  These 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.
