Dr Simone Frey

I am interested in mathematical modelling of signal transduction pathways and have been working on modelling the Snf1 Pathway.

PhD Students (from 2006-01-01 until 2011-12-31)

Research interest

A Systems Biology Approach for the AMPK/SNF1 Pathway

"I am interested in mathematical modelling of signal transduction pathways and have been working on modelling the Snf1 Pathway."

Systems biology studies the dynamics of intra- and intercellular processes that determine cell function applying mathematical modelling to manage this organized complexity. The questions we focus on are: How is the regulation of Snf1 achieved: through glucose regulated kinase and constant phosphatase, or through a glucose regulated phosphatase and a constant kinase, or even through both being glucose regulated?
Identifying dynamic interactions among components of signaling pathways leads to the understanding and characterization of their effect on the cellular behaviour. Malfunctions in those processes can lead to diseases, such as diabetes type two. Eventually, a defined model might serve as starting point to discuss potential drug targets.

In collaboration with experimentalists, a stimulus response system comprising Snf1 as a key component was selected, along with a manageable number of snf1-interrelating components. This choice mainly depends on the feasibility to generate quantitative time series data. Several experiments were done, including Mig1-GFP intensities and Snf1P Western Blots in a wild type strain as well as in strains that over-expressed the kinase, the phosphatase, or both. In parallel, several model scenarios were defined on an ODEs based framework and compared to the experimental data.

The originally selected system, comprising only kinase, phosphatase and substrates, turned out to be insufficient for describing the data. Considering a more detailed structure or adding further components have become inevitably. Regulation of Snf1 by only its kinase can be discarded. It seems that the data available is not sufficient for excluding one of the two remaining model assumptions.

Academic background

2006 - 2011 PhD Student in Systems Biology
University of Rostock, Rostock, Germany
2009 - 3 months research internship
at the Biophotonics Group of M. Goksör,
University of Gothenburg, Sweden
2000 - 2005 Diplom Biomathematik
University of Greifswald, Greifswald, Germany
2000 Abitur (University Entrance Qualification),
Gymnasium Rodenkirchen, Cologne
1997 - 1998 Student at Miss Porter's School,
Farmington, CT, USA

 

Selected publications

A mathematical analysis of nuclear intensity dynamics for Mig1-GFP under consideration of bleaching effects and background noise in Saccharomyces cerevisiae

Frey S, Sott K, Smedh M, Millat T, Dahl P, Wolkenhauer O, Goksör M (2011)

Molecular BioSystems 7: 215-223

How quantitative measures unravel design principles in multi-stage phosphorylation cascades

Frey S, Millat T, Hohmann S, Wolkenhauer O (2008)

J Theor Biol 254: 27-36

Quantifying properties of cell signaling cascades

Frey S, Wolkenhauer O, Millat T

in: Control Theory and Systems Biology; Iglesias P A, Ingalls B (eds.); MIT press 2009.

ISBN 13 (print): 9780262013345

BIB: Download file

How integrals over dynamic signals can unravel characteristic properties of signal transduction pathways

Thomas Millat, Simone Frey, Olaf Wolkenhauer

11th International Conference on Systems Biology (ICSB), Edinburgh, UK, 10-15 October 2010

Venue: Edinburgh, UK

A mathematical analysis of nuclear intensity dynamics for Mig1-GFP under consideration of bleaching effects and background noise in S. cerevisiae

Simone Frey, Kristin Sott, Maria Smedh, Thomas Millat, Peter Dahl, Olaf Wolkenhauer, Mattias Goksör

11th International Conference on Systems Biology (ICSB), Edinburgh, UK, 10-15 October 2010

Venue: Edinburgh, UK

Quantitative analysis of the SNF1-pathway in Saccharomyces cerevisiae

Garcia-Salcedo R, Frey S, Beltran G, Bosch D, Elbing K, Tian Y, Manchala S, Rateitschak K, Wolkenhauer O, Hohmann S

35thFEBS Congress 2010, Göteborg (Gothenburg), Sweden. June 26 - July 1, 2010

Venue: Gothenburg, Sweden

Quantitative analysis of the SNF1-pathway in Saccharomyces cerevisiae

Garcia-Salcedo R, Frey S, Beltran G, Bosch D, Elbing K, Tian Y, Manchala S, Rateitschak K, Wolkenhauer O, Hohmann S

35thFEBS Congress 2010, Göteborg (Gothenburg), Sweden. June 26 - July 1, 2010

Venue: Gothenburg, Sweden

How Quantitative Measures unravel Design Principles in multi-stage Phosphorylation Cascades

Frey S, Millat T, Hohmann S, Wolkenhauer O

9th International Conference on Systems Biology (ICSB), Göteborg (Gothenburg), Sweden, 23 August - 28 August 2008

Venue: Gothenburg, Sweden

Modelling Snf1 regulation in Saccharomyces cerevisiae

Frey S, Schmidt H, Rateitschak K, Beltran G, Garcia-Salcedo R, Elbing K, Bosch D, Ye T, Hohmann S, Wolkenhauer O

9th International Conference on Systems Biology, Göteborg (Gothenburg), Sweden, August 2008

Venue: Gothenburg, Sweden

Quantitative measures to characterize properties of signal transduction pathways

Frey S, Millat T, Rateitschak K, Wolkenhauer O

Winter Simulation Conference (WSC '06), December 2006

A systems biology approach to dynamic modelling of the AMP-activated kinase pathway

Frey S

2011