Quarkonium production in heavy ion collisions measured by the PHENIX detector at RHIC

Quarkonium ($c\bar{c}$ and $b\bar{b}$) production and its nuclear modification factors in heavy ion collisions offer an opportunity to gauge cold nuclear matter properties such as parton distribution modifications and $Q\bar{Q}$ breakup in the hadronic matter. Furthermore, the quarkonium can be dissociated due to the color screening in quark-gluon plasma. Consequently, the observation of its suppression can be used as a phase transition thermometer. Finally, the quark charm coalescence is likely to enhance the charmonium abundance in deconfined matter. The PHENIX Experiment at RHIC collected large data sets with $p$+$p$, $d$+Au and heavy ion collisions that were used to measure quarkonium production at $\sqrt{S_{NN}}=$200 GeV in different rapidity ranges. This presentation will summarize the up to date quarkonium measurements in $d$+Au and Au+Au collisions obtained by PHENIX and their interpretation in view of the topics described above.