Center for Systems Biology, University of Iceland, Iceland
The University of Iceland in Reykjavik has a long history of biomedical research and has recently established the Center for Systems Biology (CSB UoI). The CSB UoI is an active, dynamic, interdisciplinary center with the Schools of Medicine, Engineering, and Natural Sciences participating. A major aim of the CSB UoI is to utilize the current knowledge-base in Iceland to characterize human disease using a systems biology approach as well as driving new biotechnological approaches for generation of fine chemical from geothermal resources. Therefore, the research efforts at the CSB UoI focus on systems biology of human metabolism and industrial biotechnology. The CSB UoI poses the following key technologies which form the basis of the aforementioned research effort: cell culturing expertise, metabolomics expertise, biochemical network reconstruction expertise with focus on human metabolism and biomedical & biotechnological interesting organisms, constraint-based modeling expertise, and algorithm development expertise for computational modeling and bioinformatics.
Profile of staff members
Dr. Ines Thiele is an Assistant Professor of Bioengineering at University of Iceland. She is an expert in reconstruction and analysis of genome-scale biochemical networks, which can be converted into a mathematical format and enable computation of physiological properties. She has authored many papers on network reconstruction including a widely used standard operating procedure for network reconstruction . Her research focuses on developing computational modeling and metabolomics methods to unravel mechanisms underlying pathophysiological states in various diseases. Dr. Thiele has particular expertise in multi-scale modeling, where processes on different time or spatial scales are integrated into a single model. This research is essential to bridge the gap between molecular level processes, occurring on relatively fast timescales, and clinical level processes, which proceed on slower timescales.
Dr. Ronan Fleming is an Assistant Professor at the Department of Biochemistry & Molecular Biology, Faculty of Medicine, University of Iceland. His research is focused on integration of kinetics and thermodynamics with constraint-based modeling of genome scale human biological networks. Biochemical networks give rise to high dimensional and nonlinear systems of model equations. Off the shelf algorithms are incapable of reliably finding solutions to such systems. Fortunately, inherent mathematical structure emerges with a parsimonious perspective on biochemical networks and tailored algorithms using powerful variational analysis techniques can be used to reliably solve such systems on genome scale. This research is foundational to efforts to construct predictive models of human biochemistry.
Five recent publications relevant to the project
1) Haraldsdottir, H., Thiele, I., Fleming, R. M. F., "Quantitative Assignment of Reaction Directionality in a Multicompartmental Human Metabolic Reconstruction: Recon 1", Biophys. J., In press (2012).
2) Fleming, R. M.T., Maes, C. M., Saunders, M. A., Ye, Y., Palsson, B. O.,"A variational principle for computing nonequilibrium fluxes and potentials in genome-scale biochemical networks", J Theor Biol, 292C:71-77 (2011).
3) Thorleifsson, S. G., Thiele, I., "rBioNet: A COBRA toolbox extension for reconstructing high-quality biochemical networks", Bioinformatics, 27(14):2009-10 (2011).
4) Thiele, I. and Palsson, B. O.,"''A protocol for generating a high-quality genome-scale metabolic reconstruction'', Nat Prot, 5(1): 93 - 121(2010).
5) Duarte, N.C., Becker, S.A., Jamshidi, N., Thiele, I., Mo, M.L., Vo, T.D., Srivas, R., and Palsson, B. O. "Global reconstruction of the human metabolic network based on genomic and bibliomic data.", PNAS, 104(6):1777-82 (2007).