Heavy quarks and their bound states are ideal probes of the medium formed in heavy ion collisions.  The resulting hierarchy of scales of in-medium heavy quarkonium makes the combined system ideally suited for treatment using nonrelativistic effective field theories and the formalism of open quantum systems (OQS).  My talk will consist of three parts: in the first, I will present an introduction to nonrelativistic QCD (NRQCD), potential NRQCD (pNRQCD), and the OQS formalism; in the second, I will present the derivation of the master equation governing the evolution of in-medium heavy quarkonium; and in the third, I will discuss solutions of the master equation and present recent phenomenological results for the nuclear modification factor and the elliptic flow compared against experimental measurements.