On The Reconstruction of Interaction Networks with Applications to   Transcriptional Regulation
  A novel information-theoretic method for reconstruction of interaction networks is introduced. We prove that the method is exact for some class of networks. Performance tests on large synthetic transcriptional regulatory networks produce very encouraging results. 
Adam A. Margolin, Ilya Nemenman, Chris Wiggins, Gustavo Stolovitzky,   Andrea Califano