thesis.tex

\RequirePackage[l2tabu, orthodox]{nag}
\documentclass{thesis}

\addbibresource{references.bib}

\begin{document}

\hyphenation{%
    abun-dance
    be-twe-en
    co-don
    co-dons
    chan-ges
    hy-bri-di-sa-tion
    ri-bo-so-mal
    samp-ling
}

\titlehead{%
    \parbox{0.5\textwidth}{\includegraphics[height=12mm]{logo-uofc-cmyk}}%
    \parbox{0.5\textwidth}{\raggedleft%
        \includegraphics[height=12mm]{logo-embl-ebi-cmyk}}%
    % Obligatory logo margin
    \vspace{-1.5\baselineskip}%
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\title{Investigating the link between\\tRNA and mRNA abundance\\in mammals}
\subject{This dissertation is submitted for the degree of Doctor of Philosophy}
\author{Konrad \second{Ludwig Moritz} Rudolph}
\date{May 2015}
\publishers{%
    %\vfill doesn’t work properly on title page due to excess glue
    \vspace{6\baselineskip}
    St Edmund’s College,\\
    University of Cambridge\\[0.2\baselineskip]
    EMBL-EBI}

\lowertitleback{%
    \centering
    {\footnotesize The source code of the thesis is available at
        \url{https://github.com/klmr/thesis}.

    Licensed under Creative Commons Attribution (CC BY) 3.0}
    \\[2mm]
    \href{http://creativecommons.org/licenses/by/3.0/}{%
        \raisebox{-0.25em}{\includegraphics[width=1em]{cc}
            \includegraphics[width=1em]{by}}}}

\maketitle

\chapterfile{declaration}

\begingroup
    \hypersetup{linkcolor=thesis@toccolor}
    \tableofcontents
    \listofabbrevs
    \cleardoublepage
    \phantomsection
    \addcontentsline{toc}{chapter}{\listfigurename}
    \listoffigures
    \cleardoublepage
    \phantomsection
    \addcontentsline{toc}{chapter}{\listtablename}
    \listoftables
\endgroup

\chapterfile{summary}
\chapterfile{acknowledgements}
\chapterfile{introduction}

\chapterfile{trna-development}
\chapterfile{codons}
\chapterfile{polIII-transcriptome}

\chapterfile{conclusion}

\chapterfile{appendix}

\printbibliography[heading=bibintoc]

\end{document}