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.

Yeast Metabolic Reconstruction

We update the most comprehensive and documented reconstruction of yeast metabolism. This stemmed from a community-wide collaborative project from which a consensus model emerged. 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 reconstruction is available in SBML format from


We are part of the Manchester Centre for Integrative Systems Biology (MCISB). During its first period of funding, the Centre engaged in the development of bottom-up systems biology using yeast as a model organism. This included methods for systematic protein purification, enzyme kinetics, quantitative metabolomics, quantitative proteomics, flux-balance analysis, kinetic modelling with ODEs, metabolic control analysis, data standards and web services. This work resulted in several dynamic models of biochemical pathways of yeast central metabolism.

Oxidative stress response

We carried out a comprehensive gene expression study of the dynamic response to oxidative stress in yeast. We use these data to develop reverse engineering methods for top-down systems biology.

mRNA translation machinery

Together with the group of John McCarthy, we created a detailed model of yeast mRNA translation (protein synthesis by the ribosome). This model helped decide between alternative mechanisms in some of the steps of initiation.