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{cascade2020,
author = {Tsirvouli, Eirini and Niederdorfer, Barbara and Zobolas, John and Vasundra, Tour{\'{e}} and Flobak, {\AA}smund and Kuiper, Martin},
doi = {10.5281/zenodo.4066665},
month = {oct},
publisher = {Zenodo},
title = {{CASCADE - CAncer Signaling CAusality DatabasE}},
year = {2020}
}