Fisher J, Henzinger TA. Executable cell biology. Nat Biotechnol. 2007; 25(11):1239–49.

Article
CAS
PubMed
Google Scholar

Machado D, Costa RS, Rocha M, Ferreira EC, Tidor B, Rocha I. Modeling formalisms in systems biology. AMB Express. 2011; 1(1):1–14.

Article
Google Scholar

Barnat J, Brim L, Černá I, Dražan S, Šafránek D. Parallel model checking large-scale genetic regulatory networks with divine. Electron Notes Theor Comput Sci. 2008; 194(3):35–50. Proceedings of the First Workshop From Biology To Concurrency and back (FBTC 2007).

Article
Google Scholar

Brim L, Barnat J, Černá I, Dražan S, Fabriková J, Šafránek D. Computational analysis of large-scale multi-affine ode models. In: High Performance Computational Systems Biology, 2009. HIBI ’09. International Workshop On. Los Alamitos (CA), USA: IEEE: 2009. p. 81–90.

Google Scholar

De Jong H, Page M, Hernandez C, Geiselmann J. Qualitative simulation of genetic regulatory networks: Method and application. In: Proceedings of the 17th International Joint Conference on Artificial Intelligence - Volume 1, IJCAI’01. San Francisco: Morgan Kaufmann Publishers Inc.: 2001. p. 67–73.

Google Scholar

Di Cara A, Garg A, De Micheli G, Xenarios I, Mendoza L. Dynamic simulation of regulatory networks using squad. BMC Bioinforma. 2007; 8(1):1–10.

Article
Google Scholar

Barnat J, Brim L, Černá I, Dražan S, Fabriková J, Šafránek D. On algorithmic analysis of transcriptional regulation by {LTL} model checking. Theor Comput Sci. 2009; 410(33-34):3128–48. Concurrent Systems Biology: To Nadia Busi (1968–2007).

Article
Google Scholar

Monteiro PT, Ropers D, Mateescu R, Freitas AT, de Jong H. Temporal logic patterns for querying dynamic models of cellular interaction networks. Bioinformatics. 2008; 24(16):227–33.

Article
Google Scholar

Alur R, Dill DL. A theory of timed automata. Theor Comput Sci. 1994; 126(2):183–235.

Article
Google Scholar

Schivo S, Scholma J, Wanders B, Urquidi Camacho RA, van der Vet PE, Karperien M, Langerak R, van de Pol J, Post JN. Modelling biological pathway dynamics with Timed Automata. IEEE J Biomed Health Inform. 2014; 18(3):832–9.

Article
PubMed
Google Scholar

Scholma J, Schivo S, Urquidi Camacho RA, van de Pol J, Karperien M, Post JN. Biological networks 101: Computational modeling for molecular biologists. Gene. 2014; 533(1):379–84.

Article
CAS
PubMed
Google Scholar

Killcoyne S, Carter GW, Smith J, Boyle J. Cytoscape: a community-based framework for network modeling. Methods Mol Biol (Clifton, N.J.) 2009; 563:219–39.

Article
CAS
Google Scholar

Elowitz MB, Leibler S. A synthetic oscillatory network of transcriptional regulators. Nature. 2000; 403(6767):335.

Article
CAS
PubMed
Google Scholar

Larsen KG, Pettersson P, Yi W. UPPAAL in a nutshell. Int J Softw Tools Technol Transfer (STTT). 1997; 1:134–52.

Article
Google Scholar

Schivo S, Scholma J, Karperien HBJ, Post JN, van de Pol JC, Langerak R. Setting parameters for biological models with ANIMO In: André E, Frehse G, editors. Proceedings 1st International Workshop on Synthesis of Continuous Parameters, Grenoble, France. Electronic Proceedings in Theoretical Computer Science, vol. 145. Australia: Open Publishing Association: 2014. p. 35–47.

Google Scholar

ANIMO. 2015. http://fmt.cs.utwente.nl/tools/animo. Accessed date 11 June 2016.

Batt G, Salah RB, Maler O. Onimed models of gene networks. In: Proceedings of the 5th International Conference on Formal Modeling and Analysis of Timed Systems, FORMATS’07. Berlin, Heidelberg: Springer: 2007. p. 38–52.

Google Scholar

Goethem SV, Jacquet JM, Brim L, Šafránek D. Timed modelling of gene networks with arbitrarily precise expression discretization. Electron Notes Theor Comput Sci. 2013; 293:67–81. Proceedings of the Third International Workshop on Interactions Between Computer Science and Biology (CS2Bio’12).

Article
Google Scholar

Fathallah-Shaykh HM, Bona JL, Kadener S. Mathematical model of the drosophila circadian clock: Loop regulation and transcriptional integration. Biophys J. 2009; 97(9):2399–408.

Article
CAS
PubMed
PubMed Central
Google Scholar

Ma B, Leijten JCH, Wu L, Kip M, van Blitterswijk CA, Post JN, Karperien M. Gene expression profiling of dedifferentiated human articular chondrocytes in monolayer culture. Osteoarthr Cartil. 2013; 21(4):599–603.

Article
CAS
PubMed
Google Scholar

Leijten JCH, Emons J, Sticht C, van Gool S, Decker E, Uitterlinden A, Rappold G, Hofman A, Rivadeneira F, Scherjon S, Wit JM, van Meurs J, van Blitterswijk CA, Karperien M. Gremlin 1, Frizzled-related protein, and Dkk-1 are key regulators of human articular cartilage homeostasis. Arthritis Rheum. 2012; 64(10):3302–12.

Article
CAS
PubMed
Google Scholar

Scholma J, Schivo S, Kerkhofs J, Langerak R, Karperien HBJ, van de Pol JC, Geris L, Post JN. ECHO: the Executable CHOndrocyte. In: Tissue Engineering & Regenerative Medicine International Society, European Chapter Meeting, Genova, Italy, vol. 8. Malden: Wiley: 2014. p. 54.

Google Scholar

Scholma J, Schivo S, Karperien HBJ, Langerak R, van de Pol JC, Post JN. An ECHO in biology: Validating the Executable CHondrocyte. In: 2014 World Congress on Osteoarthritis, Paris, France. Osteoarthritis and Cartilage, vol. 22. Amsterdam: Elsevier: 2014. p. 157.

Google Scholar

Kanehisa M, Goto S. KEGG: Kyoto Encyclopedia of Genes and Genomes. Nucleic Acids Res. 2000; 28(1):27–30.

Article
CAS
PubMed
PubMed Central
Google Scholar

Hornbeck PV, Chabra I, Kornhauser JM, Skrzypek E, Zhang B. PhosphoSite: A bioinformatics resource dedicated to physiological protein phosphorylation. Proteomics. 2004; 4(6):1551–61.

Article
CAS
PubMed
Google Scholar

Gaudet S, Janes KA, Albeck JG, Pace EA, Lauffenburger DA, Sorger PK. A compendium of signals and responses triggered by prodeath and prosurvival cytokines. Mol Cell Proteomics. 2005; 4(10):1569–90.

Article
CAS
PubMed
Google Scholar

Janes KA, Gaudet S, Albeck JG, Nielsen UB, Lauffenburger DA, Sorger PK. The response of human epithelial cells to TNF involves an inducible autocrine cascade. Cell. 2006; 124(6):1225–39.

Article
CAS
PubMed
Google Scholar

Davis RJ. Signal transduction by the JNK group of MAP kinases. Cell. 2000; 103(2):239–52.

Article
CAS
PubMed
Google Scholar

Bannister AJ, Brown HJ, Sutherland JA, Kouzarides T. Phosphorylation of the c-Fos and c-Jun HOB1 motif stimulates its activation capacity. Nucleic Acids Res. 1994; 22(24):5173–6.

Article
CAS
PubMed
PubMed Central
Google Scholar

Bailly S, Fay M, Israël N, Gougerot-Pocidalo MA. The transcription factor AP-1 binds to the human interleukin 1 alpha promoter. Eur Cytokine Netw. 1996; 7(2):125–8.

CAS
PubMed
Google Scholar

Russell M, Lange-Carter CA, Johnson GL. Direct interaction between Ras and the kinase domain of mitogen-activated protein kinase kinase kinase (MEKK1). J Biol Chem. 1995; 270(20):11757–60.

Article
CAS
PubMed
Google Scholar

Dérijard B, Hibi M, Wu IH, Barrett T, Su B, Deng T, Karin M, Davis RJ. JNK1: A protein kinase stimulated by uv light and ha-ras that binds and phosphorylates the c-Jun activation domain. Cell. 1994; 76(6):1025–37.

Article
PubMed
Google Scholar

Aldridge BB, Saez-Rodriguez J, Muhlich JL, Sorger PK, Lauffenburger DA. Fuzzy logic analysis of kinase pathway crosstalk in TNF/EGF/Insulin-induced signaling. PLoS Comput Biol. 2009; 5(4):1000340.

Article
Google Scholar

Janes KA, Albeck JG, Gaudet S, Sorger PK, Lauffenburger DA, Yaffe MB. A systems model of signaling identifies a molecular basis set for cytokine-induced apoptosis. Science. 2005; 310(5754):1646–53.

Article
CAS
PubMed
Google Scholar

Terfve C, Cokelaer T, Henriques D, MacNamara A, Goncalves E, Morris M, Iersel Mv, Lauffenburger D, Saez-Rodriguez J. CellNOptR: a flexible toolkit to train protein signaling networks to data using multiple logic formalisms. BMC Syst Biol. 2012; 6(1):133.

Article
CAS
PubMed
PubMed Central
Google Scholar

Gonçalves E, Saez-Rodriguez J. Cyrface: An interface from Cytoscape to R that provides a user interface to R packages. F1000Research. 2013; 2:192.

PubMed
PubMed Central
Google Scholar

Chaouiya C, Berenguier D, Keating S, Naldi A, van Iersel M, Rodriguez N, Drager A, Buchel F, Cokelaer T, Kowal B, Wicks B, Goncalves E, Dorier J, Page M, Monteiro P, von Kamp A, Xenarios I, de Jong H, Hucka M, Klamt S, Thieffry D, Le Novere N, Saez-Rodriguez J, Helikar T. Sbml qualitative models: a model representation format and infrastructure to foster interactions between qualitative modelling formalisms and tools. BMC Syst Biol. 2013; 7(1):135.

Article
PubMed
PubMed Central
Google Scholar

Siebert H, Bockmayr A. Temporal constraints in the logical analysis of regulatory networks. Theor Comput Sci. 2008; 391(3):258–75.

Article
Google Scholar

Bartocci E, Corradini F, Merelli E, Tesei L. Model checking biological oscillators. Electron Notes Theor Comput Sci. 2009; 229(1):41–58. Proceedings of the Second Workshop From Biology to Concurrency and Back (FBTC 2008).

Article
Google Scholar

Chaouiya C, Remy E, Mossé B, Thieffry D. Qualitative analysis of regulatory graphs: A computational tool based on a discrete formal framework In: Benvenuti L, De Santis A, Farina L, editors. Positive Systems. Lecture Notes in Control and Information Sciences, vol. 294. Berlin/Heidelberg: Springer: 2003. p. 830–2.

Google Scholar

Bock M, Scharp T, Talnikar C, Klipp E. Boolesim: an interactive boolean network simulator. Bioinformatics. 2014; 30(1):131–2.

Article
CAS
PubMed
Google Scholar

Krumsiek J, Polsterl S, Wittmann D, Theis F. Odefy - from discrete to continuous models. BMC Bioinforma. 2010; 11(1):233.

Article
Google Scholar

Mendes P, Hoops S, Sahle S, Gauges R, Dada J, Kummer U. Computational modeling of biochemical networks using COPASI. In: Systems biology, Methods in Molecular Biology, vol. 500. Totowa, NJ: Humana Press: 2009. p. 17–59. Chap. 2.

Google Scholar

Matsuoka Y, Funahashi A, Ghosh S, Kitano H. Modeling and simulation using celldesigner In: Miyamoto-Sato E, Ohashi H, Sasaki H, Nishikawa J-i, Yanagawa H, editors. Transcription Factor Regulatory Networks. Methods in Molecular Biology, vol. 1164. Springer: 2014. p. 121–45.

de Jong H, Geiselmann J, Hernandez C, Page M. Genetic Network Analyzer: qualitative simulation of genetic regulatory networks. Bioinformatics. 2003; 19(3):336–44.

Article
CAS
PubMed
Google Scholar

Resasco DC, Gao F, Morgan F, Novak IL, Schaff JC, Slepchenko BM. Virtual Cell: computational tools for modeling in cell biology. Wiley Interdiscip Rev Syst Biol Med. 2012; 4(2):129–40.

Article
CAS
PubMed
Google Scholar

Ciocchetta F, Duguid A, Gilmore S, Guerriero ML, Hillston J. The Bio-PEPA Tool Suite. Int Conf Quant Eval Syst. 2009;:309–310. http://ieeexplore.ieee.org/xpl/mostRecentIssue.jsp?punumber=5290656.

COSBILab. 2012. http://www.cosbi.eu/index.php/research/cosbi-lab. Accessed date 11 June 2016.

Nagasaki M, Saito A, Jeong E, Li C, Kojima K, Ikeda E, Miyano S. Cell illustrator 4.0: a computational platform for systems biology. Stud Health Technol Inform. 2011; 162:160–81.

PubMed
Google Scholar

yEd. 2015. http://www.yworks.com/en/products/yfiles/yed. Accessed date 11 June 2016.

Palmisano A, Hoops S, Watson LT, Jones Jr TC, Tyson JJ, Shaffer CA. Multistate Model Builder (MSMB): a flexible editor for compact biochemical models. BMC Syst Biol. 2014; 8(1):1–13.

Article
Google Scholar