To cite package ‘GEM’ in publications use:

  Pan H, Holbrook JD, Karnani N, Kwoh CK (2016): Gene, Environment and
  Methylation (GEM): A tool suite to efficiently navigate large scale
  epigenome wide association studies and integrate genotype and
  interaction between genotype and environment. BMC Bioinformatics
  (submitted)

A BibTeX entry for LaTeX users is

  @Article{,
    title = {Gene, Environment and Methylation (GEM): A tool suite to efficiently navigate large scale epigenome wide association studies and integrate genotype and interaction between genotype and environment},
    author = {Pan Hong and Holbrook JD and Karnani N and Kwoh CK},
    year = {2016},
    journal = {BMC Bioinformatics},
  }

  Shabalin AA. (2012). Matrix eQTL: ultra fast eQTL analysis via large
  matrix operations. Bioinformatics 28(10): 1353-1358

A BibTeX entry for LaTeX users is

  @Article{,
    title = {Matrix eQTL: ultra fast eQTL analysis via large matrix operations},
    author = {Andrey A. Shabalin},
    year = {2012},
    journal = {Bioinformatics},
    volume = {28(10)},
    pages = {1353--1358},
  }