  Traceability between published scientific breakthroughs and their
implementation is essential, especially in the case of open-source scientific
software which implements bleeding-edge science in its code. However, aligning
the link between GitHub repositories and academic papers can prove difficult,
and the current practice of establishing and maintaining such links remains
unknown. This paper investigates the role of academic paper references
contained in these repositories. We conduct a large-scale study of 20 thousand
GitHub repositories that make references to academic papers. We use a
mixed-methods approach to identify public access, traceability and evolutionary
aspects of the links. Although referencing a paper is not typical, we find that
a vast majority of referenced academic papers are public access. These
repositories tend to be affiliated with academic communities. More than half of
the papers do not link back to any repository. We find that academic papers
from top-tier SE venues are not likely to reference a repository, but when they
do, they usually link to a GitHub software repository. In a network of arXiv
papers and referenced repositories, we find that the most referenced papers are
(i) highly-cited in academia and (ii) are referenced by repositories written in
different programming languages.
