One. 2011;6(7):e21784. doi: 10.1371/journal.pone.0021784. Epub 2011 Jul 6.

4.

Are we ready for genome-scale modeling in plants?

Collakova E, Yen JY, Senger RS.

Plant Sci. 2012 Aug;191-192:53-70. doi: 10.1016/j.plantsci.2012.04.010. Epub 2012 May 3. Review.

5.

C4GEM, a genome-scale metabolic model to study C4 plant metabolism.

Dal'Molin CG, Quek LE, Palfreyman RW, Brumbley SM, Nielsen LK.

Plant Physiol. 2010 Dec;154(4):1871-85. doi: 10.1104/pp.110.166488. Epub 2010 Oct 25.

6.

On the reconstruction of the Mus musculus genome-scale metabolic network model.

Quek LE, Nielsen LK.

Genome Inform. 2008;21:89-100.

PMID:
19425150
7.

Genome-scale reconstruction and in silico analysis of the Clostridium acetobutylicum ATCC 824 metabolic network.

Lee J, Yun H, Feist AM, Palsson BØ, Lee SY.

Appl Microbiol Biotechnol. 2008 Oct;80(5):849-62. doi: 10.1007/s00253-008-1654-4. Epub 2008 Aug 29.

PMID:
18758767
8.

An in silico assessment of gene function and organization of the phenylpropanoid pathway metabolic networks in Arabidopsis thaliana and limitations thereof.

Costa MA, Collins RE, Anterola AM, Cochrane FC, Davin LB, Lewis NG.

Phytochemistry. 2003 Nov;64(6):1097-112.

PMID:
14568076
9.

Genome-scale modeling and in silico analysis of mouse cell metabolic network.

Selvarasu S, Karimi IA, Ghim GH, Lee DY.

Mol Biosyst. 2010 Jan;6(1):152-61. doi: 10.1039/b912865d. Epub 2009 Sep 2.

PMID:
20024077
10.

Building and analysing genome-scale metabolic models.

Fell DA, Poolman MG, Gevorgyan A.

Biochem Soc Trans. 2010 Oct;38(5):1197-201. doi: 10.1042/BST0381197.

PMID:
20863283
11.

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
12.

The Edinburgh human metabolic network reconstruction and its functional analysis.

Ma H, Sorokin A, Mazein A, Selkov A, Selkov E, Demin O, Goryanin I.

Mol Syst Biol. 2007;3:135. Epub 2007 Sep 18.

13.

Principal transcriptional regulation and genome-wide system interactions of the Asp-family and aromatic amino acid networks of amino acid metabolism in plants.

Less H, Angelovici R, Tzin V, Galili G.

Amino Acids. 2010 Oct;39(4):1023-8. doi: 10.1007/s00726-010-0566-7. Epub 2010 Apr 4.

PMID:
20364431
14.

Reconstruction of Arabidopsis metabolic network models accounting for subcellular compartmentalization and tissue-specificity.

Mintz-Oron S, Meir S, Malitsky S, Ruppin E, Aharoni A, Shlomi T.

Proc Natl Acad Sci U S A. 2012 Jan 3;109(1):339-44. doi: 10.1073/pnas.1100358109. Epub 2011 Dec 19.

15.

Genome-scale metabolic network analysis of the opportunistic pathogen Pseudomonas aeruginosa PAO1.

Oberhardt MA, Puchałka J, Fryer KE, Martins dos Santos VA, Papin JA.

J Bacteriol. 2008 Apr;190(8):2790-803. doi: 10.1128/JB.01583-07. Epub 2008 Jan 11.

16.

An in silico compartmentalized metabolic model of Brassica napus enables the systemic study of regulatory aspects of plant central metabolism.

Pilalis E, Chatziioannou A, Thomasset B, Kolisis F.

Biotechnol Bioeng. 2011 Jul;108(7):1673-82. doi: 10.1002/bit.23107. Epub 2011 Mar 11.

PMID:
21337341
17.

Genome-scale metabolic network analysis and drug targeting of multi-drug resistant pathogen Acinetobacter baumannii AYE.

Kim HU, Kim TY, Lee SY.

Mol Biosyst. 2010 Feb;6(2):339-48. doi: 10.1039/b916446d. Epub 2009 Dec 8.

PMID:
20094653
18.

A genome-scale metabolic model of Arabidopsis and some of its properties.

Poolman MG, Miguet L, Sweetlove LJ, Fell DA.

Plant Physiol. 2009 Nov;151(3):1570-81. doi: 10.1104/pp.109.141267. Epub 2009 Sep 15.

19.

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.

20.

Targeted metabolic reconstruction: a novel approach for the characterization of plant-pathogen interactions.

Pinzón A, Rodriguez-R LM, González A, Bernal A, Restrepo S.

Brief Bioinform. 2011 Mar;12(2):151-62. doi: 10.1093/bib/bbq009. Epub 2010 Mar 29.

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