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

Zhang, Y. and Song, M. (2013) Deciphering interactions in causal networks without parametric assumptions. arXiv Molecular Networks, arXiv:1311.2707. Retrieved from URL https://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 Unpublished doctoral dissertation, Department of Computer Science, New Mexico State University, Las Cruces, USA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. and Song, M. (2018) A fast exact functional test for directional association and cancer biology applications. IEEE/ACM Transactions on Computational Biology and Bioinformatics. https://doi.org/10.1109/TCBB.2018.2809743

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. Retrieved from URL https://nar.oxfordjournals.org/content/42/7/e57.full

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. Retrieved from URL https://nar.oxfordjournals.org/content/43/9/4393.long

To cite the simulate_tables() function in publications use:

Sharma, R., Kumar, S., Zhong, H. and Song, M. (2017) Simulating noisy, nonparametric, and multivariate discrete patterns. The R Journal 9(2), 366--377. Retrieved from https://journal.r-project.org/archive/2017/RJ-2017-053/index.html

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 = {https://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},
  }
  @Article{zhong2018eft,
    title = {A fast exact functional test for directional association
      and cancer biology applications},
    journal = {IEEE/ACM Transactions on Computational Biology and
      Bioinformatics},
    year = {2018},
    note = {In press},
    author = {Hua Zhong and Mingzhou Song},
    url = {https://doi.org/10.1109/TCBB.2018.2809743},
  }
  @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 = {https://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 = {https://nar.oxfordjournals.org/content/43/9/4393.long},
  }
  @Article{sharma2017simulating,
    title = {Simulating noisy, nonparametric, and multivariate discrete
      patterns},
    journal = {The R Journa},
    year = {2017},
    volume = {9},
    number = {2},
    page = {366--377},
    author = {Ruby Sharma and Sajal Kumar and Hua Zhong and Mingzhou
      Song},
    url =
      {https://journal.r-project.org/archive/2017/RJ-2017-053/index.html},
  }