High energy heavy ion collisions, like those performed at the Relativistic Heavy Ion Collider (RHIC), allow us to test our understanding of nuclear physics at the highest temperatures accessible in the laboratory. At these high temperatures, a new phase of nuclear matter called the Quark Gluon Plasma (QGP), where the fundamental quarks and gluons are no longer confined within hadrons, is created. The RHIC experiments discovered that the QGP is strongly coupled and behaves as a nearly perfect fluid, contrary to initial expectations. Understanding the microscopic structure of the QGP, and its strongly coupled nature, requires calibrated probes at varying length scales. Heavy quarks, namely charm and bottom, are produced in initial hard scatterings, and therefore provide an excellent tool for these studies as they experience the full evolution of the produced medium. In this colloquium, I will discuss the use of heavy quarks as a probe of the medium produced in heavy ion collisions including recent experimental advances made possible by detector upgrades of the PHENIX experiment at RHIC.