References
Aickin, Mikel, and Helen Gensler. 1996. “Adjusting for multiple testing when reporting research results: The Bonferroni vs Holm methods.” American Journal of Public Health 86 (5): 726–28. https://doi.org/10.2105/AJPH.86.5.726.
Braschi, Bryony, Paul Denny, Kristian Gray, Tamsin Jones, Ruth Seal, Susan Tweedie, Bethan Yates, and Elspeth Bruford. 2019. “Genenames.org: The HGNC and VGNC resources in 2019.” Nucleic Acids Research 47 (D1): D786–92. https://doi.org/10.1093/nar/gky930.
Flobak, Åsmund, Anaïs Baudot, Elisabeth Remy, Liv Thommesen, Denis Thieffry, Martin Kuiper, and Astrid Lægreid. 2015. “Discovery of Drug Synergies in Gastric Cancer Cells Predicted by Logical Modeling.” Edited by Ioannis Xenarios. PLOS Computational Biology 11 (8): e1004426. https://doi.org/10.1371/journal.pcbi.1004426.
Flobak, Åsmund, Barbara Niederdorfer, Vu To Nakstad, Liv Thommesen, Geir Klinkenberg, and Astrid Lægreid. 2019. “A high-throughput drug combination screen of targeted small molecule inhibitors in cancer cell lines.” Scientific Data 6 (1): 237. https://doi.org/10.1038/s41597-019-0255-7.
Friedman, Jerome, Trevor Hastie, Rob Tibshirani, Balasubramanian Narasimhan, Kenneth Tay, and Noah Simon. 2021. Glmnet: Lasso and Elastic-Net Regularized Generalized Linear Models. https://CRAN.R-project.org/package=glmnet.
Grau, Jan, Ivo Grosse, and Jens Keilwagen. 2015. “PRROC: computing and visualizing precision-recall and receiver operating characteristic curves in R.” Bioinformatics 31 (15): 2595–97. https://doi.org/10.1093/bioinformatics/btv153.
Gu, Zuguang, Roland Eils, and Matthias Schlesner. 2016. “Complex heatmaps reveal patterns and correlations in multidimensional genomic data.” Bioinformatics 32 (18): 2847–49. https://doi.org/10.1093/bioinformatics/btw313.
Holland, John Henry. 1992. Adaptation in Natural and Artificial Systems: An Introductory Analysis with Applications to Biology, Control, and Artificial Intelligence. MIT press.
Holm, Sture. 1979. “A simple sequentially rejective multiple test procedure.” Scandinavian Journal of Statistics, 65–70.
Niederdorfer, Barbara, Vasundra Touré, Miguel Vazquez, Liv Thommesen, Martin Kuiper, Astrid Lægreid, and Åsmund Flobak. 2020. “Strategies to Enhance Logic Modeling-Based Cell Line-Specific Drug Synergy Prediction.” Frontiers in Physiology 11 (July): 862. https://doi.org/10.3389/fphys.2020.00862.
Pepe, M. S. 2000. “Combining diagnostic test results to increase accuracy.” Biostatistics 1 (2): 123–40. https://doi.org/10.1093/biostatistics/1.2.123.
Plante, Jean-Francois. 2017. MAMSE: Calculation of Minimum Averaged Mean Squared Error (MAMSE) Weights. https://CRAN.R-project.org/package=MAMSE.
Saito, Takaya, and Marc Rehmsmeier. 2015. “The Precision-Recall Plot Is More Informative than the ROC Plot When Evaluating Binary Classifiers on Imbalanced Datasets.” Edited by Guy Brock. PLOS ONE 10 (3): e0118432. https://doi.org/10.1371/journal.pone.0118432.
Sondka, Zbyslaw, Sally Bamford, Charlotte G. Cole, Sari A. Ward, Ian Dunham, and Simon A. Forbes. 2018. “The COSMIC Cancer Gene Census: describing genetic dysfunction across all human cancers.” Nature Reviews Cancer 18 (11): 696–705. https://doi.org/10.1038/s41568-018-0060-1.
Veliz-Cuba, Alan, Boris Aguilar, Franziska Hinkelmann, and Reinhard Laubenbacher. 2014. “Steady state analysis of Boolean molecular network models via model reduction and computational algebra.” BMC Bioinformatics 15 (1): 221. https://doi.org/10.1186/1471-2105-15-221.
Zobolas, John. 2020. usefun: A Collection of Useful Functions by John. https://github.com/bblodfon/usefun.
———. 2021. Rtemps: R Templates for Reproducible Data Analyses. https://github.com/bblodfon/rtemps.
Zobolas, John, Martin Kuiper, and Åsmund Flobak. 2020. “Emba: R Package for Analysis and Visualization of Biomarkers in Boolean Model Ensembles.” Journal of Open Source Software 5 (53): 2583. https://doi.org/10.21105/joss.02583.