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It was a couple of years ago that I wrote my dissertation using Pandoc, so things may have changed. At the time, I started out using pandoc-citeproc with my BibTeX database, but eventually I needed more control over formatting and I switched to writing \cite everywhere. Even with hundreds of references, it only took an afternoon, so I'm happy I did it the way I did. My approach with Pandoc is to use it until you have to invest LaTeX-level effort into making it do what you want. At that point, swapping in LaTeX is rarely painful. Often you can get away with editing Pandoc's generated LaTeX and pasting it back in to your source.



You can control the formatting pandoc-citeproc (which is now built in to pandoc) produces with a CSL file. That's great if your institution provides one, otherwise... you'll have to learn CSL ;-/




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