Genomes and Genes
Affiliation: University of Freiburg
- A tutorial on mathematical modeling of biological signaling pathwaysZhike Zi
bioss Centre for Biological Signalling Studies, University of Freiburg, Freiburg, Germany
Methods Mol Biol 880:41-51. 2012..This chapter introduces how to use the bottom-up approach to establish mathematical models for cell signaling studies...
- Sensitivity analysis approaches applied to systems biology modelsZ Zi
University of Freiburg, bioss Centre for Biological Signalling Studies, Freiburg, Germany
IET Syst Biol 5:336-6. 2011....
- A quantitative study of the Hog1 MAPK response to fluctuating osmotic stress in Saccharomyces cerevisiaeZhike Zi
Centre for Biological Signalling Studies bioss, University of Freiburg, Freiburg, Germany
PLoS ONE 5:e9522. 2010..The Hog1 mitogen-activated protein kinase (MAPK) pathway is crucial for the adaption of yeast cells to external osmotic changes...
- SBML-PET-MPI: a parallel parameter estimation tool for Systems Biology Markup Language based modelsZhike Zi
bioss Centre for Biological Signalling Studies, Center for Biological Systems Analysis ZBSA, University of Freiburg, Freiburg, Germany
Bioinformatics 27:1028-9. 2011..The tool is developed and parallelized using the message passing interface (MPI) protocol, which provides good scalability with the number of processors...
- Quantitative analysis of transient and sustained transforming growth factor-β signaling dynamicsZhike Zi
BIOSS Centre for Biological Signalling Studies and Center for Biological Systems Analysis ZBSA, University of Freiburg, Freiburg, Germany
Mol Syst Biol 7:492. 2011..Our results suggest that long-term switch-like signaling responses in the TGF-β pathway might be critical for cell fate determination...
- Dynamics of TGF-β/Smad signalingZhike Zi
bioss Centre for Biological Signalling Studies, University of Freiburg, Freiburg 79104, Germany
FEBS Lett 586:1921-8. 2012..These studies reveal many interesting dynamics of TGF-β signaling and how cells quantitatively decode variable doses of TGF-β stimulation...