To cite the GMD package in publications use:

Zhao et al (2011), Systematic Clustering of Transcription Start Site Landscapes, PLoS ONE 6(8): e23409.

Corresponding BibTeX entry:

  @Article{,
    author = {Xiaobei Zhao and Eivind Valen and Brian J Parker and
      Albin Sandelin},
    title = {Systematic Clustering of Transcription Start Site
      Landscapes},
    journal = {PLoS ONE},
    year = {2011},
    volume = {6},
    pages = {e23409},
    number = {8},
    url = {http://dx.plos.org/10.1371/journal.pone.0023409},
  }