Heavy flavor production is a sensitive probe of all stages in the evolution of a heavy ion collision system, and in particular heavy quarkonia could be direct probes of quark deconfinement in $A+A$ collisions. The characterization of the competing effects on the yield in heavy ion collisions (like energy loss or suppression by collisions with initial partons or co-movers) requires a detailed description of the production, from $p+p$ and $p+A$ to $A+A$ collisions.
The unique versatility and increasing performance of the BNL/RHIC collider has provided several beams combinations at $\sqrt{S_{NN}}$ from $7$ to $500 GeV$. Also, improvements of the PHENIX experiment allow deeper study than has been previously published.
This talk aims at presenting recent PHENIX results on $J/\psi$, $\psi’$ and open charm and beauty productions at $\sqrt{S_{NN}} = 200GeV$ in several collision systems and focus on the additional degrees of freedom in $p+A$ and $A+A$ collisions have compared to $p+p$ collisions.