Commentariat is a dark syntax theme explicitly designed for writing papers, essays, academic articles, and others in markdown. Despite the maturity of Atom's theming framework, there are few options available for dark themes to those interested in using Atom as an academic toolkit, and I find that writing with darker backgrounds and lighter text makes it easier to focus on the task at hand. If you want a light theme, I highly recommend Pen-Paper-Coffee).
The theme features a pastel-based color scheme for a decent amount of contrast while writing the syntactic elements of markdown. The colors are mapped to a variety of different elements for differentiation, and the end result is being able to see each independent change or addition to your own plain text writing without the contrast between each element causing a headache, obviously important to writing the types of long documents characteristic of academic writing.
For an effective and seamless academic workflow writing in markdown in atom, I suggest the following extensions:
Here's a screenshot of the markup backend for this post
This syntax theme started from an edit of monokai-solarized-dark.
Good catch. Let us know what about this package looks wrong to you, and we'll investigate right away.