The fundamental theory of the strong interaction -- quantum chromodynamics (QCD) -- provides the foundational framework with which to describe and understand the key properties of atomic nuclei. A deep understanding of the explicit role of quarks and gluons in nuclei remains elusive however, as these effects have thus far been well-disguised by confinement effects in QCD which are encapsulated by a successful description in terms of effective hadronic degrees of freedom. The observation of the EMC effect has provided an enduring indication for explicit QCD effects in nuclei, and points to the medium modification of the bound protons and neutrons in the nuclear medium. Understanding the EMC effect is a major challenge for modern nuclear physics, and several key questions remain, such as understanding its flavor, spin, and momentum dependence. This manuscript provides a contemporary snapshot of our understanding of the role of QCD in nuclei and outlines possible pathways in experiment and theory that will help deepen our understanding of nuclei in the context of QCD.