To cite annotationTools, please use:

  Kuhn A, Luthi-Carter R, Delorenzi M (2008) Cross-species and
  cross-platform gene expression studies with the
  Bioconductor-compliant R package annotationTools. BMC Bioinformatics
  9(1):26

A BibTeX entry for LaTeX users is

  @Article{,
    author = {Alexandre Kuhn and Ruth Luthi-Carter and Mauro Delorenzi},
    title = {Cross-species and cross-platform gene expression studies with the Bioconductor-compliant R package annotationTools},
    journal = {BMC Bioinformatics},
    volume = {9},
    year = {2008},
    pages = {26},
    url = {http://www.biomedcentral.com/1471-2105/9/26},
  }