To cite the R package 'simone' in publications use:

J. Chiquet, Y. Grandvalet, and C. Ambroise (preprint). Inferring multiple graphical structures. preprint available on ArXiv : http://arxiv.org/abs/0912.4434.

C. Charbonnier, J. Chiquet, and C. Ambroise (2010). Weighted-Lasso for Structured Network Inference from Time Course Data. Statistical Applications in Genetics and Molecular Biology, vol. 9, iss. 1, article 15. http://www.bepress.com/sagmb/vol9/iss1/art15/

C. Ambroise, J. Chiquet, and C. Matias (2009). Inferring sparse Gaussian graphical models with latent structure. Electronic Journal of Statistics, vol. 3, pp. 205--238. http://dx.doi.org/10.1214/08-EJS314

Corresponding BibTeX entries:

  @TechReport{,
    title = {Inferring multiple graphical structures},
    institution = {arXiv},
    year = {2010},
    author = {Julien Chiquet and Yves Grandvalet and Christophe
      Ambroise},
  }

  @Article{,
    title = {Weighted-Lasso for Structured Network Inference from Time
      Course Data},
    journal = {Statistical Applications in Genetics and Molecular
      Biology},
    volume = {9},
    number = {1},
    year = {2010},
    author = {Camille Charbonnier and Julien Chiquet and Christophe
      Ambroise},
  }

  @Article{,
    title = {Inferring sparse Gaussian graphical models with latent
      structure},
    journal = {Electronic Journal of Statistics},
    volume = {3},
    pages = {205--238},
    year = {2009},
    author = {Christophe Ambroise and Julien Chiquet and Catherine
      Matias},
  }