-
Notifications
You must be signed in to change notification settings - Fork 0
/
Copy paththesis.tex
executable file
·142 lines (125 loc) · 3.17 KB
/
thesis.tex
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
\RequirePackage[l2tabu,orthodox]{nag}
\documentclass[paper=a4
%a4paper
,fontsize=11pt
%,12pt
,headinclude
,footinclude
,BCOR=1cm
,parskip=half*
,open=right
,floatperchapter
,numbers=noendperiod
,twoside=true
,headings=big
,bibliography=totoc
]{scrbook}
\KOMAoptions{headsepline = true, footsepline = false}
%TC:ignore
\input{config.tex}
\input{glossary.tex}
%TC:endignore
\title{Investigating\\Normal Human Gene Expression in Tissues\\
with High-throughput Transcriptomic\\and Proteomic Data.}
\subject{This dissertation is submitted for the degree of Doctor of Philosophy}
\author{Mitra Parissa Barzine}
\publishers{%
\includegraphics[width=0.3\textwidth]{HughesHallShield}
\\[0.5\baselineskip]
Hughes Hall,\\
University of Cambridge\\[0.2\baselineskip]
EMBL-EBI}
\lowertitleback{%
\centering
{\footnotesize Licensed under Creative Commons Attribution International (CC BY) 4.0}
\\[2mm]
\href{http://creativecommons.org/licenses/by/4.0/}{%
\raisebox{-0.25em}{\includegraphics[width=1em]{cc.pdf}
\includegraphics[width=1em]{by.pdf}}}}
%\addtokomafont{section}{\Large}
%\addtokomafont{subsection}{\large}
%\tolerance=1
\emergencystretch=\maxdimen
\hyphenpenalty=10000
\hbadness=10000
\begin{document}
\hyphenation{%
abun-dance
be-twe-en
chan-ges
ri-bo-so-mal
samp-ling
ENS-EMBL
}
\pagenumbering{roman}
\setcounter{page}{1}
\maketitle
\pagestyle{scrheadings}
%TC:ignore
\input{disclaimer.tex}
\addtocontents{toc}{\vspace{-30pt}}
\input{summary.tex}
\input{acknowledgements.tex}
%% problem with page numbering fixed with:
%% http://tex.stackexchange.com/a/125090/102519
\begingroup
%\hypersetup{linkcolor=thesis@toccolor}
\cleardoublepage
\pdfbookmark{\contentsname}{toc}
{\small
\tableofcontents
\phantomsection
\printglossary[title={Terms and Abbreviations},toctitle=List of Terms and Abbreviations]\raggedbottom
\phantomsection
\listoffigures
\addcontentsline{toc}{chapter}{\listfigurename}\raggedbottom\ %\clearpage \thispagestyle{empty}
\phantomsection
\listoftables
\addcontentsline{toc}{chapter}{\listtablename}\raggedbottom\ \clearpage \thispagestyle{empty}
}
\cleardoublepage
\endgroup
%TC:endignore
\cleardoublepage
%\mainmatter\
\pagenumbering{arabic}
\setcounter{page}{1}
\setcounter{table}{0}
\phantomsection
\input{introduction.tex}
\input{background.tex}
\input{datasets.tex}
\input{expressed.tex}
\input{transcriptomics.tex}
\input{proteomics.tex}
\input{integration.tex}
\input{conclusion.tex}
%TC:ignore
%\backmatter\
\appendix\
\crefalias{section}{appsec}
\crefalias{subsection}{appsubsec}
\crefalias{subsubsection}{appsubsubsec}
\part*{APPENDIX}
\addcontentsline{toc}{part}{APPENDIX}
\renewcommand\thechapter{\Alph{chapter}}
\changelocaltocdepth{1}
\begingroup
\input{app/back-suppl}
\input{app/express-supl}
\input{app/transc-supl}
\input{app/prot-suppl}
\input{app/IntegSuppl}
\input{app/concl-suppl.tex}
\chapter{List of publications}
\begin{refsection}[ownpubs]
\small
\nocite{*} % is local to the enclosing refsection
\printbibliography[heading=none]
\end{refsection}
\endgroup
\bookmarksetup{startatroot}
\printbibliography[title={References}]
%\printglossaries\
%TC:endignore
\end{document}