To cite CQN in publications use:

  KD Hansen, RA Irizarry, and Z Wu, Removing technical variability in
  RNA-seq data using conditional quantile normalization. Biostatistics
  2012 vol. 13(2) pp. 204-216.

A BibTeX entry for LaTeX users is

  @Article{,
    title = {{Removing technical variability in RNA-seq data using conditional quantile normalization}},
    author = {Kasper D. Hansen and Rafael A. Irizarry and Zhijin Wu},
    year = {2012},
    journal = {Biostatistics},
    volume = {13},
    number = {2},
    pages = {204--216},
  }