references.bib

@article{Mendoza2006,
abstract = {},
author = {Mendoza, Luis and Xenarios, Ioannis},
doi = {10.1186/1742-4682-3-13},
issn = {17424682},
journal = {Theoretical Biology and Medical Modelling},
keywords = {Biomedicine general,Cellular and Medical Topics,Health Sciences,Medicine,Physiological,Statistics for Life Sciences,Systems Biology},
mendeley-groups = {Dynamics/Others},
month = {mar},
number = {1},
pages = {13},
publisher = {BioMed Central},
title = {{A method for the generation of standardized qualitative dynamical systems of regulatory networks}},
url = {http://tbiomed.biomedcentral.com/articles/10.1186/1742-4682-3-13},
volume = {3},
year = {2006}
}

@article{Friedman2010,
annote = {glmnet R paper},
author = {Friedman, Jerome and Hastie, Trevor and Tibshirani, Robert},
journal = {Journal of Statistical Software},
mendeley-groups = {Statistics/Software},
number = {1},
pages = {1--22},
title = {{Regularization Paths for Generalized Linear Models via Coordinate Descent}},
url = {http://www.jstatsoft.org/v33/i01/},
volume = {33},
year = {2010}
}

@article{Liaw2002,
annote = {randomForest R package citation},
author = {Liaw, Andy and Wiener, Matthew},
journal = {R News},
mendeley-groups = {Statistics/Software},
number = {3},
pages = {18--22},
title = {{Classification and Regression by randomForest}},
url = {https://cran.r-project.org/doc/Rnews/},
volume = {2},
year = {2002}
}

@article{McInnes2018a,
archivePrefix = {arXiv},
arxivId = {1802.03426},
author = {McInnes, Leland and Healy, John and Melville, James},
eprint = {1802.03426},
mendeley-groups = {Machine Learning},
month = {feb},
title = {{UMAP: Uniform Manifold Approximation and Projection for Dimension Reduction}},
url = {http://arxiv.org/abs/1802.03426},
year = {2018}
}

@article{Wright2017,
author = {Wright, Marvin and Ziegler, Andreas},
doi = {10.18637/jss.v077.i01},
issn = {1548-7660},
journal = {Journal of Statistical Software, Articles},
keywords = {C++,R,Rcpp,classification,machine learning,random forests,recursive partitioning,survival analysis},
mendeley-groups = {Statistics,Statistics/Software},
number = {1},
pages = {1--17},
title = {{ranger: A Fast Implementation of Random Forests for High Dimensional Data in C++ and R}},
url = {https://www.jstatsoft.org/v077/i01},
volume = {77},
year = {2017}
}

@article{Flobak2015,
author = {Flobak, {\AA}smund and Baudot, Ana{\"{i}}s and Remy, Elisabeth and Thommesen, Liv and Thieffry, Denis and Kuiper, Martin and L{\ae}greid, Astrid},
doi = {10.1371/journal.pcbi.1004426},
editor = {Xenarios, Ioannis},
file = {:home/john/.local/share/data/Mendeley Ltd./Mendeley Desktop/Downloaded/Flobak et al. - 2015 - Discovery of Drug Synergies in Gastric Cancer Cells Predicted by Logical Modeling.pdf:pdf},
issn = {1553-7358},
journal = {PLOS Computational Biology},
mendeley-groups = {Modeling/Cancer},
month = {aug},
number = {8},
pages = {e1004426},
publisher = {Public Library of Science},
title = {{Discovery of Drug Synergies in Gastric Cancer Cells Predicted by Logical Modeling}},
url = {http://dx.plos.org/10.1371/journal.pcbi.1004426},
volume = {11},
year = {2015}
}

@misc{emba-site,
author = {Zobolas, John},
publisher = {GitHub Pages},
title = {{Emba Package Website}},
url = {https://bblodfon.github.io/emba/},
year = {2020}
}

@article{Zobolas2020,
  doi = {10.21105/joss.02583},
  url = {https://doi.org/10.21105/joss.02583},
  year = {2020},
  publisher = {The Open Journal},
  volume = {5},
  number = {53},
  pages = {2583},
  author = {John Zobolas and Martin Kuiper and Åsmund Flobak},
  title = {emba: R package for analysis and visualization of biomarkers in boolean model ensembles},
  journal = {Journal of Open Source Software}
}

@article{Cury2019,
archivePrefix = {arXiv},
arxivId = {1901.07623},
author = {Cury, Jos{\'{e}} E. R. and Monteiro, Pedro T. and Chaouiya, Claudine},
eprint = {1901.07623},
month = {jan},
title = {{Partial Order on the set of Boolean Regulatory Functions}},
url = {http://arxiv.org/abs/1901.07623},
year = {2019}
}

@article{Chaouiya2013,
author = {Chaouiya, Claudine and Ourrad, Ouerdia and Lima, Ricardo},
doi = {10.1371/journal.pone.0069626},
issn = {19326203},
journal = {PLoS ONE},
keywords = {Cell cycle and cell division,Fungal evolution,Gene regulation,Gene regulatory networks,Inertia,Markov models,Regulator genes,Yeast and fungal models},
mendeley-groups = {Dynamics/Threshold Functions},
month = {jul},
number = {7},
pages = {69626},
pmid = {23922761},
publisher = {Public Library of Science},
title = {{Majority Rules with Random Tie-Breaking in Boolean Gene Regulatory Networks}},
url = {www.plosone.org},
volume = {8},
year = {2013}
}

@article{Landis1977,
author = {Landis, J. Richard and Koch, Gary G.},
doi = {10.2307/2529310},
file = {:home/john/Downloads/2529310.pdf:pdf},
issn = {0006341X},
journal = {Biometrics},
mendeley-groups = {Statistics},
month = {mar},
number = {1},
pages = {159},
pmid = {843571},
publisher = {JSTOR},
title = {{The Measurement of Observer Agreement for Categorical Data}},
volume = {33},
year = {1977}
}

@article{McHugh2012a,
author = {McHugh, Mary L.},
doi = {10.11613/bm.2012.031},
issn = {13300962},
journal = {Biochemia Medica},
keywords = {Interrater,Kappa,Rater,Reliability},
mendeley-groups = {Statistics},
month = {oct},
number = {3},
pages = {276--282},
pmid = {23092060},
publisher = {Biochemia Medica, Editorial Office},
title = {{Interrater reliability: The kappa statistic}},
url = {https://www.biochemia-medica.com/en/journal/22/10.11613/BM.2012.031},
volume = {22},
year = {2012}
}

@article{Mussel2010,
annote = {BoolNet paper},
author = {M{\"{u}}ssel, Christoph and Hopfensitz, Martin and Kestler, Hans A.},
doi = {10.1093/bioinformatics/btq124},
issn = {1460-2059},
journal = {Bioinformatics},
mendeley-groups = {Dynamics/Tools},
month = {may},
number = {10},
pages = {1378--1380},
publisher = {Narnia},
title = {{BoolNet—an R package for generation, reconstruction and analysis of Boolean networks}},
url = {https://doi.org/10.1093/bioinformatics/btq124},
volume = {26},
year = {2010}
}

@article{Aldana2003,
author = {Aldana, Maximino and Goldstein, R E},
doi = {10.1016/S0167-2789(03)00174-X},
file = {:home/john/.local/share/data/Mendeley Ltd./Mendeley Desktop/Downloaded/Aldana, Goldstein - 2003 - Boolean dynamics of networks with scale-free topology.pdf:pdf},
journal = {Physica D: Nonlinear Phenomena},
keywords = {Boolean networks,Dynamical phase transition,Evolvability,PACS,Scale-free topology,Stability},
mendeley-groups = {Dynamics/Others},
title = {{Boolean dynamics of networks with scale-free topology}},
url = {https://doi.org/10.1016/S0167-2789(03)00174-X},
year = {2003}
}

@book{crama2011boolean,
author = {Crama, Yves and Hammer, Peter L},
publisher = {Cambridge University Press},
title = {{Boolean functions: Theory, algorithms, and applications}},
year = {2011}
}

@article{Gherardi2016,
archivePrefix = {arXiv},
arxivId = {1603.03337},
author = {Gherardi, Marco and Rotondo, Pietro},
journal = {Complexity},
keywords = {Boolean complexity,canalization,gene regulation,propositional calculus,robustness},
mendeley-groups = {Dynamics/Others},
month = {mar},
pages = {397--408},
publisher = {John Wiley and Sons Inc.},
title = {{Measuring logic complexity can guide pattern discovery in empirical systems}},
url = {http://arxiv.org/abs/1603.03337},
volume = {21},
year = {2016}
}

@book{wegener1987complexity,
author = {Wegener, Ingo},
publisher = {BG Teubner},
title = {{The complexity of Boolean functions}},
year = {1987}
}

@book{Graham1994,
address = {USA},
author = {Graham, Ronald L and Knuth, Donald E and Patashnik, Oren},
edition = {2nd},
isbn = {0201558025},
mendeley-groups = {Books},
publisher = {Addison-Wesley Longman Publishing Co., Inc.},
title = {{Concrete Mathematics: A Foundation for Computer Science}},
year = {1994}
}

@inproceedings{Benjamini2005,
address = {New York, USA},
author = {Benjamini, Itai and Schramm, Oded and Wilson, David B.},
booktitle = {Proceedings of the Annual ACM Symposium on Theory of Computing},
doi = {10.1145/1060590.1060627},
issn = {07378017},
pages = {244--250},
publisher = {ACM Press},
title = {{Balanced Boolean functions that can be evaluated so that every input bit is unlikely to be read}},
url = {http://portal.acm.org/citation.cfm?doid=1060590.1060627},
year = {2005}
}

@article{Bornholdt2008,
author = {Bornholdt, Stefan},
doi = {10.1098/rsif.2008.0132.focus},
issn = {1742-5689},
journal = {Journal of The Royal Society Interface},
keywords = {Boolean networks,Computer simulation,Regulatory networks},
mendeley-groups = {Modeling/Threshold Functions},
month = {aug},
publisher = {Royal Society},
title = {{Boolean network models of cellular regulation: prospects and limitations}},
url = {https://royalsocietypublishing.org/doi/10.1098/rsif.2008.0132.focus},
volume = {5},
year = {2008}
}

@article{Ravasz2003,
archivePrefix = {arXiv},
arxivId = {cond-mat/0206130},
author = {Ravasz, Erzs{\'{e}}bet and Barab{\'{a}}si, Albert L{\'{a}}szl{\'{o}}},
doi = {10.1103/PhysRevE.67.026112},
eprint = {0206130},
issn = {1063651X},
journal = {Physical Review E - Statistical Physics, Plasmas, Fluids, and Related Interdisciplinary Topics},
month = {feb},
number = {2},
pages = {7},
primaryClass = {cond-mat},
publisher = {American Physical Society},
title = {{Hierarchical organization in complex networks}},
url = {https://journals.aps.org/pre/abstract/10.1103/PhysRevE.67.026112},
volume = {67},
year = {2003}
}