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Just use the flag --biblatex when converting with pandoc: pandoc --biblatex --chapters ../Source/Chapters/Content.md -o ../Example/Chapters/Content.tex The result: Connecting these native implementations to the Python world is enabled by the \href{http://cython.org/}{Cython} toolchain \autocite{behnel2011cython}. You have to use the biblatex package ...

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This is happening because pandoc is interpreting (@) signs as list markers, specifically an ordered list enclosed in parentheses. As can be seen if you inspect the latex output of pandoc: Input: (@) $$(K_{0}^{-1}x)^{T}E(K_{1}^{-1}x')=0$$ Output: \begin{enumerate} \def\labelenumi{(\arabic{enumi})} \item $(K_{0}^{-1}x)^{T}E(K_{1}^{-1}x')=0$ ...

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I verified the first part of my concept based on the link Steven (@steven-b-segletes) provided in his comment. Here is a short, working example for A4 sized pdf as a background (don't mind the coordinates...): \documentclass[finnish,a4paper,11pt]{article} \usepackage[a4paper]{geometry} \usepackage{setspace} \usepackage[utf8]{inputenc} \usepackage{graphicx} ...

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