To cite the functional chi-square test in publications use:

Zhang, Y., & Song, M. (2013). Deciphering interactions in causal networks without parametric assumptions. arXiv Molecular Networks, arXiv:1311.2707. Retrieved from URL http://arxiv.org/pdf/1311.2707v3.pdf

To cite the comparative functional chi-square test in publications use:

Zhang, Y. (2014). Nonparametric Statistical Methods for Biological Network Inference. Unpublished doctoral dissertation, Department of Computer Science, New Mexico State University, Las Cruces, USA

To cite the exact functional test in publications use:

Zhong, H. (2014). An Exact and Fast Statistical Test for Nonparametric Functional Dependencies. Unpublished M.S. thesis, Department of Computer Science, New Mexico State University, Las Cruces, USA

To cite the comparative chi-square test in publications use:

Song, M., Zhang, Y., Katzaroff, A. J., Edgar, B. A., and Buttitta, L. (2014) Hunting complex differential gene interaction patterns across molecular contexts. Nucleic Acids Research 42(7), e57

Zhang, Y., Liu, Z. L., and Song, M. (2015) ChiNet uncovers rewired transcription subnetworks in tolerant yeast for advanced biofuels conversion. Nucleic Acids Research 43(9), 4393-4407

Corresponding BibTeX entries:

  @Article{zhang2013deciphering,
    title = {Deciphering interactions in causal networks without
      parametric assumptions},
    journal = {arXiv Molecular Networks},
    year = {2013},
    page = {arXiv:1311.2707},
    author = {Yang Zhang and Mingzhou Song},
    url = {http://arxiv.org/pdf/1311.2707v3.pdf},
  }

  @PhdThesis{zhang2014nonparametric,
    author = {Yang Zhang},
    year = {2014},
    title = {Nonparametric Statistical Methods for Biological Network
      Inference},
    school = {New Mexico State University},
  }

  @MastersThesis{zhong2014an,
    author = {Hua Zhong},
    year = {2014},
    title = {An Exact and Fast Statistical Test for Nonparametric
      Functional Dependencies},
    school = {New Mexico State University},
  }

  @Article{song2014hunting,
    title = {Hunting complex differential gene interaction patterns
      across molecular contexts},
    journal = {Nucleic Acids Research},
    year = {2014},
    volume = {42},
    number = {7},
    page = {e57},
    author = {Mingzhou Song and Yang Zhang and Alexia Katzaroff and
      Bruce Edgar and Laura Buttitta},
    url = {http://nar.oxfordjournals.org/content/42/7/e57.full},
  }

  @Article{zhang2015chinet,
    title = {{ChiNet} uncovers rewired transcription subnetworks in
      tolerant yeast for advanced biofuels conversion},
    journal = {Nucleic Acids Research},
    year = {2015},
    volume = {43},
    number = {9},
    page = {4393-4407},
    author = {Yang Zhang and Lewis Liu and Mingzhou Song},
    url = {http://nar.oxfordjournals.org/content/43/9/4393.long},
  }