There isn't really a research exemption in the US. From your cited article, citing Madey v. Duke University (2002):

    The court did not reject the defense, but left only a "very
    narrow and strictly limited experimental use defense" for
    "amusement, to satisfy idle curiosity, or for strictly
    philosophical inquiry." The court also precludes the
    defense where, regardless of profit motive, the research 
    was done "in furtherance of the alleged infringer’s 
    legitimate business." In the case of a research university
    like Duke University, the court held that the alleged use
    was in furtherance of its legitimate business, and thus
    the defense was inapplicable.

Practically speaking, it's difficult to sue a university or an individual for patent infringement when they are conducting research without looking like a monster. Considering the costs of litigation, time wasted, hit to PR, nebulous damages to recover, etc., it doesn't sound very worthwhile. Legally speaking, one would appear to have case law on their side.