This is a LaTeX template for ES100 taught at Harvard. It contains both a template for a thesis and a fair amount of introductory information on the use of LaTeX.
More details and instructions can be found here: https://github.com/CapraLab/lab-manuscript-template
The goal of this template is to make formatting and writing a scientific manuscript easier and more standardized. This should be appropriate as a basic academic journal template, but the Capra Lab is an evolutionary genomics lab (submitting to journals like MBE, AJHG, Genome Biology, Nat Eco Evo, etc). Some of these suggestions are subjective and there is ultimately no one-size-fits-all for writing a paper. However, this will hopefully serve as a great place to start.