To cite PADOG package in publications use:

  Adi L. Tarca, Sorin Draghici, Gaurav Bhatti, Roberto Romero,
  Down-weighting overlapping genes improves gene set analysis, BMC
  Bioinformatics, 13(136), 2012.

A BibTeX entry for LaTeX users is

  @Article{,
    author = {Adi L. Tarca and Sorin Draghici and Gaurav Bhatti and Roberto Romero},
    title = {Down-weighting overlapping genes improves gene set analysis},
    journal = {BMC Bioinformatics},
    year = {2012},
    volume = {13},
    number = {136},
  }

  Adi L. Tarca, Gaurav Bhatti and Roberto Romero, A Comparison of Gene
  Set Analysis Methods in Terms of Sensitivity, Prioritization and
  Specificity, PLoS One, 8(11), 2013.

A BibTeX entry for LaTeX users is

  @Article{,
    author = {Adi L. Tarca and Gaurav Bhatti and Roberto Romero},
    title = {A Comparison of Gene Set Analysis Methods in Terms of Sensitivity, Prioritization and Specificity},
    journal = {PLoS One},
    year = {2013},
    volume = {8},
    number = {11},
  }