When Pandoc converts Markdown to LaTeX, it uses a template that speciefies what header and footer material to add (<a href="http:&#x2F;&#x2F;pandoc.org&#x2F;README.html#templates" rel="nofollow">http:&#x2F;&#x2F;pandoc.org&#x2F;README.html#templates</a>).<p>You could modify the default template to use whatever style file you want.<p>Pandoc also supports references with a .bib file, and inserting TeX math formulae between dollar signs.