Please cite the following if utilizing the ACME software:

  Scacheri, P. C.; Crawford, G. E. & Davis, S. Statistics for ChIP-chip
  and DNase hypersensitivity experiments on NimbleGen arrays. Methods
  Enzymol, 2006, 411, 270-282

A BibTeX entry for LaTeX users is

  @Article{,
    author = {Peter C Scacheri and Gregory E Crawford and Sean Davis},
    title = {Statistics for ChIP-chip and DNase hypersensitivity experiments on NimbleGen arrays.},
    journal = {Methods Enzymol},
    year = {2006},
    volume = {411},
    pages = {270--282},
  }