The references section is actually a big problem with patents. Having worked with attorneys in the past on patents, they actually want you to find all prior art and to put it in the references of the patent. Why? Because patents are rarely invalidated due to 3rd party prior art listed in references -- even if it really would invalidate the patent looked at objectively. But it effectively takes that prior art off the table for future litigation.
I'd be surprised if Google didn't list Kleinberg's work as it was really well known in academic circles at the time. But if Google ever sued you with PageRank, and you tried to say, "Look -- prior art in Kleinberg!" They'd just say, "The USPTO already examined it and determined it isn't prior art. Sorry." You could almost certainly do a better job than the examiner in looking at the evidence, but the burden is proof is so high for you at this point that unless Larry Page wrote in his code, "This is a copy of Kleinberg's work that we slipped past the UPSTO" you're not likely to invalidate it.
I don't buy that at all. "Look -- prior art in Kleinberg!" is your opinion, not some kind of objective truth that was nefariously "slipped past" the patent office. The differences between PageRank and that prior work are crucial--they are what the patent actually covers.
I'd be surprised if Google didn't list Kleinberg's work as it was really well known in academic circles at the time. But if Google ever sued you with PageRank, and you tried to say, "Look -- prior art in Kleinberg!" They'd just say, "The USPTO already examined it and determined it isn't prior art. Sorry." You could almost certainly do a better job than the examiner in looking at the evidence, but the burden is proof is so high for you at this point that unless Larry Page wrote in his code, "This is a copy of Kleinberg's work that we slipped past the UPSTO" you're not likely to invalidate it.