Cold Nuclear Matter Effects and Heavy Quark Production in PHENIX

The PHENIX experiment uses semileptonic decay channels to measure open and closed heavy flavor cross sections across the rapidity range $-2.2<y<2.4$. High luminosity data are now available for p+p, d+Au, Cu+Cu and Au+Au collisions at $\sqrt{s_{NN}}$=200 GeV, and for Au+Au collisions at $\sqrt{s_{NN}}$= 62 GeV. We discuss recent d+Au results for open heavy flavor and $J\mathrm{/}\psi$ production, and discuss their implications for the cold nuclear matter contributions to heavy flavor production in heavy ion collisions.