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

Song M, Zhang Y, Katzaroff AJ, Edgar BA, Buttitta L (2014). “Hunting complex differential gene interaction patterns across molecular contexts.” Nucleic Acids Research, 42(7), e57. doi: 10.1093/nar/gku086.

Zhang Y, Liu ZL, Song M (2015). “ChiNet uncovers rewired transcription subnetworks in tolerant yeast for advanced biofuels conversion.” Nucleic Acids Research, 43(9), 4393–4407. doi: 10.1093/nar/gkv358.

To cite the Sharma-Song test in publications use:

Sharma R, Song M (2020). DiffXTables: Pattern Analysis Across Contingency Tables. R package, https://CRAN.R-project.org/package=DiffXTables.

To cite the marginal-change test, the strength test, and type analysis on multiple contingency tables in publications use:

Sharma R, Luo X, Kumar S, Song M (2020). “Three co-expression pattern types across microbial transcriptional networks of plankton in two oceanic waters.” In Proceedings of the 11th ACM International Conference on Bioinformatics, Computational Biology, and Health Informatics (BCB '20). In press.

Corresponding BibTeX entries:

  @Article{song2014hunting,
    title = {Hunting complex differential gene interaction patterns
      across molecular contexts},
    journal = {Nucleic Acids Research},
    year = {2014},
    volume = {42},
    number = {7},
    pages = {e57},
    author = {Mingzhou Song and Yang Zhang and Alexia J. Katzaroff and
      Bruce A. Edgar and Laura Buttitta},
    doi = {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},
    pages = {4393--4407},
    author = {Yang Zhang and Z. Lewis Liu and Mingzhou Song},
    doi = {10.1093/nar/gkv358},
  }
  @Manual{sharma2020diffxtables,
    title = {DiffXTables: Pattern Analysis Across Contingency Tables},
    author = {Ruby Sharma and Mingzhou Song},
    year = {2020},
    note = {R package},
    url = {https://CRAN.R-project.org/package=DiffXTables},
  }
  @InProceedings{sharma2020COPTYP,
    author = {Ruby Sharma and Xuye Luo and Sajal Kumar and Mingzhou
      Song},
    booktitle = {Proceedings of the 11th ACM International Conference
      on Bioinformatics, Computational Biology, and Health Informatics
      {(BCB '20)}},
    title = {Three co-expression pattern types across microbial
      transcriptional networks of plankton in two oceanic waters},
    year = {2020},
    note = {In press},
  }