Russell's "Why I am Not a Christian" is an excellent primer on the atheist viewpoint. Nietzsche's approach to religion is also at the core of many (but not all or even most) atheist's conceptions. Really,
the Skeptic's Annotated Bible almost makes everything else obsolete. The thing is it's hard to figure out what's most relevant in the flood of information there. Also it makes me look unbiased (really, it's that bad). The overall best basis may just be a google search for "arguments against Christianity." That's really what the atheist position consists of. And when the Bible comes up, you'll notice certain frequent examples that almost every educated atheist will use (including the Midianites, because it has great "stopping power").
I don't think atheistic interpretations of the Bible are the best place to look, because atheists frequently interpret the Bible as a work of fiction. And as a work of fiction, there's really nothing wrong with it (other than the boring lineages). So the position on Christianity (rather than the Bible per se) tends to be more organic.