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Okay, I found the reference someone cited as "Nate Silver openly rooting for Obama". It's from March 2008, before he joined the NYTimes:

I'm skeptical that that statement should be taken at face value. Nate Silver isn't the smoothest in in-person interviews.

That's weird - I thought I read that he was personally pulling for Obama somewhere on 538. I'll go look for that.

Here he says: "I would describe myself as being somewhere between a liberal and a Libertarian."