main.tex

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%% File: main.tex
%% Author: Matthias Zepper
%% Based on: John Liaperdos (ioannis.liaperdos@gmail.com)
%% Last update: March 31, 2017
%% Description: Provides an example of a PhD Thesis 
%% using the wwubio-thesis-en pdfLaTeX class.
%%
%% Character encoding: UTF-8
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% 1. use the "modern" or "classic" option to switch between 
% a modern or classic font, respectively.
%
% 2. add/remove the "hyperref" option to enable/disable hyperlinks:
% (remember to remove auxiliary files after adding/removing 
% the "hyperref" option).
%
% 3. add/remove the "printer" option to typeset a printer-friendly 
% (grayscale)/color version of the thesis.
%
% 4. use the "watermark" option to indicate a draft copy of the thesis
%
% 5. use the "histinit" option to enable "historiated initials".
% (If used, all chapter initials declared by the \InitialCharacter{}
% macro are enlarged. If ommitted, arguments of \InitialCharacter{}
% are typeset as normal text.)
%
% 6. use the "plain" option to disable tikz graphics in title page
% and part/chapter headers (might help to avoid compilation timeouts).
% Note that "plain" disables CD label and CD cover creation.
%
% 7. use the "noindex" option to (hopefully) avoid compilation timeouts
% when compiling online (disables index generation - note that "\indexGR",
% "\index" invocations need not be removed when toggling this option).
%
% 8. use the "frontispiece" option to typeset a frontispiece at the back of the cover page
%
% 9. use the "letter" option for a US letter page layout, instead of A4
%
% 10. use the "minitoc" option to load and properly initialize the "minitoc" package, 
% that allows typesetting individual tables of contents per chapter.
% (remember to remove auxiliary files after adding/removing 
% the "minitoc" option).
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	\documentclass[modern,hyperref,histinit,minitoc,plain]{wwubio-thesis-en}
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%% UNIVERSITY INFO 
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% University Name
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	\UniversityName{Westfälische Wilhelms-Universität}
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% School Name
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	\SchoolName{Institut für Molekulare Tumorbiologie}
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% Department Name
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	\DepartmentName{}
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% Location
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	\UniversityLocation{Münster}
%----
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%% THESIS INFO 
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%% -------------------------------------------------------------------
% Thesis Type
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\ThesisType{}
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%% -------------------------------------------------------------------
% Thesis Title 
%
% To force line breaks in title, use "\\".
% If different line break locations are to be used for the cover page and the inner title page (page 3) 
% repeat the cover page title as an optional argument of the \title macro, including line breaks.
%
% Examples:
% 1. Automatic title line breaks in cover page and inner title page: 
%	 \title{This is my title}
% 2. Title breaking after ''my'' in both cover page and inner title page:
%	 \title{This is my \\ title}
% 3. Title breaking after ''my'' in cover page, and after ''is'' in inner title page:
%	 \title[This is my \\ title]{This is \\ my title}
%
	\title{Epigenetic characterization of murine Dnmt1-deficient MLL-AF9 leukemia}
%%
%
%% -------------------------------------------------------------------
%% Thesis subtitle (optional)
%
% If no subtitle is required, set argument to blank, or comment-out the \subtitle macro.
%
% Example:
%%	\subtitle{This is my subtitle}
	\subtitle{DNA methylation in large regions and at cis-regulatory elements dissected in the \dnmtchip mouse model}
%
%% -------------------------------------------------------------------
%
%% Author name
%
% For more than one authors, separate with ",".
% Example:
	\authorName{Matthias Lutz Zepper} 
	\authorBirthplace{Ludwigsburg} 
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%% -------------------------------------------------------------------
%
%% Supervisor's name
% 
	\supervisor{Frank Rosenbauer}
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%% -------------------------------------------------------------------
%% Supervisor's title
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	\supervisorTitle{Prof.~Dr.rer.nat.}
%
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%% Place and date of publication
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	\thesisPlaceDate{2020}
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%% Place and date in acknowledgements (if applicable).
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	\ackPlaceDate{Münster, February 2020}
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%% Approval information
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	\examinationDate{October XX, 2020}
	\approvalStatement{Approved by ...}
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%% Copyright Year
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	\copyrightYear{2020}
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%% Name of first examiner
%
\dean{Susanne Fetzner}
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%% Title of first examiner
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\deanTitle{Prof.~Dr.rer.nat.}
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%% Name of first examiner
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	\firstExaminer{Joachim Kurtz}
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%% -------------------------------------------------------------------
%% Title of first examiner
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	\firstExaminerTitle{Prof.~Dr.rer.nat.}
%
%% -------------------------------------------------------------------
%% Name of second examiner
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	\secondExaminer{Martin Dugas}
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%% -------------------------------------------------------------------
%% Title of second examiner
%
	\secondExaminerTitle{Prof.~Dr.med.}
%%
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%% THESIS COLORS: 
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\definecolor{wwugreen}{HTML}{7ab51d}
\definecolor{wwulime}{HTML}{b1c800}
\definecolor{wwublue}{HTML}{009dd1}
\definecolor{wwudark}{HTML}{006e89}
\definecolor{wwuteal}{HTML}{008e96}
\definecolor{wwugray}{HTML}{666666}

\definecolor{fbbioblue}{HTML}{5685b9}
\definecolor{fbbiolight}{HTML}{a2c3e6}



%%
%% Color for cover and chapters
	\chaptercolor{fbbioblue}
%%
%% Color for appendices
	\appendixcolor{fbbiolight}
%%
%% hyperlink color (ignored if the "hyperref" option is omitted)
 	\hyperlinkcolor{fbbioblue}
%%
%% Thesis title foreground color in cover page (ignored if the "plain" option is used)
 	\titlecolor{fbbioblue}
%%
%% Thesis title background color in cover page (ignored if the "plain" option is used)
 	\titlebackgroundcolor{white} 
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%% COVER PAGE IMAGE: 
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%%
 \coverpageimage{0.2}{logo/biouni.jpg}
%%
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%% MISCELLANEOUS SETTINGS: 
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%%
% Path to University Logo (all supported formats are allowed)
	\UniversityLogoPath{logo/logo_wwu.eps}
%
% Path to University Logo (grayscale version to be used with the `printer' option)
	\UniversityBWLogoPath{logo/logo_wwu.eps}
%
% Scalefactor for University logos (1 for 100%)
	\LogoScaleFactor{2}
% Draft Indication (watermark text to be used with the `watermark' option)
	\draftIndication{--- DRAFT v.0.3 ---}
%
% Frontispiece settings (ignored if the `frontispiece' option is omitted)
%	Syntax: \setFrontispiece[scale factor]{path to frontispiece image}{frontispiece image legend}
	\setFrontispiece[0.8]{figures/aesop.png}{Aesop}
%
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%
% add custom hyphenation rules here
%\hyphenation{} 
%
% Custom formatting
\input{macros}	
\input{hyphenation} % suppress hyphenation of some terms and abbreviations

%textwidth: 14.99786cm
%linewidth: 14.99786cm

\renewcommand{\arraystretch}{1.4}
\setlength{\parindent}{0em}
%\setlength{\parskip}{1em} 

\begin{document}
 
\maketitle

\beginfrontmatter
	
% Abstract (content in `abstract.tex')
	\include{abstract}
% Dedication
	%\thesisDedication{To someone you love or so}
% Acknowledgements (content in `acknowledgements.tex')
	\include{acknowledgements}
% Table of Contents
	\tableofcontents
	\herestoyoufrank{\item For this thesis, additional figures and more detailed method descriptions are available as supplementary online content. 
		\item All supplements can be found at \url{https://thesis.matthias-zepper.de}}
% List of Figures
%	\listoffigures
% List of Illustrations
	%\listofillustrations
% List of Tables
	%\listoftables
% List of Algorithms
	%\listofalgorithms
% Preface (content in `preface.tex') 
	%\include{preface}
	
\beginmainmatter


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%% INCLUDE YOUR CHAPTERS/SECTIONS HERE
%%
% Introduction
 %\part{Introduction}
 	\include{introduction_abridged}
% Parts/Chapters
 \part{Methylomes of MLL-AF9 c-Kit+ leukemia} 
	\include{results_wgbs}
	\include{results_wgbs_betadist}
	%\include{results_gammodels_intro}
	\include{results_gammodels} 
    \include{results_gam_chromatin}
	\include{results_wgbs_cchip}
	\part{Deregulated genes and pathways}
	\include{results_deregulated_genes}
	\include{results_deregulated_genes_tinats}
 \part{Enhancer delineation}
	\include{results_enhancer_clustering}
	\include{results_enhancer_motifsregulation}
	%\include{results_enhancer_targetgenes}
	\part{Discussion}
	\include{discussion_nuevageneracion}
	% \include{discussion_mice}
	 \include{discussion_methylation_persistence}
	 %\include{discussion_transcriptionalcontrol}
	 \include{discussion_enhanceractivation}
	 %\include{discussion_enhancer_gskj4}
% Appendices
	\appendices
	\include{appendix_thirdpartydata}
	\include{appendix_samples}
	%\include{appendix_degenes} 
	%\include{appendix_enhancers} 
	%\include{cv2019}
    \include{cv2019strip}		
% Bibliography/References (BiBTeX items in `references.bib')
 \cleardoublepage\phantomsection\addcontentsline{toc}{chapter}{Bibliography}%
 %\bibliographystyle{plos2015}
	\bibliography{references.bib}
% Abbreviations (content in `abbreviations.tex') 
	\includeabbreviations{abbreviations}
% Glossary (content in `glossary.tex') 
	%\includeglossary{glossary}

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% Index
	\printindices
%
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%% Create CD labels:

	\definecdlabeloffsets{0}{-0.65}{0}{0.55} % upper label x offset [cm] (default=0) / upper label y offset [cm] (default=0) / lower label x offset [cm] (default=0) / lower label y offset [cm] (default=0) -- For Q-Connect KF01579 labels use the following offset values: {0}{-0.65}{0}{0.55}

	\createcdlabel{This is my PhD \\ Thesis Title}{My Name}{October}{2014}{8} % thesis title / author name / month / year / title area width in cm (recommended value: 8) 

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%% Create CD case covers:

	\createcdcover{This is my PhD \\ Thesis Title}{My Name}{October}{2014}{10} % thesis title / author name / month / year / title area width in cm (recommended value: 10) 

%%
%
\end{document}

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