Please cite the paper below for the qusage software itself. Please also try to cite the appropriate methodology articles when using either the QGen mixed model framework or the gene set meta-analysis pipeline. To cite QuSAGE, use the following publication: To cite the QGen mixed model framework, use the following publication: To cite the QuSAGE meta-analysis framework, use the following publication:

Yaari G, Bolen CR, Thakar J, Kleinstein SH. Quantitative set analysis for gene expression: a method to quantify gene set differential expression including gene-gene correlations. Nucleic Acids Res. 2013 Aug 5.

Turner JA, Bolen CR, Blankenship DM. Quantitative gene set analysis generalized for repeated measures, confounder adjustment, and continuous covariates. BMC Bioinformatics. 2015 Aug 28

Meng H, Yaari G, Bolen CR, Avey S, Kleinstein SH. Gene set meta-analysis with Quantitative Set Analysis for Gene Expression (QuSAGE). PLoS Comput Biol. 2019

Corresponding BibTeX entries:

  @Article{,
    title = {Quantitative set analysis for gene expression: a method to
      quantify gene set differential expression including gene-gene
      correlations.},
    author = {Gur Yaari and Christopher R. Bolen and Juilee Thakar and
      Steven H. Kleinstein},
    journal = {Nucleic Acids Res.},
    year = {2013},
  }

  @Article{,
    title = {Quantitative gene set analysis generalized for repeated
      measures, confounder adjustment, and continuous covariates.},
    author = {Jacob A. Turner and Christopher R. Bolen and Derek M.
      Blankenship},
    journal = {BMC Bioinformatics.},
    year = {2015},
  }

  @Article{,
    title = {Gene set meta-analysis with Quantitative Set Analysis for
      Gene Expression (QuSAGE). .},
    author = {Hailong Meng and Gur Yaari and Christopher R. Bolen and
      Stefan Avey and Steven H. Kleinstein},
    journal = {PLoS Computat Biol.},
    year = {2019},
  }