Hmm...
Assuming this isn't the aloof HE (and seeing as this is a forum fight, it wouldn't be), I'd say HE not only wins, but could also, arguably, be considered smarter than Doom overall, and in genetics in particular. HE turned himself into, essentially, a God, via his intellect. Doom, fan worship notwithstanding, has just stolen other beings godlike abilities via tech and mastered sorcery. Pretty much every field Doom has mastered HE has as well, with HE being far better in the field of genetics, and HE having more personal power. Doom's simply more diabolical and popular.