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