org-mode does indeed support footnotes[fn:1], but I was recently saddened to find that Github doesn't render them (it does render more basic org-mode features, though).

org-ref[fn:2] has extensive support for for citations and is explicitly designed for scientific papers and output to LaTeX.

[fn:1] Check out http://orgmode.org/manual/Footnotes.html

[fn:2] Check out https://github.com/jkitchin/org-ref/blob/master/org-ref.org

> org-mode does indeed support footnotes[fn:1], but I was recently saddened to find that Github doesn't render them (it does render more basic org-mode features, though).

GitHub uses this org-ruby project[1] to render Org files. If someone loves Org and knows Ruby too (I don't), please open PR's on that repo to improve Org parsing.

[1]: https://github.com/wallyqs/org-ruby

Slightly off topic but I have to ask: would you be willing to share your markdown workflow for academic writing? I am very interested in graduating from latex :)

This is somehwat geared toward my specific preferences as a social scientist, but my cookiecutter template contains pretty much everything you need for academic writing using pandoc: https://bitbucket.org/jboy1/cookiecutter-pandoc-paper

You can also consult Kieran Healy's guide here: http://plain-text.co (again, this targets social scientists)

Me too. Particularly I am interested in knowing if the setup auto-suggests items from the bibfile when typing [@

That's a big one for me that I've only gotten to work in online latex tools.

There are plugins to do this in Vim, Atom and I'm sure other editors as well. See one academic's description of how to tie it all together here: http://wcm1.web.rice.edu/plain-text-citations.html

I would second this, having written a lot of documentation recently (markdown + template + pandoc -> pdf) I am very interested in improving this workflow.

Yeah, bibliography works with org-mode. You can also do cross references in org-mode, which last I checked were a showstopper for me with Markdown.

I've tried doing academic writing in both org-mode and markdown. Org-mode ended up being the only one that did everything I needed.