Doctoral Training Centre - Integrative Systems Biology
Publications by DTC students:
2012
M. Goodfellow, K. Schindler, G. Baier, Self-organised transients in a neural mass model of epileptogenic tissue dynamics. NeuroImage 59, 2644-2660 (2012).
M. Goodfellow, P. Taylor, Y. Wang, D. Garry, G. Baier, Modelling the role of tissue heterogeneity in epileptic rhythms. Eur. J. Neurosci. (2012) accepted for publication.
2011
S. Geenen, F.B. du Preez, M. Reed, H. Frederik Nijhout, J. Gerry Kenna, I.D. Wilson, H.V. Westerhoff, J.L. Snoep. A mathematical modelling approach to assessing the reliability of biomarkers of glutathione metabolism. Eur J Pharm Sci. 2011 Aug 24. [Epub ahead of print]
B.G. Small, B.W. McColl, R. Allmendinger, J. Pahle, G. Lopez-Castejon, N.J. Rothwell, J. Knowles, P. Mendes, D. Brough, D.B. Kell, Anti-inflammatory small molecule combinations discovered using evolutionary computing. Nature Chem Biol. 7, 902-908 (2011).
S. Rehman, R. Goodacre, P.J. Day, A. Bayat and H.V. Westerhoff, Dupuytren's: a Systems Biology Disease. Arthritis Research & Therapy 13, 238 (2011).
S. Geenen, Michopoulos F, Kenna JG, Kolaja KL, Westerhoff HV, Wilson I. HPLC-MS/MS methods for the quantitative analysis of 5-oxoproline (pyroglutamate) in rat plasma and hepatic cell line culture medium. J Pharm Biomed Anal. 2011 Nov 1; 56 (3):655-663.
S. Geenen, Michopoulos F, Kenna JG, Kolaja KL, Westerhoff HV, Wilson I. HPLC-MS/MS methods for the quantitative analysis of ophthalmic acid in rodent plasma and hepatic cell line culture medium. J Pharm Biomed Anal. 2011 Apr 5;54(5):1128-35. Epub 2010 Dec 2.
M. Goodfellow, K. Schindler, G. Baier, Intermittent spike-wave dynamics in a heterogeneous, spatially extended neural mass model. NeuroImage 55, 920-932 (2011).
B. Bonev, A. Pisco, and N. Papalopulu, microRNA-9 reveals regional diversity of neural progenitors along the anterior-posterior axis. Dev. Cell 20 (1), 19-32 (2011).
P. Taylor, G. Baier, A Spatially Extended Neural Field Model for Spike-Wave Dynamics. J. Comput. Neurosci. 31, 679-684 (2011). Online: DOI 10.1007/s10827-011-0332-1.
M. Swat, S. M. Kielbasa, S. Polak, B. Olivier, F.J. Bruggeman, M. Quinton Tulloch, J.L. Snoep, A.J. Verhoeven, and H.V. Westerhoff. What it takes to understand and cure a living system: computational systems biology and a systems biology-driven pharmacokinetics–pharmacodynamics platform. Interface Focus 1 (1), 16-23 (2011). Published ahead of print December 8, 2010, doi:10.1098/rsfs.2010.0011
2010
Maya-Mendoza A, Olivares-Chauvet P, Shaw A, Jackson DA, 2010. S Phase Progression in Human Cells Is Dictated by the Genetic Continuity of DNA Foci. PLoS Genet 6(4): e1000900. doi:10.1371/journal.pgen.1000900
Martin C, Chen S, Heilos D, Sauer G, Hunt J, Shaw AG, Sims PF, Jackson DA, Lovric J. (2010). Changed genome heterochromatinization upon prolonged activation of Raf/ERK signalling pathway. PLoS ONE, 5(10), e13322. eScholarID:111927
Shaw A, Olivares-Chauvet P, Maya-Mendoza A and Jackson DA. (2010). S-phase progression in mammalian cells: modelling the influence of nuclear organization. Chromosome Research, 18(1), 163-178. eScholarID:111910 | DOI:10.1007/s10577-010-9114-2
K. Li, W. Zhu, K. Zeng, Z. Zhang, J. Ye, W. Ou, S. Rehman, B. Heuer, S. Chen, Proteome characterization of cassava (Manihot esculenta Crantz) somatic embryos, plantlets and tuberous roots. Proteome Science 8(10), (2010). doi:10.1186/1477-5956-8-10
J.A. Logan, M.E. Kelly, D. Ayers. N. Shipillis, G. Baier, P.J.R. Day, Systems Biology and Modelling in Neuroblastoma: practicalities and perspectives. Expert Reviews in Molecular Diagnosics 10, 131-145 (2010).
Y. Al-Nuaimi, G. Baier, R. Watson, C.M. Chuong, R. Paus, The Cycling Hair Follicle as an Ideal Systems Biology Research Model. Exp. Dermatol. 19(8), 707-713(2010).
J.E. Kloepper, K. Sugawara, Y. Al-Nuaimi, E. Gaspar, N. van Beek and R. Paus. Methods in hair research: how to objectively distinguish between anagen and catagen in human hair follicle organ culture. Experimental Dermatology, Vol. 19, Issue 3, p 305-312 (2010).
Murabito E, Smallbone K, Swinton J, Westerhoff H V, Steuer R: A probabilistic approach to identify putative drug targets in biochemical networks. Journal of the Royal Society Interface. Published online before print, December 1, 2010
PD Dobson, K Smallbone, D Jameson, E Simeonidis, K Lanthaler, P Pir, C Lu, N Swainston, WB Dunn, P Fisher, D Hull, M Brown, O Oshota, NJ Stanford, DB Kell, RD King, SG Oliver, RD Stevens, P Mendes (2010). Further developments towards a genome-scale metabolic model of yeast. BMC Syst Biol 4:145.
doi:10.1186/1752-0509-4-145
E Simeonidis, E Murabito, K Smallbone, HV Westerhoff (2010). Why does yeast ferment? A flux balance analysis study. Biochem Soc Trans 38: 1225-1229. doi:10.1042/BST0381225
2009
E Murabito, E Simeonidis, K Smallbone, J Swinton (2009). Capturing the essence of a
metabolic network: A flux balance analysis approach. J Theor Biol 260: 445-452.
2008
S. Rehman, Salway F, Stanley JK, Ollier WE, Day P, Bayat A., Molecular phenotypic descriptors of Dupuytren's disease defined using informatics analysis of the transcriptome, J. Hand Surg.33 (3) (2008), pp. 359-372.
A. Bevilacqua, S.J. Wilkinson, R. Dimelow, Ettore Murabito, Samrina Rehman, M. Nardelli, K. van Eunen, S. Rossell, F.J. Bruggeman, N. Blüthgen, D. de Vos, J. Bouwman, B.M. Bakker and H.V.Westerhoff, Vertical systems biology; from DNA to flux and back. Chapter 4, in: A. Hetherington & C. Grierson (eds.), Practical Systems Biology, (2008), pp. 65-91. New York, Abington: Taylor & Francis.