For use of the original simulated annealing algorithm, please cite:

  Almudevar A, McCall MN, McMurray H, Land H (2011). Fitting Boolean
  Networks from Steady State Perturbation Data, Statistical
  Applications in Genetics and Molecular Biology, 10(1): Article 47.

A BibTeX entry for LaTeX users is

  @Article{,
    author = {Anthony Almudevar and Matthew N McCall and Helene McMurray and Hartmut Land},
    title = {Fitting Boolean Networks from Steady State Perturbation Data},
    journal = {Statistical Applications in Genetics and Molecular Biology},
    volume = {10},
    number = {1},
    year = {2011},
    pages = {47},
    publisher = {Berkeley Electronic Press},
  }

For use of the replica exchange algorithm, please cite:

  Gene network modeling via TopNet reveals robust epistatic
  interactions between functionally diverse tumor critical mediator
  genes (2020). Helene R. McMurray, Aslihan Ambeskovic, Laurel A.
  Newman, Jordan Aldersley, Vijaya Balakrishnan, Bradley Smith, Harry
  A. Stern, Hartmut Land, Matthew N. McCall bioRxiv; doi:
  https://doi.org/10.1101/2020.10.07.328542

A BibTeX entry for LaTeX users is

  @Article{,
    author = {{McMurray} and Helene R and {Ambeskovic} and {Aslihan} and {Newman} and Laurel A and {Aldersley} and {Jordan} and {Balakrishnan} and {Vijaya} and {Smith} and {Bradley} and {Stern} and Harry A and {Land} and {Hartmut} and {McCall} and Matthew N},
    title = {Gene network modeling via TopNet reveals robust epistatic interactions between functionally diverse tumor critical mediator genes},
    journal = {bioRxiv},
    year = {2020},
    publisher = {Cold Spring Harbor Laboratory},
  }