References

[BHZ+16]

Alexis R Barr, Frank S Heldt, Tongli Zhang, Chris Bakal, and Béla Novák. A dynamical framework for the all-or-none g1/s transition. Cell systems, 2(1):27–37, 2016. URL: https://www.sciencedirect.com/science/article/pii/S2405471216000028, doi:https://doi.org/10.1016/j.cels.2016.01.001.

[HMW+17]

Helge Hass, Kristina Masson, Sibylle Wohlgemuth, Violette Paragas, John E Allen, Mark Sevecka, Emily Pace, Jens Timmer, Joerg Stelling, Gavin MacBeath, and others. Predicting ligand-dependent tumors from multi-dimensional signaling features. NPJ systems biology and applications, 3(1):1–15, 2017. doi:10.1038/s41540-017-0030-3.

[HBC+18]

Frank S Heldt, Alexis R Barr, Sam Cooper, Chris Bakal, and Béla Novák. A comprehensive model for the proliferation–quiescence decision in response to endogenous dna damage in human cells. Proceedings of the National Academy of Sciences, 115(10):2532–2537, 2018. URL: https://www.pnas.org/doi/10.1073/pnas.1715345115, doi:https://doi.org/10.1073/pnas.1715345115.

[IYO22]

Hiroaki Imoto, Sawa Yamashiro, and Mariko Okada. A text-based computational framework for patient-specific modeling for classification of cancers. iScience, 25(3):103944, 2022. URL: https://www.cell.com/iscience/fulltext/S2589-0042(22)00214-0, doi:10.1016/ j.isci.2022.103944.

[KHWB97]

Boris N Kholodenko, Jan B Hoek, Hans V Westerhoff, and Guy C Brown. Quantification of information transfer via cellular signal transduction pathways. FEBS letters, 414(2):430–434, 1997. doi:https://doi.org/10.1016/S0014-5793(97)01018-1.

[Kho00]

Boris N. Kholodenko. Negative feedback and ultrasensitivity can bring about oscillations in the mitogen-activated protein kinase cascades. European Journal of Biochemistry, 267(6):1583–1588, 2000. URL: https://febs.onlinelibrary.wiley.com/doi/abs/10.1046/j.1432-1327.2000.01197.x, arXiv:https://febs.onlinelibrary.wiley.com/doi/pdf/10.1046/j.1432-1327.2000.01197.x, doi:https://doi.org/10.1046/j.1432-1327.2000.01197.x.

[KNT+12]

Hiroyuki Kubota, Rei Noguchi, Yu Toyoshima, Yu-ichi Ozaki, Shinsuke Uda, Kanako Watanabe, Wataru Ogawa, and Shinya Kuroda. Temporal coding of insulin action through multiplexing of the akt pathway. Molecular Cell, 46(6):820–832, 2012. URL: https://www.sciencedirect.com/science/article/pii/S1097276512003401, doi:https://doi.org/10.1016/j.molcel.2012.04.018.

[LG03]

Jean-Christophe Leloup and Albert Goldbeter. Toward a detailed computational model for the mammalian circadian clock. Proceedings of the National Academy of Sciences, 100(12):7051–7056, 2003. URL: https://www.pnas.org/content/100/12/7051, arXiv:https://www.pnas.org/content/100/12/7051.full.pdf, doi:10.1073/pnas.1132112100.

[LSK+18]

Philippe Lucarelli, Marcel Schilling, Clemens Kreutz, Artyom Vlasov, Martin E. Boehm, Nao Iwamoto, Bernhard Steiert, Susen Lattermann, Marvin Wäsch, Markus Stepath, Matthias S. Matter, Mathias Heikenwälder, Katrin Hoffmann, Daniela Deharde, Georg Damm, Daniel Seehofer, Maria Muciek, Norbert Gretz, Wolf D. Lehmann, Jens Timmer, and Ursula Klingmüller. Resolving the combinatorial complexity of smad protein complex formation and its link to gene expression. Cell Systems, 6(1):75–89.e11, 2018. URL: https://www.sciencedirect.com/science/article/pii/S2405471217305380, doi:https://doi.org/10.1016/j.cels.2017.11.010.

[MT08]

Thomas Maiwald and Jens Timmer. Dynamical modeling and multi-experiment fitting with potterswheel. Bioinformatics, 24(18):2037–2043, 2008. doi:10.1093/bioinformatics/btn350.

[NBS+10]

Takashi Nakakuki, Marc R. Birtwistle, Yuko Saeki, Noriko Yumoto, Kaori Ide, Takeshi Nagashima, Lutz Brusch, Babatunde A. Ogunnaike, Mariko Okada-Hatakeyama, and Boris N. Kholodenko. Ligand-specific c-fos expression emerges from the spatiotemporal control of erbb network dynamics. Cell, 141(5):884–896, 2010. URL: https://www.sciencedirect.com/science/article/pii/S0092867410003739, doi:https://doi.org/10.1016/j.cell.2010.03.054.

[OKH+18]

Angela Oppelt, Daniel Kaschek, Suzanna Huppelschoten, Rowena Sison-Young, Fang Zhang, Marie Buck-Wiese, Franziska Herrmann, Sebastian Malkusch, Carmen L Krüger, Mara Meub, and others. Model-based identification of tnfα-induced ikkβ-mediated and iκbα-mediated regulation of nfκb signal transduction as a tool to quantify the impact of drug-induced liver injury compounds. NPJ systems biology and applications, 4(1):1–16, 2018. URL: https://www.nature.com/articles/s41540-018-0058-z, doi:https://doi.org/10.1038/s41540-018-0058-z.