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  "Title": "Signaling Pathway Impact Analysis (SPIA) using combined evidence\nof pathway over-representation and unusual signaling\nperturbations",
  "Author": "Adi Laurentiu Tarca <atarca@med.wayne.edu>, Purvesh Kathri\n<purvesh@cs.wayne.edu> and Sorin Draghici <sorin@wayne.edu>",
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