Current position
I work as an Experimental Officer for the Manchester Centre for Integrative Systems Biology (MCISB) at the University of Manchester, with Prof. Hans Westerhoff (Professor of Systems Biology at the School of CEAS and MCISB director). I am officially affiliated to the School of Chemical Engineering and Analytical Science (CEAS).
Research interests
Systems Biology
My research focuses on the development of mathematical models for the analysis of biological systems. These range from fully parameterised, kinetic models of pathways to genome-scale models of either kinetic or purely stoichiometric nature. The analysis and control of metabolic flux is also among my main interests. The techniques I use for the modelling of these systems vary from kinetic, ODE-based modelling, to stoichiometric, optimization-based approaches (e.g. Flux Balance Analysis). At the same time, I develop novel, hybrid approaches for the characterization of metabolic behaviour.
Yeast metabolism
My main responsibility at the MCISB is the mathematical modelling of the metabolism of baker's yeast. The MCISB is pioneering the development of new technologies in Systems Biology, a new conceptual view on biological research that uses complex computational and mathematical analysis to advance traditional methods. We are developing the necessary Systems Biology methods and techniques using yeast (Saccharomyces cerevisiae) as a model organism, but we are also very interested in applying our methodologies to mammalian and human systems.
Mathematical Programming and Integer Optimisation
The object of this research is the application of mathematical programming and optimisation methodologies to problems of biological and biochemical nature. Main research areas that I have examined include:
- Protein folding
- Metabolic pathway analysis
- p53 apoptotic control network
- Synthesis of peptide purification tags for downstream protein processing
Selected publications
E. Simeonidis, E. Murabito, K. Smallbone and H.V. Westerhoff (2010) Why does yeast ferment? A Flux Balance Analysis study. Biochemical Society Transactions, in press.
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) 
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)
A complete publication list can be accessed here. (pdf)
Curriculum Vitae
A 2-page CV is available for download (pdf). A detailed CV can be provided upon request.
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