Journal publications
K. Smallbone, N. Malys, H.L. Messiha, J.A. Wishart and 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 and P. Mendes (2010) Further developments towards a genome-scale metabolic model of yeast. BMC Systems Biology, 4:145. (doi) (pdf)
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 and N.W. Paton (2010) Systematic integration of experimental data and models in systems biology. BMC Bioinformatics, 11:582. (doi) (pdf)
E. Simeonidis, E. Murabito, K. Smallbone and H.V. Westerhoff (2010) Why does yeast ferment? A Flux Balance Analysis study. Biochemical Society Transactions, 38 (5), 1225-1229. (doi) (pdf)
K. Smallbone, N. Malys, H.L. Messiha, J.A. Wishart and 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 and P. Mendes (2010) Further developments towards a genome-scale metabolic model of yeast. BMC Systems Biology, 4:145. (doi) (pdf)
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 and N.W. Paton (2010) Systematic integration of experimental data and models in systems biology. BMC Bioinformatics, 11:582. (doi) (pdf)
E. Simeonidis, E. Murabito, K. Smallbone and 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 and P. Mendes (2010) Towards a genome-scale kinetic model of cellular metabolism. BMC Systems Biology, 4:6. (doi) (pdf)
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 and 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)
K. Smallbone, E. Simeonidis, N. Swainston and P. Mendes (2010) Towards a genome-scale kinetic model of cellular metabolism. BMC Systems Biology, 4:6. (doi) (pdf)
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 and 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 and 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 and 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 and 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 and 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, 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, 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, J.M. Pinto and L.G. Papageorgiou (2005) An MILP model for optimal design of purification tags and synthesis of downstream processing. In European Symposium on Computer-Aided Process Engineering-15, L. Puigjaner and A. Espuña (eds.), pp. 1537-1542.
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.
E. Simeonidis, J.M. Pinto and L.G. Papageorgiou (2004) Optimal peptide tag design and synthesis of downstream protein processing. In European Symposium on Computer-Aided Process Engineering-14, A. Barbosa-Povoa and H. Matos (eds.), pp.289-294.
Theses
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.
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, 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, 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, J.M. Pinto and L.G. Papageorgiou (2005) An MILP model for optimal design of purification tags and synthesis of downstream processing. In European Symposium on Computer-Aided Process Engineering-15, L. Puigjaner and A. Espuña (eds.), pp. 1537-1542.
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.
E. Simeonidis, J.M. Pinto and L.G. Papageorgiou (2004) Optimal peptide tag design and synthesis of downstream protein processing. In European Symposium on Computer-Aided Process Engineering-14, A. Barbosa-Povoa and H. Matos (eds.), pp.289-294.
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.
