To cite the functional chi-squared test in publications, use

Zhang Y, Song M (2013). “Deciphering interactions in causal networks without parametric assumptions.” arXiv Molecular Networks, arXiv:1311.2707. https://arxiv.org/abs/1311.2707.

To cite the exact functional test using dynamic and quadratic programming in publications, use

Nguyen HH, Zhong H, Song M (2020). “Optimality, accuracy, and efficiency of an exact functional test.” In Proceedings of the Twenty-Ninth International Joint Conference on Artificial Intelligence, IJCAI-20, 2683–2689. doi:10.24963/ijcai.2020/372.

To cite the exact functional test using quadratic programming 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), 818–826. doi:10.1109/TCBB.2018.2809743.

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 Journal, 9(2), 366–377. doi:10.32614/RJ-2017-053.

To cite the function index in publications, use

Zhong H, Song M (2019b). “Directional association test reveals high-quality putative cancer driver biomarkers including noncoding RNAs.” BMC Med Genomics, 12(7), 129. doi:10.1186/s12920-019-0565-9.

and

Kumar S, Zhong H, Sharma R, Li Y, Song M (2018). “Scrutinizing functional interaction networks from RNA-binding proteins to their targets in cancer.” In IEEE International Conference on Bioinformatics and Biomedicine, 185–190. doi:10.1109/BIBM.2018.8621502.

To cite the adapted functional chi-squared test in publications, use

Kumar S, Song M (2022). “Overcoming biases in causal inference of molecular interactions.” Bioinformatics, 38(10), 2818–2825. doi:10.1093/bioinformatics/btac206.

Corresponding BibTeX entries:

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

  @InProceedings{Nguyen2020EFT,
    author = {Hien H. Nguyen and Hua Zhong and Mingzhou Song},
    booktitle = {Proceedings of the Twenty-Ninth International Joint
      Conference on Artificial Intelligence, {IJCAI-20}},
    title = {Optimality, accuracy, and efficiency of an exact
      functional test},
    year = {2020},
    pages = {2683--2689},
    doi = {10.24963/ijcai.2020/372},
  }

  @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},
    pages = {818--826},
    author = {Hua Zhong and Mingzhou Song},
    doi = {10.1109/TCBB.2018.2809743},
  }

  @Article{sharma2017simulating,
    title = {Simulating noisy, nonparametric, and multivariate discrete
      patterns},
    journal = {The R Journal},
    year = {2017},
    volume = {9},
    number = {2},
    pages = {366--377},
    author = {Ruby Sharma and Sajal Kumar and Hua Zhong and Mingzhou
      Song},
    doi = {10.32614/RJ-2017-053},
  }

  @Article{Zhong2019FANTOM5,
    author = {Hua Zhong and Mingzhou Song},
    doi = {10.1186/s12920-019-0565-9},
    journal = {BMC Med Genomics},
    number = {7},
    pages = {129},
    title = {Directional association test reveals high-quality putative
      cancer driver biomarkers including noncoding RNAs},
    volume = {12},
    year = {2019b},
  }

  @InProceedings{KumarZSLS18,
    address = {Madrid, Spain},
    author = {Sajal Kumar and Hua Zhong and Ruby Sharma and Yiyi Li and
      Mingzhou Song},
    booktitle = {IEEE International Conference on Bioinformatics and
      Biomedicine},
    doi = {10.1109/BIBM.2018.8621502},
    pages = {185--190},
    title = {Scrutinizing functional interaction networks from
      {RNA}-binding proteins to their targets in cancer},
    year = {2018},
  }

  @Article{Kumar2022AFT,
    title = {Overcoming biases in causal inference of molecular
      interactions},
    journal = {Bioinformatics},
    year = {2022},
    volume = {38},
    number = {10},
    pages = {2818--2825},
    author = {Sajal Kumar and Mingzhou Song},
    doi = {10.1093/bioinformatics/btac206},
  }