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.

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

Corresponding BibTeX entries:

  @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},
  }

  @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},
  }