Vikas Rawal has an excellent introduction to using Org-mode for writing academic research papers. Rawal is mainly interested in statistical studies so his introduction emphasizes R but not in a way that excludes using his notes for other languages. Almost everything he says about using R (except the R code itself, of course) applies to other languages as well.
Rawal practices reproducible research so his paper writing environment is structured to make that easy. All the analysis for his papers is performed by embedded code blocks so anyone who has his Org file and external data sets can reproduce his results. He doesn't say but presumably small amounts of data are also included in the file even if they aren't exported.
Export to PDF and HTML is handled by the excellent Org export system. Org can also export to ODT for use with Word but Rawal needs a bit more flexibility so he first exports to LaTeX and then uses
pandoc to complete the conversion.
I really like these notes. If you're writing papers (scientific or not) either as part of your job or as a student, Rawal's note tells you how to do it easily using the much simpler Org-mode markdown instead of LaTeX itself. You need only add a bit of LaTeX boilerplate to your Org file to make things work. Rawal shows you what you need to do. He also includes a brief introduction to Emacs and Org but most Irreal readers will already be familiar with that material.
This is a great resource. If you're writing papers, give it a read.