Modeling a Minimal CDK Network
This paper reports a computational analysis of the minimal CDK network engineered in fission yeast (doi:10.1038/nature09543). It had been observed that a Cdk-inhibitory mechanism working through tyrosine phosphorylation of the kinase subunit, which is essential for modern fission yeast, is dispensable...
Minimal Cell Cycle
This is a great example of a paper where synthetic biology meets systems biology. The authors developed a minimal cell cycle regulatory network by engineering a synthetic CDK. To simplify the cell cycle control machinery, a cassette expressing a fusion of cdc13 and cdc2under...
Testing of a New Integrated Model of the Yeast START Transition
We propose a new model of the yeast start transition. We tested the accuracy of the model by simulating various mutants not described in the literature. The cell cycle is composed of bistable molecular switches that govern the transitions between...
Parameterization of a Stochastic Model of Gene Expression from Adaptive Imaging Cytometry Data
Supplementary material to a manuscript under review. The manuscript can be downloaded from the link below.
Abstract
Recent decades have yielded an understanding of cellular behavior as arising from a complicated soup of noisy molecular interactions. Systems biologists [...]
Parameter estimation preprint
We just submitted a revised version of a manuscript describing the analysis of data collected using our GenoSIGHT software. The paper shows that this data can be used to estimate parameters of gene network models. This manuscript is under consideration...
Adaptive Imaging Cytometry
The use of microfluidics in live cell imaging allows the acquisition of dense time-series from individual cells that can be perturbed through computer-controlled changes of growth medium. Systems and synthetic biologists frequently perform gene expression studies that require changes in...
Adaptive imaging cytometry to estimate parameters of gene networks models in systems and synthetic biology
Supplementary material to a manuscript under review. The manuscript can be downloaded from the link below.
Abstract
Recent decades have yielded an understanding of cellular behavior as arising from a complicated soup of noisy molecular interactions. Systems biologists [...]
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