author-contributions.tex

\chap{Author Contributions}

My contributions to the studies included in this thesis were as follows:
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\I    & \textbf{The Sweden Cancerome Analysis Network-Breast (\scanb{}) Initiative: a large-scale multicenter infrastructure towards implementation of breast cancer genomic analyses in the clinical routine} \vspace{1mm} \\
      & I contributed the software described in study \II as well as input to the development of the \scanb{} computational pipeline, performed subtyping, compared microarray and RNA-seq based expression and intrinsic subtypes, contributed to data analysis, deposited the data in the NCBI Gene Expression Omnibus (GEO), and contributed to writing the manuscript. \vspace{1mm} \\
      & \vspace{5mm} \\

% Paper II
\II   & \textbf{TopHat-Recondition: A post-processor for TopHat unmapped reads} \vspace{1mm} \\
      & I diagnosed the problems in TopHat/TopHat2, designed and developed the software TopHat-Recondition, and drafted and revised the manuscript. \vspace{1mm} \\
      & \vspace{5mm} \\

% Paper III
\III  & \textbf{Clinical Value of RNA Sequencing-Based Classifiers for Prediction of the Five Conventional Breast Cancer Biomarkers: A Report From the Population-Based Multicenter Sweden Cancerome Analysis Network--Breast Initiative} \vspace{1mm} \\
      & I evaluated different machine learning approaches on training data, trained and evaluated the final classifiers, performed classification and survival analysis in the 3,273 patient validation cohort, deposited the data in NCBI GEO, and drafted and revised the manuscript. \vspace{1mm} \\
      & \vspace{5mm} \\

% Paper IV
\IV   & \textbf{The mutational landscape of the SCAN-B real-world primary breast cancer transcriptome} \vspace{1mm} \\
      & I participated in study design, implemented the DNA/RNA mutation calling pipeline, performed the mutation calling, and co-supervised a masters student who worked on variant filtering. I performed all downstream analysis of the mutations, performed the survival analysis, developed the \scanb{} MutationExplorer web application, and drafted and revised the manuscript. \vspace{1mm} \\

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