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Bacterial Molecular Networks pp 463–479Cite as

Logical Modelling of Gene Regulatory Networks with GINsim

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Part of the book series: Methods in Molecular Biology ((MIMB,volume 804))

Abstract

Discrete mathematical formalisms are well adapted to model large biological networks, for which detailed kinetic data are scarce. This chapter introduces the reader to a well-established qualitative (logical) framework for the modelling of regulatory networks. Relying on GINsim, a software implementing this logical formalism, we guide the reader step by step towards the definition and the analysis of a simple model of the lysis–lysogeny decision in the bacteriophage λ.

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References

  1. Thieffry D, Thomas R. (1995) Dynamical behaviour of biological regulatory networks, II. Immunity control in bacteriophage lambda. Bull Math Biol, 57(2):277–297.

    CAS  Google Scholar 

  2. Filopon D, Mérieau A, Bernot G, Comet JP, LeBerre R, Guery B, Polack B, Guespin-Michel J. (2006) Epigenetic acquisition of inducibility of type III cytotoxicity in aeruginosa. BMC Bioinformatics 2006, 7:272.

    Google Scholar 

  3. Simão E, Remy E, Thieffry D, Chaouiya C. (2005) Qualitative modelling of regulated metabolic pathways: application to the tryptophan biosynthesis in E. coli. Bioinformatics, 21(Suppl 2):190–196.

    Google Scholar 

  4. Chaves M, Albert R, Sontag ED. (2005) Robustness and fragility of Boolean models for genetic regulatory networks. J Theor Biol, 235(3):431–449.

    Article  PubMed  Google Scholar 

  5. Sánchez L, Chaouiya C, Thieffry D. (2008) Segmenting the fly embryo: a logical analysis of the segment polarity cross-regulatory module. Int J Dev Biol, 52(8):1059–1075.

    Article  PubMed  Google Scholar 

  6. González A, Chaouiya C, Thieffry D. (2008) Logical modelling of the role of the Hh pathway in the patterning of the Drosophila wing disc. Bioinformatics, 24:i234–i240.

    Article  PubMed  Google Scholar 

  7. Fauré A, Naldi A, Lopez F, Chaouiya C, Ciliberto A, Thieffry D. (2009) Modular logical modelling of the budding yeast cell cycle. Mol Biosyst, 5:1787–1796.

    Article  PubMed  Google Scholar 

  8. Irons DJ. (2009) Logical analysis of the budding yeast cell cycle. J Theor Biol, 257(4): 543–559.

    Article  PubMed  CAS  Google Scholar 

  9. Mendoza L. (2006) A network model for the control of the differentiation process in Th cells. Biosystems, 84(2):101–114.

    Article  PubMed  CAS  Google Scholar 

  10. Ptashne M. (2004) A Genetic Switch: Phage Lambda Revisited. 3rd ed. Cold Spring Harbor Laboratory Press, Cold Spring Harbor.

    Google Scholar 

  11. Ackers GK, Johnson AD, Shea MA. (1982) Quantitative model for gene regulation by lambda phage repressor. Proc Natl Acad Sci U S A, 79(4):1129–1133.

    Article  PubMed  CAS  Google Scholar 

  12. Arkin A, Ross J, McAdams HH. (1998) Stochastic kinetic analysis of a developmental pathway bifurcation in phage lambda-infected Escherichia coli cells. Genetics, 149:1633–1648.

    PubMed  CAS  Google Scholar 

  13. Matsuno H, Doi A, Nagasaki M, Miyano S. (2000) Hybrid Petri net representation of gene regulatory network. In Pac Symp Biocomput 2000:341–352.

    Google Scholar 

  14. Naldi A, Berenguier D, Fauré A, Lopez F, Thieffry D, Chaouiya C. (2009) Logical modelling of regulatory networks with GINsim 2.3. Biosystems, 97(2):134–139.

    Google Scholar 

  15. Naldi A, Thieffry D, Chaouiya C. (2007) Decision diagrams for the representation of logical models of regulatory networks. Lect Notes Comput Sci, 4695:233–247.

    Article  Google Scholar 

  16. Naldi A, Remy E, Thieffry D, Chaouiya C. (2009) A reduction of logical regulatory graphs preserving essential dynamical properties. Lect Notes Comput Sci, 5688:266–280.

    Article  Google Scholar 

  17. Hartwell L, Hopfield J, Leibler S, Murray A. (1999) From molecular to modular cell biology. Nature, 402:C47–C52.

    Article  PubMed  CAS  Google Scholar 

  18. Mirschel S, Steinmetz K, Rempel M, Ginkel M, Gilles ED. (2009) ProMoT: modular modeling for systems biology. Bioinformatics, 25(5):687–689.

    Article  PubMed  CAS  Google Scholar 

  19. Fauré A, Naldi A, Chaouiya C, Thieffry D. (2006) Dynamical analysis of a generic Boolean model for the control of the mammalian cell cycle. Bioinformatics, 22(14):124–131.

    Article  Google Scholar 

  20. Thieffry D. (2007) Dynamical roles of biological regulatory circuits. Brief Bioinformatics, 8(4):220–225.

    Article  PubMed  CAS  Google Scholar 

  21. Remy E, Ruet P. (2008) From minimal signed circuits to the dynamics of Boolean regulatory networks. Bioinformatics, 24(16):i220–i226.

    Article  PubMed  Google Scholar 

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Acknowledgments

A.N. has been supported by a PhD grant from the French Ministry of Research and Technology. This project was further supported by research grants from the EU FP6 (DIAMONDS STREP) and FP7 (APOSYS large scale project) programs, and by the Belgian Science Policy Office (IAP BioMaGNet).

Author information

Authors and Affiliations

  1. Instituto Gulbenkian de Ciência, Oeiras, Portugal

    Claudine Chaouiya

  2. TAGC, INSERM U928, Marseille, France

    Aurélien Naldi

  3. Institut de Biologie de l’Ecole Normale Supérieure (IBENS), UMR ENS, CNRS 8197, INSERM 1024, Paris, France

    Denis Thieffry

Authors
  1. Claudine Chaouiya
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  2. Aurélien Naldi
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  3. Denis Thieffry
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Corresponding author

Correspondence to Claudine Chaouiya .

Editor information

Editors and Affiliations

  1. Labo. Bioinformatique des, Génomes et des Réseaux (BiGRe), Université Libre de Bruxelles, bd. du Triomphe, Bruxelles, 1050, Belgium

    Jacques van Helden

  2. Labo. Bioinformatique des, Génomes et des Réseaux (BiGRe), Université Libre de Bruxelles, Bvd. du Triomphe, Bruxelles, 1050, Belgium

    Ariane Toussaint

  3. INSERM 1024, Institut de Biologie de l'Ecole Normale, rue d'Ulm 46, Paris, 75230, France

    Denis Thieffry

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Chaouiya, C., Naldi, A., Thieffry, D. (2012). Logical Modelling of Gene Regulatory Networks with GINsim. In: van Helden, J., Toussaint, A., Thieffry, D. (eds) Bacterial Molecular Networks. Methods in Molecular Biology, vol 804. Springer, New York, NY. https://doi.org/10.1007/978-1-61779-361-5_23

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  • DOI: https://doi.org/10.1007/978-1-61779-361-5_23

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  • Publisher Name: Springer, New York, NY

  • Print ISBN: 978-1-61779-360-8

  • Online ISBN: 978-1-61779-361-5

  • eBook Packages: Springer Protocols

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