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Items: 1 to 20 of 26


The clinical impact of platelet-rich plasma on tendinopathy compared to placebo or dry needling injections: A meta-analysis.

Tsikopoulos K, Tsikopoulos I, Simeonidis E, Papathanasiou E, Haidich AB, Anastasopoulos N, Natsis K.

Phys Ther Sport. 2016 Jan;17:87-94. doi: 10.1016/j.ptsp.2015.06.003. Epub 2015 Jun 18. Review.


Integrating food webs with metabolic networks: modeling contaminant degradation in marine ecosystems.

Basler G, Simeonidis E.

Front Genet. 2015 Feb 3;6:20. doi: 10.3389/fgene.2015.00020. eCollection 2015. No abstract available.


Genome-scale modeling for metabolic engineering.

Simeonidis E, Price ND.

J Ind Microbiol Biotechnol. 2015 Mar;42(3):327-38. doi: 10.1007/s10295-014-1576-3. Epub 2015 Jan 13. Review.


Macromolecular networks and intelligence in microorganisms.

Westerhoff HV, Brooks AN, Simeonidis E, García-Contreras R, He F, Boogerd FC, Jackson VJ, Goncharuk V, Kolodkin A.

Front Microbiol. 2014 Jul 22;5:379. doi: 10.3389/fmicb.2014.00379. eCollection 2014.


MediaDB: a database of microbial growth conditions in defined media.

Richards MA, Cassen V, Heavner BD, Ajami NE, Herrmann A, Simeonidis E, Price ND.

PLoS One. 2014 Aug 6;9(8):e103548. doi: 10.1371/journal.pone.0103548. eCollection 2014.


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.


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.


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.


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.


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.


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.


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.


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.


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.


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.


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.


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.


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.


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.


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.

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