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. 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. Ph.D. thesis, New Mexico State University.

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

Nguyen H (2018). Inference of Functional Dependency via Asymmetric, Optimal, and Model-free Statistics. Ph.D. thesis, New Mexico State University.

To cite the exact functional test in publications use:

Zhong H, Song M (2019). “A fast exact functional test for directional association and cancer biology applications.” IEEE/ACM Transactions on Computational Biology and Bioinformatics, 16(3). https://doi.org/10.1109/TCBB.2018.2809743.

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

Song M, Zhang Y, Katzaroff A, Edgar B, Buttitta L (2014). “Hunting complex differential gene interaction patterns across molecular contexts.” Nucleic Acids Research, 42(7). https://doi.org/10.1093/nar/gku086.

Zhang Y, Liu L, Song M (2015). “ChiNet uncovers rewired transcription subnetworks in tolerant yeast for advanced biofuels conversion.” Nucleic Acids Research, 43(9). https://doi.org/10.1093/nar/gkv358.

To cite the simulate_tables() function in publications use:

Sharma R, Kumar S, Zhong H, Song M (2017). “Simulating noisy, nonparametric, and multivariate discrete patterns.” The R Journa, 9(2). https://doi.org/10.32614/RJ-2017-053.

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},
  }
  @PhdThesis{nguyen2018modelfree,
    author = {Hien Nguyen},
    year = {2018},
    title = {Inference of Functional Dependency via Asymmetric,
      Optimal, and Model-free Statistics},
    school = {New Mexico State University},
  }
  @Article{zhong2019eft,
    title = {A fast exact functional test for directional association
      and cancer biology applications},
    journal = {IEEE/ACM Transactions on Computational Biology and
      Bioinformatics},
    year = {2019},
    volume = {16},
    number = {3},
    page = {818--826},
    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://doi.org/10.1093/nar/gku086},
  }
  @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://doi.org/10.1093/nar/gkv358},
  }
  @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://doi.org/10.32614/RJ-2017-053},
  }