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\begin{document}
\selectlanguage{ngerman}%

\subject{Dissertation zur Erlangung des Doktorgrades der 
Fakultät f\"ur Biologie
der Albert-Ludwigs-Universität Freiburg im Breisgau}

\selectlanguage{english}%

\title{A Network View of the Dynamic Transcriptome Response}


\author{Jie Bao}


\date{}

\selectlanguage{ngerman}%

\publishers{\includegraphics[width=0.4\columnwidth]{fig/Uni_Logo-Grundversion_E1_A4_CMYK}\vspace{\baselineskip}\\
Albert-Ludwigs-Universität Freiburg im Breisgau\\
Fakultät f\"ur Biologie\\
%Institut für zzz\vspace{-3cm}
}

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%\maketitle

%\thispagestyle{empty}
%\lowertitleback{
%\mbox{}\par\vfill
%\textbf{Dekan}\smallskip{}
%\\ 
%Prof. Dr. Ad Aertsen\bigskip{}
%\\
%\textbf{Promotionsvorsitzender}\smallskip{}
%\\
%Prof. Dr. Stefan Rotter\bigskip{}
%\\
%\textbf{Betreuer der Arbeit}\smallskip{}
%\\
%Dr. Hauke Busch\bigskip{}
%\\
%\textbf{Datum der Promotion (only necessary for final publication)}\smallskip{}
%\\
%xx.yy.zzzz}

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The whole is more than the sum of its parts. 
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--- Aristotle\\
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wirkungslos, Praxis ohne Theorie ist blind.
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--- Immanuel Kant\\
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%\begin{itemize}
%  \item introduction
%  \begin{itemize}
%    \item signal flow: protein interaction network $\rightarrow$ transcriptome
%    \item failure of biomarker
%    \item why predict dynamics of complex systems (Derek Ruths)
%    \item advantage of predictive analysis: time and labor-intensive lab work
%    \item complexity can only be understood within the
%      network context~\citep{Barabasi2012}, Understanding a complex network's 
%      structure is beneficial to understanding its function
%  \end{itemize}
%  \item network dynamics and topology
%  \begin{itemize}
%    \item fireworks: sequence of events, dynamics
%    \item elephant in the room: what we can and cannot see from
%    the transcriptome data
%    \item gene expression heavy-tailed distributed, discuss 
%    bimodal distribution 
%    \item normalization assumption: most genes do not change
%    expressions
%    \item few genes respond: sparsity assumption in reverse-%
%    engineering
%    \item Network inference in the yeast is already hard because absence of correlation
%    between TF expression and activity~\cite{Marbach2012}
%    \item CRNT: structure of the reaction network determines the number and type of
%    steady states
%  \end{itemize}
%  \item signal flow
%  \begin{itemize}
%    \item TF important in disease, but not detectable: many of the TFs that regulate physiological
%    targets are constitutively present, and their activity is determined
%    by posttranslational modifications such as phosphorylation%
%    ~\cite{Messina2004}
%  \end{itemize}
%  \item discussion
%  \begin{itemize}
%    \item attractor 
%    \item reverse-engineering: topological constraint
%  \end{itemize}
%\end{itemize}

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\appendix
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\chapter*{Acknowledgements}
\addcontentsline{toc}{chapter}{Acknowledgements}

First off, I am grateful that Dr. Hauke Busch offered me the opportunity to 
perform this work in the Cell Control and Communication group.
The unique composition of the group by people with different
background proved to be truly fruitful.
Hauke's role as an academic mentor includes, but is not
limited to, stimulating discussions, introducing me to the
scientific community, responsible conduct of research, etc.

Dr. Dr. Melanie Boerries is not only the wet lab expert, but
the one that connects experimentalists and
theoretians together as well. I greatly appreciate when Melanie
can quickly turn a not-so-well-formulated analytical idea
into a comprehensible explanation; or when she critically 
reviews the analysis results.

Thanks also go to Prof. Ad Aertsen and Prof. Stefan Rensing,
who agreed to be part of my thesis committee and provided
useful input during the work.

There are numerous people, both experimentalists and theoreticians, 
whom I have had discussion with and who have read
and commented on the working copies of this thesis. I would
especially like to thank Marisa, Ju, Silke, Amit, Sebastian
Ohse, Sebastian Weber, Moritz, Nurgazy, Martin, Okko, Julia,
Hendrik.

I am thankful to my wife, Huili, who has constantly been a 
motivating
source; to my son and daughter, Yichen and Yimeng, for 
the quiet nights during the writing and the enormous joy brought by them; to my parents for their unconditional support.

%\newpage
%\chapter*{Erkl\"arung}
%\addcontentsline{toc}{chapter}{Declaration}
%\begin{enumerate}
%\item Ich erkl\"are hiermit, dass ich die vorliegende Arbeit ohne unzul\"assige Hilfe Dritter und ohne Benutzung anderer als der angegebenen Hilfsmittel angefertigt habe. Die aus anderen Quellen direkt 
%oder indirekt \"ubernommenen Daten und Konzepte sind unter Angabe der Quellen gekennzeichnet. Insbesondere habe ich hierf\"ur 
%nicht die entgeltliche Hilfe von Vermittlungs- beziehungsweise 
%Beratungsdiensten (Promotionsberater oder anderer Personen) 
%in Anspruch genommen. Niemand hat von mir unmittelbar oder 
%mittelbar geldwerte Leistungen f\"ur Arbeiten erhalten, die im Zusammenhang mit dem Inhalt der vorgelegten Dissertation stehen.
%\item Die Arbeit wurde bisher weder im In- noch im Ausland in gleicher 
%oder \"ahnlicher Form einer anderen Pr\"ufungsbeh\"orde vorgelegt.
%\item Die Bestimmungen der Promotionsordnung der Fakult\"at f\"ur Biologie der Universit\"at Freiburg sind mir bekannt, insbesondere 
%wei\ss ich, dass ich vor Vollzug der Promotion zur F\"uhrung des 
%Doktortitels nicht berechtigt bin.
%\end{enumerate}
%\vskip 3cm
%Berlin, den \ddmmyyyydate\today \hspace{6cm} Jie Bao

\end{document}