Modeling of Cellular Processes
Supported generously by NSF
We also have been active in the area of engineering-based bioinformatics. In
collaboration with Prof. Vassily
Hatzimanikatis from EPFL (Ecole Polytechnique Fédérale de Lausanne) we are interested
in the relationship between mRNA and proteome expression profiles. We consider the effect of post-transcriptional
and translational regulation of mRNA expression profiles to predict proteome expression profiles. Basically,
can one predict a proteome expression profile given chip data (or vice-versa)?
We are also developing mathematical models for intracellular signaling in PC12 cells in collaboration with
Prof.
Rick Cerione (Departments of
Chemistry and Chemical Biology and
Molecular Medicine),
and Prof. Jim Sethna
(Laboratory of Atomic and Solid State Physics).
Together with the these groups, we are exploring methods for building ensembles of models
that offer key insights into the structure of models and experimental data. This overall approach
has been termed Sloppy Modeling.
A new area that has been initiated in collaboration with Jordi Garcia-Ojalvo is to develop an
improved understanding of the evolution of the mechanism of circadian rhythms. We have built a
mechanistic model for circadian oscillations in gene expression from Drosophila that is able
to achieve a 24 hour period without introducing artificial time-delays into the network.
These models and mathematical tools we develop both guide and complement our
experimental program (Area 1, Area 2, and
Area 3) and provide opportunities to develop a deeper insight into the data we generate.
DNA chip analysis and proteome analysis provide important tools for monitoring gene expression.
We would like to develop mathematical frameworks to relate these data sets and the corresponding DNA sequence.
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