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**Harvard**

Gennemark, P. (2005) *Modeling and identification of biological systems with emphasis on osmoregulation in yeast *. Göteborg : Chalmers University of Technology (Doktorsavhandlingar vid Chalmers tekniska högskola. Ny serie, nr: 2329).

** BibTeX **

@book{

Gennemark2005,

author={Gennemark, Peter},

title={Modeling and identification of biological systems with emphasis on osmoregulation in yeast },

isbn={91-7291-647-8},

abstract={This thesis deals with two topics in the area of systems biology. The
first topic, model identification, concerns the problem of
automatically identifying a mathematical model of a biochemical system
from experimental data. We present algorithms for model selection and
parameter estimation that identify both the structure and the
parameters of a differential equation model from experimental data.
The algorithms are designed to handle problems of realistic size,
where reactions can be non-linear in the parameters and where data can
be sparse and noisy. To achieve computational efficiency, parameters
are estimated for one equation at a time, giving a fast and accurate
parameter estimation algorithm compared to other algorithms in the
literature. The model selection is done with an efficient heuristic
search algorithm, where the structure is built incrementally. The main
strengths of our algorithms are that a complete model, and not only a
structure, is identified, and that they are considerably faster
compared to other identification algorithms.
</p>
The second topic concerns mathematical modeling of osmoregulation in
the yeast \emph{Saccharomyces cerevisiae}. This system involves the
biophysical and biochemical responses of a cell when it is exposed to
an osmotic shock. We present two different differential equation
models based on experimental data of this system. The first model is
a detailed model taking into account an extensive amount of molecular
detail, while the second is a simple model with less detail. We
demonstrate that both models agree well with experimental data on
wild-type cells. Moreover, the models predict the behavior of other
genetically modified strains and input signals.},

publisher={Institutionen för data- och informationsteknik, Datavetenskap, Bioinformatik (Chalmers), Chalmers tekniska högskola,},

place={Göteborg},

year={2005},

series={Doktorsavhandlingar vid Chalmers tekniska högskola. Ny serie, no: 2329Technical report D - School of Computer Science and Engineering, Chalmers University of Technology, no: 10D},

keywords={model identification, model selection, parameter estimation, ordinary differential equations, Saccharomyces cerevisiae, osmotic stress},

note={59},

}

** RefWorks **

RT Dissertation/Thesis

SR Print

ID 8053

A1 Gennemark, Peter

T1 Modeling and identification of biological systems with emphasis on osmoregulation in yeast

YR 2005

SN 91-7291-647-8

AB This thesis deals with two topics in the area of systems biology. The
first topic, model identification, concerns the problem of
automatically identifying a mathematical model of a biochemical system
from experimental data. We present algorithms for model selection and
parameter estimation that identify both the structure and the
parameters of a differential equation model from experimental data.
The algorithms are designed to handle problems of realistic size,
where reactions can be non-linear in the parameters and where data can
be sparse and noisy. To achieve computational efficiency, parameters
are estimated for one equation at a time, giving a fast and accurate
parameter estimation algorithm compared to other algorithms in the
literature. The model selection is done with an efficient heuristic
search algorithm, where the structure is built incrementally. The main
strengths of our algorithms are that a complete model, and not only a
structure, is identified, and that they are considerably faster
compared to other identification algorithms.
</p>
The second topic concerns mathematical modeling of osmoregulation in
the yeast \emph{Saccharomyces cerevisiae}. This system involves the
biophysical and biochemical responses of a cell when it is exposed to
an osmotic shock. We present two different differential equation
models based on experimental data of this system. The first model is
a detailed model taking into account an extensive amount of molecular
detail, while the second is a simple model with less detail. We
demonstrate that both models agree well with experimental data on
wild-type cells. Moreover, the models predict the behavior of other
genetically modified strains and input signals.

PB Institutionen för data- och informationsteknik, Datavetenskap, Bioinformatik (Chalmers), Chalmers tekniska högskola,

T3 Doktorsavhandlingar vid Chalmers tekniska högskola. Ny serie, no: 2329Technical report D - School of Computer Science and Engineering, Chalmers University of Technology, no: 10D

LA eng

OL 30