To cite bnlearn in publications use:

Marco Scutari (2010). Learning Bayesian Networks with the bnlearn R Package. Journal of Statistical Software, 35(3), 1-22. URL http://www.jstatsoft.org/v35/i03/.

Corresponding BibTeX entry:

  @Article{,
    title = {Learning Bayesian Networks with the {bnlearn} {R}
      Package},
    author = {Marco Scutari},
    journal = {Journal of Statistical Software},
    year = {2010},
    volume = {35},
    number = {3},
    pages = {1--22},
    url = {http://www.jstatsoft.org/v35/i03/},
  }