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Re:Madoko – Write full-blown academic articles in Markdown by jamessb on Thursday September 03, 2015 @03:24PM (#10166995)
When Pandoc converts Markdown to LaTeX, it uses a template that speciefies what header and footer material to add (http://pandoc.org/README.html#templates).

You could modify the default template to use whatever style file you want.

Pandoc also supports references with a .bib file, and inserting TeX math formulae between dollar signs.

Re:Madoko – Write full-blown academic articles in Markdown by lelandbatey on Thursday September 03, 2015 @07:51PM (#10168146)
Exactly. I've been using raw markdown processed with Pandoc as my sole document-creation tool for the past 3 years and it's worked excellently so far. Pandoc's pretty awesome.