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Results: 1 to 20 of 33


BioPreDyn-bench: a suite of benchmark problems for dynamic modelling in systems biology.

Villaverde AF, Henriques D, Smallbone K, Bongard S, Schmid J, Cicin-Sain D, Crombach A, Saez-Rodriguez J, Mauch K, Balsa-Canto E, Mendes P, Jaeger J, Banga JR.

BMC Syst Biol. 2015 Feb 20;9(1):8. doi: 10.1186/s12918-015-0144-4.


Playing off the curve - testing quantitative predictions of skill acquisition theories in development of chess performance.

Gaschler R, Progscha J, Smallbone K, Ram N, Bilalić M.

Front Psychol. 2014 Aug 22;5:923. doi: 10.3389/fpsyg.2014.00923. eCollection 2014.


A mathematical model of the colon crypt capturing compositional dynamic interactions between cell types.

Smallbone K, M Corfe B.

Int J Exp Pathol. 2014 Feb;95(1):1-7. doi: 10.1111/iep.12062. Epub 2013 Dec 20.


Systematic construction of kinetic models from genome-scale metabolic networks.

Stanford NJ, Lubitz T, Smallbone K, Klipp E, Mendes P, Liebermeister W.

PLoS One. 2013 Nov 14;8(11):e79195. doi: 10.1371/journal.pone.0079195. eCollection 2013.


Version 6 of the consensus yeast metabolic network refines biochemical coverage and improves model performance.

Heavner BD, Smallbone K, Price ND, Walker LP.

Database (Oxford). 2013 Aug 9;2013:bat059. doi: 10.1093/database/bat059. Print 2013.


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.


Kinetic modeling of metabolic pathways: application to serine biosynthesis.

Smallbone K, Stanford NJ.

Methods Mol Biol. 2013;985:113-21. doi: 10.1007/978-1-62703-299-5_7.


Mechanistic modelling of cancer: some reflections from software engineering and philosophy of science.

Cañete-Valdeón JM, Wieringa R, Smallbone K.

Naturwissenschaften. 2012 Dec;99(12):973-83. doi: 10.1007/s00114-012-0991-4. Epub 2012 Nov 13.


Improving metabolic flux predictions using absolute gene expression data.

Lee D, Smallbone K, Dunn WB, Murabito E, Winder CL, Kell DB, Mendes P, Swainston N.

BMC Syst Biol. 2012 Jun 19;6:73. doi: 10.1186/1752-0509-6-73.


Yeast 5 - an expanded reconstruction of the Saccharomyces cerevisiae metabolic network.

Heavner BD, Smallbone K, Barker B, Mendes P, Walker LP.

BMC Syst Biol. 2012 Jun 4;6:55. doi: 10.1186/1752-0509-6-55.


Modelling acidosis and the cell cycle in multicellular tumour spheroids.

Tindall MJ, Dyson L, Smallbone K, Maini PK.

J Theor Biol. 2012 Apr 7;298:107-15. doi: 10.1016/j.jtbi.2011.11.009. Epub 2011 Dec 8.


The SuBliMinaL Toolbox: automating steps in the reconstruction of metabolic networks.

Swainston N, Smallbone K, Mendes P, Kell D, Paton N.

J Integr Bioinform. 2011 Nov 18;8(2):186. doi: 10.2390/biecoll-jib-2011-186.


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.


A probabilistic approach to identify putative drug targets in biochemical networks.

Murabito E, Smallbone K, Swinton J, Westerhoff HV, Steuer R.

J R Soc Interface. 2011 Jun 6;8(59):880-95. doi: 10.1098/rsif.2010.0540. Epub 2010 Dec 1.


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.


Enzyme kinetics informatics: from instrument to browser.

Swainston N, Golebiewski M, Messiha HL, Malys N, Kania R, Kengne S, Krebs O, Mir S, Sauer-Danzwith H, Smallbone K, Weidemann A, Wittig U, Kell DB, Mendes P, Müller W, Paton NW, Rojas I.

FEBS J. 2010 Sep;277(18):3769-79. doi: 10.1111/j.1742-4658.2010.07778.x. Epub 2010 Aug 3.

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