dissertation.tex

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% Modify the following line to match your school
% Available options include `Harvard`, `Princeton`, and `NYU`.
\documentclass[School=Harvard]{Dissertate}
\usepackage{textgreek}
\usepackage{nomencl}
\usepackage{etoolbox}
\usepackage{tabularx}
\usepackage{geometry}
\makenomenclature
\setlength{\nomlabelwidth}{2.5cm}

% define function
\renewcommand\nomgroup[1]{%
  \ifstrequal{#1}{A}{%
    \item[\bfseries\large Abbreviations]\vspace{10pt} % Adjust the space as needed
  }{%
    \ifstrequal{#1}{N}{%
      \item[\bfseries\large Notation]\vspace{10pt} % Adjust the space as needed
    }{}%
  }%
}

\begin{document}

% the front matter
\input{frontmatter/personalize}
\maketitle
\copyrightpage





% nomenclature
\renewcommand{\nomname}{List of Abbreviations and Notation}
% abbreviation section
\nomenclature[A]{AUC}{Area under the curve}
\nomenclature[A]{CIMP}{CpG island methylator phenotype}
\nomenclature[A]{CIN}{Chromosomal instability}
\nomenclature[A]{CRC}{Colorectal cancer}
\nomenclature[A]{PDO}{Patient Derived Organoid}
\nomenclature[A]{CRISPR}{Clustered Regularly Interspaced Short Palindromic Repeats}
\nomenclature[A]{DMEM}{Dulbecco’s Modified Eagle Medium}
\nomenclature[A]{DMSO}{Dimethyl sulfoxide}
\nomenclature[A]{FDR}{False discovery rate}
\nomenclature[A]{MSI}{Microsatellite instability}
\nomenclature[A]{MSS}{Microsatellite stability}
\nomenclature[A]{AUROC}{Area under the receiver operating characteristic}
\nomenclature[A]{UICC}{Union for International Cancer Control}
\nomenclature[A]{sgRNA}{Single guide RNA}
\nomenclature[A]{5FU}{5-fluorouracil}
\nomenclature[A]{HexCer}{Hexosylceramide}
\nomenclature[A]{PA}{Phosphatidate}
\nomenclature[A]{Cer}{Ceramide}
\nomenclature[A]{SM}{Sphingomyelin}
\nomenclature[A]{LPC}{Lysophosphatidylcholine}
\nomenclature[A]{PS}{Phosphatidylserine}
\nomenclature[A]{PE}{Phosphatidylethanolamine}
\nomenclature[A]{PI}{Phosphatidylinositol}
\nomenclature[A]{PG}{Phosphatidylglycerol}
\nomenclature[A]{DAG}{Diacylglycerol}
\nomenclature[A]{PC}{Phosphatidylcholine}
\nomenclature[A]{Hex2Cer}{Dihexosylceramide}
\nomenclature[A]{CE}{Cholesterol Ester}
\nomenclature[A]{Chol}{Cholesterol}
\nomenclature[A]{TAG}{Triacylglycerol}
\nomenclature[A]{ARD}{Automatic Relevance Determination}
\nomenclature[A]{FOLFOX}{Folinic Acid, 5-Fluorouracil, and Oxaliplatin}
\nomenclature[A]{FOLFIRI}{Folinic Acid, 5-Fluorouracil, and Irinotecan}
\nomenclature[A]{FOLFOXIRI}{Folinic Acid, 5-Fluorouracil, Oxaliplatin, and Irinotecan}
\nomenclature[A]{BMP}{Bone Morphogenic Protein}
\nomenclature[A]{HRP}{Horse Radish Peroxidase}
\nomenclature[A]{RIPA}{Radioimmunoprecipitation Assay Buffer}
\nomenclature[A]{DTT}{Dithiothreitol}
\nomenclature[A]{TRITC}{Tetramethylrhodamine}
\nomenclature[A]{DAPI}{4′,6-Diamidino-2-Phenylindole}
\nomenclature[A]{HDF5}{Hierarchical Data Format Version 5}
\nomenclature[A]{PCA}{Principal Component Analysis}
\nomenclature[A]{ICA}{Independent Component Analysis}
\nomenclature[A]{NMF}{Non-negative Matrix Factorization}
\nomenclature[A]{ANOVA}{Analysis of Variance}
\nomenclature[A]{RMA}{Robust Multiarray Average}
\nomenclature[A]{MOFA}{Multi-omics Factor Analysis}
\nomenclature[A]{CMS}{Consensus Molecular Subtype}
\nomenclature[A]{GSEA}{Gene Set Enrichment Analysis}
\nomenclature[A]{BCA}{Bicinchoninic Acid Assay}
\nomenclature[A]{WENRAS}{Organoid Medium containing Wnt3a, Egf, Noggin, R-Spondin, A83-01, and SB202190}
\nomenclature[A]{ENA}{Organoid Medium containing Egf, Noggin, and A83-01}
\nomenclature[A]{ENAS}{Organoid Medium containing Egf, Noggin, A83-01, and SB202190}
\nomenclature[A]{UMAP}{Uniform Manifold Approximation and Projection}
\nomenclature[A]{CRIS}{CRC Intrinsic Subtypes}
\nomenclature[A]{MCR}{Mutation Cluster Region}
%\nomenclature[A]{WT}{Wildtype}
\nomenclature[A]{HEPES}{4-(2-Hydroxyethyl)-1-Piperazineethanesulfonic Acid}
\nomenclature[A]{DPBS}{Dulbecco's Phosphate Buffered Saline}
\nomenclature[A]{CTG}{Cell Titer Glo Viability Assay}
\nomenclature[A]{ATP}{Adenosine triphosphate}
\nomenclature[A]{PBS}{Phosphate Buffered Saline}
\nomenclature[A]{PBS-T}{Phosphate Buffered Saline containing 0.1\% (v/v) Triton X-100}
\nomenclature[A]{ACN}{Acetonitrile}
\nomenclature[A]{PAINS}{Pan Assay INterference compoundS}
\nomenclature[A]{siRNA}{small interfering RNA}
%\nomenclature[A]{SREBP}{Sterol regulatory element binding proteins (SREBP)}

% notation section
\nomenclature[N]{$\mathbf{X}$}{Matrix}
\nomenclature[N]{$\mathbf{X}^T$}{Matrix Transpose}
\nomenclature[N]{$\mathbf{X}^+$}{Pseudoinverse of a Matrix}
\nomenclature[N]{$\mathbf{Y_m}$}{Measured data matrix of modality $m$}
\nomenclature[N]{$\mathbf{Z}$}{Factor score matrix}
\nomenclature[N]{$\mathbf{W_m}$}{Factor weight matrix (also called loading matrix) of modality $m$ }
\nomenclature[N]{$\boldsymbol{\epsilon_m}$}{Error terms of modality $m$}




% continuing with frontmatter
\tableofcontents
\listoffigures
\addcontentsline{toc}{chapter}{List of Figures}
\listoftables
\addcontentsline{toc}{chapter}{List of Tables}
\printnomenclature
\addcontentsline{toc}{chapter}{List of Abbreviations and Notation}
\doublespacing



% include each chapter...
\setcounter{chapter}{0}  % start chapter numbering at 1 (set to -1 to start at 0)
\include{chapters/introduction}
\include{chapters/methods}
\include{chapters/chapter2}
\include{chapters/chapter3}
\include{chapters/conclusion}
% the back matter
\abstractpage
\addcontentsline{toc}{chapter}{\numberline{6}Summary}
\addcontentsline{toc}{chapter}{\numberline{7}Zusammenfassung}
\singlespacing
\clearpage
\printbibliography
\addcontentsline{toc}{chapter}{\numberline{9}References}
%\bibliographystyle{harvard}
\eigenanteil
\addcontentsline{toc}{chapter}{Eigenanteil}
\curriculumvitae
\addcontentsline{toc}{chapter}{Curriculum Vitae}
\acknowledgments
\addcontentsline{toc}{chapter}{Acknowledgments}
\eidesstaat
\addcontentsline{toc}{chapter}{Eidesstaatliche Versicherung}
\end{document}