To cite bnlearn in publications use the most appropriate among:

A teaching book about Bayesian networks based on bnlearn:

Marco Scutari, Jean-Baptiste Denis. (2014) Bayesian Networks with Examples in R. Chapman and Hall, Boca Raton. ISBN 978-1-4822-2558-7.

To cite applications of Bayesian networks in genetics and systems biology you may want to use:

Radhakrishnan Nagarajan, Marco Scutari, Sophie Lebre. (2013) Bayesian Networks in R with Applications in Systems Biology. Springer, New York. ISBN 978-1-4614-6445-7.

To cite parallel computing for bnlearn in publications use:

Marco Scutari (2017). Bayesian Network Constraint-Based Structure Learning Algorithms: Parallel and Optimized Implementations in the bnlearn R Package. Journal of Statistical Software, 77(2), 1-20.<doi:10.18637/jss.v077.i02>

To cite general use of 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/.

This last is the original JSS paper for the package.

Corresponding BibTeX entries:

  @Book{,
    title = {Bayesian Networks with Examples in {R}},
    author = {Marco Scutari and Jean-Baptiste Denis},
    publisher = {Chapman and Hall},
    address = {Boca Raton},
    year = {2014},
    note = {ISBN 978-1-4822-2558-7, 978-1-4822-2560-0},
  }

  @Book{,
    title = {Bayesian Networks in {R} with Applications in Systems
      Biology},
    author = {Radhakrishnan Nagarajan and Marco Scutari},
    publisher = {Springer},
    address = {New York},
    year = {2013},
    note = {ISBN 978-1-4614-6445-7, 978-1-4614-6446-4},
    doi = {10.1007/978-1-4614-6446-4},
  }

  @Article{,
    title = {Bayesian Network Constraint-Based Structure Learning
      Algorithms: Parallel and Optimized Implementations in the
      {bnlearn} {R} Package},
    author = {Marco Scutari},
    journal = {Journal of Statistical Software},
    year = {2017},
    volume = {77},
    number = {2},
    pages = {1--20},
    doi = {10.18637/jss.v077.i02},
  }

  @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},
    doi = {10.18637/jss.v035.i03},
  }