BMC Sys. Biol.
Yeast Systems Biology
The yeast Saccharomyces cerevisiae is perhaps the best model organism to establish new techniques and methodologies due to its easy growth, non-pathogenicity, and the wide availability of genetic and molecular tools. This is also the case for systems biology, so yeast is used in many projects in our group.
We are part of the Manchester Centre for Integrative Systems Biology which is using yeast to develop the methodologies needed for construction of large-scale metabolic kinetic models. This includes methods such as protein purification, enzyme kinetics, metabolomics, proteomics, flux-balance analysis, kinetic modelling with ODEs, metabolic control analysis, data standards and web services.
We update the most comprehensive and documented reconstruction of yeast metabolism YEASTNET. This stemmed from a community-wide collaborative project from which a consensus model emerged 1. We have subsequently continued to update this reconstruction by filling in gaps and adding parts of metabolism that were previously not well covered by reconstructions. The most up to date model is available in SBML format and also queriable by a simple web interface here.
We are also members of the European Union FP7 project UNICELLSYS which is using systems biology to understand growth and division using yeast as a model organism. Within this consortium we are developing methods for multiscale simulation.
Another collaborative research project is MOSES, funded by SysMO, which is studying the importance and centrality of ATP in metabolism. Our participation has been mostly of enzyme kinetics, parameter estimation and kinetic modelling.
With colleagues at VBI we are studying the yeast response to oxidative stress and creating top-down models of this process.
 Herrgård MJ, Swainston N, Dobson P, Dunn WB, Arga KY, Arvas M, Blüthgen N, Borger S, Costenoble R, Heinemann M, Hucka M, Le Novère N, Li P, Liebermeister W, Mo ML, Oliveira AP, Petranovic D, Pettifer S, Simeonidis E, Smallbone K, Spasić I, Weichart D, Brent R, Broomhead DS, Westerhoff HV, Kirdar B, Penttilä M, Klipp E, Palsson BØ, Sauer U, Oliver SG, Mendes P, Nielsen J, Kell DB (2008) A consensus yeast metabolic network reconstruction obtained from a community approach to systems biology, Nature Biotechnol. 26, 1155-1160. [ abstract ] [ full text ].