Publications

K. Smallbone, H.L. Messiha, K.M. Carroll, C.L. Winder, N. Malys, W.B. Dunn, E. Murabito, N. Swainston, J.O. Dada, F. Khan, P. Pir, E. Simeonidis, I. Spasic, J. Wishart, D. Weichart, N.W. Hayes, D. Jameson, D.S. Broomhead, S.G. Oliver, S.J. Gaskell, J.E.G. McCarthy, N.W. Paton, H.V. Westerhoff, D.B. Kell, P. Mendes (2013) A model of yeast glycolysis based on a consistent kinetic characterisation of all its enzymes. FEBS Letters, 587(17), 2832-2841. (doi) (pdf)

E. Simeonidis, S. Chandrasekaran, N.D. Price (2013) A guide to integrating transcriptional regulatory and metabolic networks using PROM (Probabilistic Regulation Of Metabolism).Methods in Molecular Biology, 985, 103-112. (doi) (pdf)

I. Thiele, N. Swainston, R.M.T. Fleming, A. Hoppe, S. Sahoo, M.K. Aurich, H. Haraldsdottir, M.L. Mo, O. Rolfsson, M.D. Stobbe, S.G. Thorleifsson, R. Agren, C. Bölling, S. Bordel, A.K. Chavali, P. Dobson, W.B. Dunn, L. Endler, D. Hala, M. Hucka, D. Hull, D. Jameson, N. Jamshidi, J.J. Jonsson, N. Juty, S. Keating, I. Nookaew, N. Le Novère, N. Malys, A. Mazein, J.A. Papin, N.D. Price, E.Selkov Sr, M.I. Sigurdsson, E. Simeonidis, N. Sonnenschein, K. Smallbone, A. Sorokin, J.H.G.M. van Beek, D. Weichart, I. Goryanin, J. Nielsen, H.V. Westerhoff, D.B. Kell, P. Mendes, B.Ø. Palsson (2013) A community-driven global reconstruction of human metabolism, Nature Biotechnology, 31(5), 419-425.  (doi) (pdf)

V. Sangar, J.A. Eddy, E. Simeonidis, N. Price (2012) Mechanistic modeling of aberrant energy metabolism in human disease. Frontiers in Computational Physiology and Medicine, 3:404. (doi) (pdf)  

A. Kolodkin, E. Simeonidis, H.V. Westerhoff (2012) Computing life: add Logos to biology and Bios to physics. Progress in Biophysics and Molecular Biology, 111(2-3), 69-74. (doi) (pdf)
 
A. Kolodkin, E. Simeonidis, R. Balling, H.V. Westerhoff (2012) Understanding complexity in neurodegenerative diseases: in silico reconstruction of emergence. Frontiers in Systems Physiology, 3:291. (doi) (pdf)

K. Smallbone, N. Malys, H.L. Messiha, J.A. Wishart, E. Simeonidis (2011) Building a kinetic model of trehalose biosynthesis in Saccharomyces cerevisiae. Methods in Enzymology, 500, 355-370. (doi) (pdf)

P.D. Dobson, K. Smallbone, D. Jameson, E. Simeonidis, K. Lanthaler, P. Pir, C. Lu, N. Swainston, W.B. Dunn, P. Fisher, D. Hull, M. Brown, O. Oshota, N.J. Stanford, D.B. Kell, R.D. King, S.G. Oliver, R.D. Stevens, P. Mendes (2010) Further developments towards a genome-scale metabolic model of yeast. BMC Systems Biology, 4:145. (doi) (pdf) highly accessed    

P. Li, J.O. Dada, D. Jameson, I. Spasic, N. Swainston, K. Carroll, W. Dunn, F. Khan, H.L. Messiha, E. Simeonidis, D. Weichart, C. Winder, D. Broomhead, C.A. Goble, S.J. Gaskell, D.B. Kell, H.V. Westerhoff, P. Mendes, N.W. Paton (2010) Systematic integration of experimental data and models in systems biology. BMC Bioinformatics, 11:582. (doi) (pdf) highly accessed

E. Simeonidis, E. Murabito, K. Smallbone, H.V. Westerhoff (2010) Why does yeast ferment? A Flux Balance Analysis study. Biochemical Society Transactions, 38 (5), 1225-1229. (doi) (pdf)

H.V. Westerhoff, M. Verma, M. Nardelli, M. Adamczyk, K. Van Eunen, E. Simeonidis, B.M. Bakker (2010) Systems Biochemistry in practice: experimenting with modelling and understanding, with regulation and control. Biochemical Society Transactions, 38 (5), 1189-1196. (doi) (pdf)

K. Smallbone, E. Simeonidis, N. Swainston, P. Mendes (2010) Towards a genome-scale kinetic model of cellular metabolism. BMC Systems Biology, 4:6. (doi) (pdf) highly accessed

H.V. Westerhoff, C. Winder, H. Messiha, E. Simeonidis, M. Adamczyk, M. Verma, F.J. Bruggeman, W. Dunn (2009) Systems Biology: the elements and principles of Life. FEBS Letters,583 (24), 3882-3890. (doi) (pdf)

E. Murabito, E. Simeonidis, K. Smallbone, J. Swinton (2009) Capturing the essence of a metabolic network: A Flux Balance Analysis approach. Journal of Theoretical Biology, 260 (3), 445-452. (doi) (pdf)

I. Spasić, E. Simeonidis, H.L. Messiha, N.W. Paton, D.B. Kell (2009) KiPar, a tool for systematic information retrieval regarding parameters for kinetic modelling of yeast metabolic pathways.Bioinformatics, 25 (11), 1404-1411. (doi) (pdf)
K. Smallbone, E. Simeonidis (2009) Flux balance analysis: A geometric perspective. Journal of Theoretical Biology, 258 (2), 311-315. (doi) (pdf)
M.J. Herrgård, N. Swainston, P. Dobson, W.B. Dunn, K.Y. Arga, M. Arvas, N. Blüthgen, S. Borger, R. Costenoble, M. Heinemann, M. Hucka, N. Le Novère, P. Li, W. Liebermeister, M.L. Mo, A.P. Oliveira, D. Petranovic, S. Pettifer, E. Simeonidis, K. Smallbone, I. Spasić, D. Weichart, R. Brent, D.S. Broomhead, H.V. Westerhoff, B. Kırdar, M. Penttilä, E. Klipp, B.Ø. Palsson, U. Sauer, S.G. Oliver, P. Mendes, J. Nielsen, D.B. Kell (2008) A consensus yeast metabolic network reconstruction obtained from a community approach to systems biology. Nature Biotechnology, 26(10), 1155-1160. (doi) (pdf)
K. Smallbone, E. Simeonidis, D.S. Broomhead, D.B. Kell (2007) Something from nothing – Bridging the gap between constraint-based and kinetic modelling. FEBS Journal, 274 (21), 5576-5585. (doi) (pdf)

L. Dartnell, E. Simeonidis, M. Hubank, S. Tsoka, I.D.L. Tsoka, L.G. Papageorgiou (2005) Robustness of the p53 network and biological hackers. FEBS Letters, 579 (14), 3037-3042. (doi) (pdf)

E. Simeonidis, J.M. Pinto and L.G. Papageorgiou (2005) An MILP model for optimal design of purification tags and synthesis of downstream processing. Computer Aided Chemical Engineering,20, 1537-1542. (doi) (pdf)

E. Simeonidis, M.E. Lienqueo, S. Tsoka, J.M. Pinto, L.G. Papageorgiou (2005) MINLP models for the synthesis of optimal peptide tags and downstream protein processing. Biotechnology Progress,21 (3), 875-884. (doi) (pdf)

E. Simeonidis, J.M. Pinto and L.G. Papageorgiou (2004) Optimal peptide tag design and synthesis of downstream protein processing. Computer Aided Chemical Engineering, 18, 289-294. (doi) (pdf)

E. Simeonidis, S.C.G. Rison, J.M. Thornton, I.D.L. Bogle, L.G. Papageorgiou (2003) Analysis of biochemical networks using a pathway distance metric through linear programming. Metabolic Engineering, 5 (3), 211-219. (doi) (pdf)

Proceedings
E. Simeonidis, L. Dartnell, I.D.L. Bogle and L.G. Papageorgiou (2005) Analysis of biochemical networks using linear programming, 7th World Congress of Chemical Engineering, Glasgow, Scotland, UK. (pdf)

Theses

E. Simeonidis (2005) Optimisation of Biochemical Systems, PhD Thesis, University of London (UCL), London, United Kingdom.
 E. Simeonidis (2000) A re-configurable supply chain simulation system, MSc dissertation, Imperial College, London, United Kingdom.

E. Simeonidis, E. Stivaktakis (1999) Spectrophotometric determination of bromate ions using phenothiazines, Diploma thesis, Aristotle University of Thessaloniki, Greece.

C. Mantelis, I. Oxyzidis, E. Simeonidis (1998) Design of an industrial unit for polypropylene production, Design project, Aristotle University of Thessaloniki, Greece.