To cite pcalg in publications use:

Markus Kalisch, Martin Maechler, Diego Colombo, Marloes H. Maathuis, Peter Buehlmann (2012). Causal Inference Using Graphical Models with the R Package pcalg. Journal of Statistical Software, 47(11), 1-26. URL http://www.jstatsoft.org/v47/i11/.

Alain Hauser, Peter Buehlmann (2012). Characterization and greedy learning of interventional Markov equivalence classes of directed acyclic graphs Journal of Machine Learning Research, 13, 2409-2464. URL http://jmlr.org/papers/v13/hauser12a.html.

Corresponding BibTeX entries:

  @Article{,
    title = {Causal Inference Using Graphical Models with the {R}
      Package {pcalg}},
    author = {Markus Kalisch and Martin M\"achler and Diego Colombo and
      Marloes H. Maathuis and Peter B\"uhlmann},
    journal = {Journal of Statistical Software},
    year = {2012},
    volume = {47},
    number = {11},
    pages = {1--26},
    url = {http://www.jstatsoft.org/v47/i11/},
  }
  @Article{,
    title = {Characterization and greedy learning of interventional
      {M}arkov equivalence classes of directed acyclic graphs},
    author = {Alain Hauser and Peter B\"uhlmann},
    journal = {Journal of Machine Learning Research},
    year = {2012},
    volume = {13},
    pages = {2409--2464},
    url = {http://jmlr.org/papers/v13/hauser12a.html},
  }