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Results: 1 to 20 of 21

1.

A model of yeast glycolysis based on a consistent kinetic characterisation of all its enzymes.

Smallbone K, Messiha HL, Carroll KM, Winder CL, Malys N, Dunn WB, Murabito E, Swainston N, Dada JO, Khan F, Pir P, Simeonidis E, Spasić I, Wishart J, Weichart D, Hayes NW, Jameson D, Broomhead DS, Oliver SG, Gaskell SJ, McCarthy JE, Paton NW, Westerhoff HV, Kell DB, Mendes P.

FEBS Lett. 2013 Sep 2;587(17):2832-41. doi: 10.1016/j.febslet.2013.06.043. Epub 2013 Jul 4.

PMID:
23831062
[PubMed - indexed for MEDLINE]
Free PMC Article
2.

A community-driven global reconstruction of human metabolism.

Thiele I, Swainston N, Fleming RM, Hoppe A, Sahoo S, Aurich MK, Haraldsdottir H, Mo ML, Rolfsson O, Stobbe MD, Thorleifsson SG, Agren R, Bölling C, Bordel S, Chavali AK, Dobson P, Dunn WB, Endler L, Hala D, Hucka M, Hull D, Jameson D, Jamshidi N, Jonsson JJ, Juty N, Keating S, Nookaew I, Le Novère N, Malys N, Mazein A, Papin JA, Price ND, Selkov E Sr, Sigurdsson MI, Simeonidis E, Sonnenschein N, Smallbone K, Sorokin A, van Beek JH, Weichart D, Goryanin I, Nielsen J, Westerhoff HV, Kell DB, Mendes P, Palsson BØ.

Nat Biotechnol. 2013 May;31(5):419-25. doi: 10.1038/nbt.2488. Epub 2013 Mar 3.

PMID:
23455439
[PubMed - indexed for MEDLINE]
Free PMC Article
3.

A guide to integrating transcriptional regulatory and metabolic networks using PROM (probabilistic regulation of metabolism).

Simeonidis E, Chandrasekaran S, Price ND.

Methods Mol Biol. 2013;985:103-12. doi: 10.1007/978-1-62703-299-5_6.

PMID:
23417801
[PubMed - indexed for MEDLINE]
4.

Mechanistic modeling of aberrant energy metabolism in human disease.

Sangar V, Eddy JA, Simeonidis E, Price ND.

Front Physiol. 2012 Oct 25;3:404. doi: 10.3389/fphys.2012.00404. eCollection 2012.

PMID:
23112774
[PubMed]
Free PMC Article
5.

Computing life: Add logos to biology and bios to physics.

Kolodkin A, Simeonidis E, Westerhoff HV.

Prog Biophys Mol Biol. 2013 Apr;111(2-3):69-74. doi: 10.1016/j.pbiomolbio.2012.10.003. Epub 2012 Oct 24.

PMID:
23103359
[PubMed - indexed for MEDLINE]
6.

Understanding complexity in neurodegenerative diseases: in silico reconstruction of emergence.

Kolodkin A, Simeonidis E, Balling R, Westerhoff HV.

Front Physiol. 2012 Jul 23;3:291. doi: 10.3389/fphys.2012.00291. eCollection 2012.

PMID:
22934043
[PubMed]
Free PMC Article
7.

Building a kinetic model of trehalose biosynthesis in Saccharomyces cerevisiae.

Smallbone K, Malys N, Messiha HL, Wishart JA, Simeonidis E.

Methods Enzymol. 2011;500:355-70. doi: 10.1016/B978-0-12-385118-5.00018-9.

PMID:
21943906
[PubMed - indexed for MEDLINE]
8.

Systematic integration of experimental data and models in systems biology.

Li P, Dada JO, Jameson D, Spasic I, Swainston N, Carroll K, Dunn W, Khan F, Malys N, Messiha HL, Simeonidis E, Weichart D, Winder C, Wishart J, Broomhead DS, Goble CA, Gaskell SJ, Kell DB, Westerhoff HV, Mendes P, Paton NW.

BMC Bioinformatics. 2010 Nov 29;11:582. doi: 10.1186/1471-2105-11-582.

PMID:
21114840
[PubMed - indexed for MEDLINE]
Free PMC Article
9.

Further developments towards a genome-scale metabolic model of yeast.

Dobson PD, Smallbone K, Jameson D, Simeonidis E, Lanthaler K, Pir P, Lu C, Swainston N, Dunn WB, Fisher P, Hull D, Brown M, Oshota O, Stanford NJ, Kell DB, King RD, Oliver SG, Stevens RD, Mendes P.

BMC Syst Biol. 2010 Oct 28;4:145. doi: 10.1186/1752-0509-4-145.

PMID:
21029416
[PubMed - indexed for MEDLINE]
Free PMC Article
10.

Why does yeast ferment? A flux balance analysis study.

Simeonidis E, Murabito E, Smallbone K, Westerhoff HV.

Biochem Soc Trans. 2010 Oct;38(5):1225-9. doi: 10.1042/BST0381225.

PMID:
20863289
[PubMed - indexed for MEDLINE]
11.

Systems biochemistry in practice: experimenting with modelling and understanding, with regulation and control.

Westerhoff HV, Verma M, Nardelli M, Adamczyk M, van Eunen K, Simeonidis E, Bakker BM.

Biochem Soc Trans. 2010 Oct;38(5):1189-96. doi: 10.1042/BST0381189. Review.

PMID:
20863282
[PubMed - indexed for MEDLINE]
12.

Towards a genome-scale kinetic model of cellular metabolism.

Smallbone K, Simeonidis E, Swainston N, Mendes P.

BMC Syst Biol. 2010 Jan 28;4:6. doi: 10.1186/1752-0509-4-6.

PMID:
20109182
[PubMed - indexed for MEDLINE]
Free PMC Article
13.

Systems biology: the elements and principles of life.

Westerhoff HV, Winder C, Messiha H, Simeonidis E, Adamczyk M, Verma M, Bruggeman FJ, Dunn W.

FEBS Lett. 2009 Dec 17;583(24):3882-90. doi: 10.1016/j.febslet.2009.11.018. Epub . Review.

PMID:
19913018
[PubMed - indexed for MEDLINE]
Free Article
14.

Capturing the essence of a metabolic network: a flux balance analysis approach.

Murabito E, Simeonidis E, Smallbone K, Swinton J.

J Theor Biol. 2009 Oct 7;260(3):445-52. doi: 10.1016/j.jtbi.2009.06.013. Epub 2009 Jun 21.

PMID:
19540851
[PubMed - indexed for MEDLINE]
15.

Flux balance analysis: a geometric perspective.

Smallbone K, Simeonidis E.

J Theor Biol. 2009 May 21;258(2):311-5. doi: 10.1016/j.jtbi.2009.01.027. Epub 2009 Feb 7.

PMID:
19490860
[PubMed - indexed for MEDLINE]
16.

KiPar, a tool for systematic information retrieval regarding parameters for kinetic modelling of yeast metabolic pathways.

Spasic I, Simeonidis E, Messiha HL, Paton NW, Kell DB.

Bioinformatics. 2009 Jun 1;25(11):1404-11. doi: 10.1093/bioinformatics/btp175. Epub 2009 Mar 31.

PMID:
19336445
[PubMed - indexed for MEDLINE]
Free Article
17.

A consensus yeast metabolic network reconstruction obtained from a community approach to systems biology.

Herrgård MJ, Swainston N, Dobson P, Dunn WB, Arga KY, Arvas M, Blüthgen N, Borger S, Costenoble R, Heinemann M, Hucka M, Le Novère N, Li P, Liebermeister W, Mo ML, Oliveira AP, Petranovic D, Pettifer S, Simeonidis E, Smallbone K, Spasić I, Weichart D, Brent R, Broomhead DS, Westerhoff HV, Kirdar B, Penttilä M, Klipp E, Palsson BØ, Sauer U, Oliver SG, Mendes P, Nielsen J, Kell DB.

Nat Biotechnol. 2008 Oct;26(10):1155-60. doi: 10.1038/nbt1492.

PMID:
18846089
[PubMed - indexed for MEDLINE]
Free PMC Article
18.

Something from nothing: bridging the gap between constraint-based and kinetic modelling.

Smallbone K, Simeonidis E, Broomhead DS, Kell DB.

FEBS J. 2007 Nov;274(21):5576-85. Epub 2007 Oct 8.

PMID:
17922843
[PubMed - indexed for MEDLINE]
19.

MINLP models for the synthesis of optimal peptide tags and downstream protein processing.

Simeonidis E, Pinto JM, Lienqueo ME, Tsoka S, Papageorgiou LG.

Biotechnol Prog. 2005 May-Jun;21(3):875-84.

PMID:
15932268
[PubMed - indexed for MEDLINE]
20.

Robustness of the p53 network and biological hackers.

Dartnell L, Simeonidis E, Hubank M, Tsoka S, Bogle ID, Papageorgiou LG.

FEBS Lett. 2005 Jun 6;579(14):3037-42.

PMID:
15896791
[PubMed - indexed for MEDLINE]
Free Article

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