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Items: 1 to 20 of 26

1.

Can the whole be less than the sum of its parts? Pathway analysis in genome-scale metabolic networks using elementary flux patterns.

Kaleta C, de Figueiredo LF, Schuster S.

Genome Res. 2009 Oct;19(10):1872-83. doi: 10.1101/gr.090639.108. Epub 2009 Jun 18.

2.

Detecting structural invariants in biological reaction networks.

Behre J, de Figueiredo LF, Schuster S, Kaleta C.

Methods Mol Biol. 2012;804:377-407. doi: 10.1007/978-1-61779-361-5_20. Review.

PMID:
22144164
3.

Advances in network-based metabolic pathway analysis and gene expression data integration.

Rezola A, Pey J, Tobalina L, Rubio Á, Beasley JE, Planes FJ.

Brief Bioinform. 2015 Mar;16(2):265-79. doi: 10.1093/bib/bbu009. Epub 2014 Mar 13. Review.

PMID:
24626528
4.

Flux analysis and metabolomics for systematic metabolic engineering of microorganisms.

Toya Y, Shimizu H.

Biotechnol Adv. 2013 Nov;31(6):818-26. doi: 10.1016/j.biotechadv.2013.05.002. Epub 2013 May 13. Review.

PMID:
23680193
5.

Constraining the metabolic genotype-phenotype relationship using a phylogeny of in silico methods.

Lewis NE, Nagarajan H, Palsson BO.

Nat Rev Microbiol. 2012 Feb 27;10(4):291-305. doi: 10.1038/nrmicro2737. Review.

6.

Elementary flux modes in a nutshell: properties, calculation and applications.

Zanghellini J, Ruckerbauer DE, Hanscho M, Jungreuthmayer C.

Biotechnol J. 2013 Sep;8(9):1009-16. doi: 10.1002/biot.201200269. Epub 2013 Jun 21. Review.

7.

Software applications toward quantitative metabolic flux analysis and modeling.

Dandekar T, Fieselmann A, Majeed S, Ahmed Z.

Brief Bioinform. 2014 Jan;15(1):91-107. doi: 10.1093/bib/bbs065. Epub 2012 Nov 9. Review.

PMID:
23142828
8.

Hierarchical decomposition of metabolic networks using k-modules.

Reimers AC.

Biochem Soc Trans. 2015 Dec;43(6):1146-50. doi: 10.1042/BST20150143. Review.

PMID:
26614652
9.

Genome-scale metabolic networks.

Terzer M, Maynard ND, Covert MW, Stelling J.

Wiley Interdiscip Rev Syst Biol Med. 2009 Nov-Dec;1(3):285-97. doi: 10.1002/wsbm.37. Review.

PMID:
20835998
10.

[Applications of elementary mode analysis in biological network and pathway analysis].

Zhao Q, Yu S, Shi J.

Sheng Wu Gong Cheng Xue Bao. 2013 Jun;29(6):701-15. Review. Chinese.

PMID:
24063231
11.

Metabolic network modeling with model organisms.

Yilmaz LS, Walhout AJ.

Curr Opin Chem Biol. 2017 Feb;36:32-39. doi: 10.1016/j.cbpa.2016.12.025. Epub 2017 Jan 12. Review.

PMID:
28088694
12.

Genome-Scale Modeling of Thermophilic Microorganisms.

Dahal S, Poudel S, Thompson RA.

Adv Biochem Eng Biotechnol. 2017;160:103-119. doi: 10.1007/10_2016_45. Review.

PMID:
27913830
13.

Exploiting stoichiometric redundancies for computational efficiency and network reduction.

Ingalls BP, Bembenek E.

In Silico Biol. 2015;12(1-2):55-67. doi: 10.3233/ISB-140464. Review.

14.

From elementary flux modes to elementary flux vectors: Metabolic pathway analysis with arbitrary linear flux constraints.

Klamt S, Regensburger G, Gerstl MP, Jungreuthmayer C, Schuster S, Mahadevan R, Zanghellini J, Müller S.

PLoS Comput Biol. 2017 Apr 13;13(4):e1005409. doi: 10.1371/journal.pcbi.1005409. eCollection 2017 Apr. Review.

15.

Applications of genome-scale metabolic network model in metabolic engineering.

Kim B, Kim WJ, Kim DI, Lee SY.

J Ind Microbiol Biotechnol. 2015 Mar;42(3):339-48. doi: 10.1007/s10295-014-1554-9. Epub 2014 Dec 3. Review.

PMID:
25465049
16.

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.

17.

Genome-scale modelling of microbial metabolism with temporal and spatial resolution.

Henson MA.

Biochem Soc Trans. 2015 Dec;43(6):1164-71. doi: 10.1042/BST20150146. Review.

18.

Metabolic pathways in the post-genome era.

Papin JA, Price ND, Wiback SJ, Fell DA, Palsson BO.

Trends Biochem Sci. 2003 May;28(5):250-8. Review.

PMID:
12765837
19.

Which metabolic pathways generate and characterize the flux space? A comparison among elementary modes, extreme pathways and minimal generators.

Llaneras F, Picó J.

J Biomed Biotechnol. 2010;2010:753904. doi: 10.1155/2010/753904. Epub 2010 May 11. Review.

20.

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.

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