hese proceedings are dedicated to Miklos Gyulassy's 70$^{\rm th}$ birthday. In his long and distinguished career he has made seminal contributions to many areas of heavy ion theory, including early papers on quarkonium phenomenology in fixed-target heavy ion experiments. Theoretical and experimental studies of the $J/\psi$ and $\Upsilon$ states have evolved considerably in the past decades, and I describe a recent generalization of non-relativistic Quantum Chromodynamics to include interactions in a generic nuclear medium. NRQCD with Glauber gluons aims to provide a universal microscopic description of the interaction of heavy quarkonia in a range of phases that include cold nuclear matter, dense hadron gas, and quark-gluon plasma. Such effective field theory is an important step toward understanding the common trends in proton-nucleus and nucleus-nucleus data on quarkonium suppression.