Heavy quark production in heavy ion collisions has been used as a probe of
the strongly coupled quark gluon plasma in two ways. One is the study of
the collision centrality and transverse momentum dependence of the
modification of open heavy flavor yields in A+A collisions, which
provides information about the coupling of the heavy quark to the medium.
The other is the study of the modification of heavy quarkonia in A+A
collisions, which provides information about the effect of the medium on
the binding of these closed heavy flavor mesons. PHENIX has the ability
to study both probes at midrapidity and at forward/backward rapidity.
Recently, measurements of quarkonia production in $p(d)$+A collisions have
shown strong modification of the more weakly bound quarkonia, at the same
time that evidence of the formation of a small QGP in
these light systems has been found. This proceedings presents results of
measurements of separated charm and bottom open heavy flavor modification
in Au+Au collisions, and charmonia production
in $p$+Al and $p$+Au collisions.