Petri net representation of multi-valued logical regulatory graphs

Claudine Chaouiya1,2, Aurélien Naldi2,3, Élisabeth Rémy4, Denis Thieffry2,3,5
1Instituto Gulbenkian de Ciência, Oeiras, Portugal
2INSERM U928—TAGC, Marseille, France
3Université de la Méditerranée. Marseille, France
4Institut de Mathématiques de Luminy, Marseille, France
5CONTRAINTES Project, INRIA-Paris-Rocquencourt, Le Chesnay, France

Tóm tắt

Từ khóa


Tài liệu tham khảo

Ahmad J, Richard A, Bernot G, Comet J-P, Roux O (2006) Delays in biological regulatory networks (BRN). Lect Notes Comput Sci 3992:887–894

Alberts B, Johnson A, Lewis J, Raff M, Roberts K, Walter P (2008) Molecular biology of the cell, 5th edn. Garland Science/Taylor & Francis, New York

Chaouiya C, Remy E, Mossé B, Thieffry D (2003) Qualitative analysis of regulatory graphs: a computational tool based on a discrete formal framework. Lect Notes Control Inf Sci 294:119–126

Chaouiya C, Remy E, Ruet P, Thieffry D (2004) Qualitative modelling of genetic networks: from logical regulatory graphs to standard Petri nets. Lect Notes Comput Sci 3099:137–156

Chaouiya C, Remy E, Thieffry D (2006) Qualitative Petri net modelling of genetic networks. Lect Notes Comput Sci 4220:95–112

Chaouiya C, Remy E, Thieffry D (2008) Petri net modelling of biological regulatory networks. J Discrete Algorithms 6(2):165–177

Comet J-P, Klaudel H, Liauzu S (2005) Modeling multi-valued genetic regulatory networks using high-level Petri nets. Lect Notes Comput Sci 3536:208–227

de Jong H (2002) Modeling and simulation of genetic regulatory systems: a literature review. J Comput Biol 1:67–103

Doi A, Nagasaki M, Matsuno H, Miyano S (2006) Simulation-based validation of the p53 transcriptional activity with hybrid functional Petri net. In Silico Biol 6:1–13

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 22:124–131

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

Garg A, Xenarios I, Mendoza L, De Micheli G (2007) An efficient method for dynamic analysis of gene regulatory networks and in-silico gene perturbation experiments. Lect Notes Comput Sci 4453:62–76

GINsim web page: http://gin.univ-mrs.fr/GINsim/

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

Goss PJ, Peccoud J (1998) Quantitative modeling of stochastic systems in molecular biology by using stochastic Petri nets. Proc Natl Acad Sci USA 95:6750–6755

Grafahrend-Belau E, Schreiber F, Heiner M, Sackmann A, Junker BH, Grunwald S, Speer A, Winder K, Koch I (2008) Modularization of biochemical networks based on classification of Petri net t-invariants. BMC Bioinformatics 9:90

Heiner M, Gilbert D, Donaldson R (2008) Petri nets for systems and synthetic biology. Lect Notes Comput Sci 5016:215–264

INA, Integrated Net Analyzer, tool for the analysis of (Coloured) PNs: http://www.informatik.hu-berlin.de/~starke/ina.html

Kam T, Villa T, Brayton RK, Sangiovanni-Vincentelli AL (1998) Multi-valued decision diagrams: theory and applications. Int J Multiple-Valued Logic 4:9–62

Kauffman S (1993) The origins of order: self-organization and selection in evolution. Oxford University Press, New York

Klamt S, Saez-Rodriguez J, Lindquist JA, Simeoni L, Gilles ED (2006) A methodology for the structural and functional analysis of signaling and regulatory networks. BMC Bioinformatics 7:56

Li C, Ge QW, Nakata M, Matsuno H, Miyano S (2007) Modelling and simulation of signal transductions in an apoptosis pathway by using timed Petri nets. J Biosci 32:113–127

Marsan MA, Balbo G, Conte G, Donatelli S, Franceschinis G (1994) Modelling with generalized stochastic Petri nets. Wiley, New York

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

Mura I, Csikasz-Nagy A (2008) Stochastic Petri net extension of a yeast cell cycle model. J Theor Biol 254(4):850–860

Nagasaki M, Doi A, Matsuno H, Miyano S (2004) A versatile Petri net based architecture for modeling and simulation of complex biological processes. Genome Inform 15:180–197

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

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

Naldi A, Remy E, Thieffry D, Chaouiya C (2009b) A reduction method for logical regulatory graphs preserving essential dynamical properties. Lect Notes Bioinform 5688:266–280

Remy E, Ruet P, Thieffry D (2006a) Positive or negative regulatory circuit inference from multilevel dynamics. Lect Notes Control Inf Sci 341:263–270

Remy E, Ruet P, Mendoza L, Thieffry D, Chaouiya C (2006b) From logical regulatory graphs to standard Petri nets: dynamical roles and functionality of feedback circuits. Lect Notes Comput Sci 4230:55–72

Richard A, Comet J-P (2007) Necessary conditions for multistationarity in discrete dynamical systems. Discret Appl Math 155(18):2403–2413

Sackmann A, Heiner M, Koch I (2006) Application of Petri net based analysis techniques to signal transduction pathways. BMC Bioinformatics 7:482

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

Schlitt T, Brazma A (2007) Current approaches to gene regulatory network modelling. BMC Bioinformatics 8:S9

Siebert H, Bockmayr A (2006) Incorporating time delays into the logical analysis of gene regulatory networks. Lect Notes Comput Sci 4210:169–183

Siebert H, Bockmayr A (2007) Context sensitivity in logical modeling with time delays. Lect Notes Comput Sci 4695:64–79

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:ii190–ii196

Soulé C (2006) Mathematical approaches to gene regulation and differentiation. CR Acad Sci Paris (Biol) 329:13–20

Srivastava R, Peterson MS, Bentley WE (2001) Stochastic kinetic analysis of the Escherichia coli stress circuit using σ32-targeted antisense. Biotechnol Bioeng 75:120–129

Steggles LJ, Banks R, Shaw O, Wipat A (2007) Qualitatively modelling and analysing genetic regulatory networks: a Petri net approach. Bioinformatics 23:336–343

Thieffry D (2007) Dynamical roles of biological regulatory circuits. Brief Bioinform 8:220–225

Thomas R (1991) Regulatory networks seen as asynchronous automata: a logical description. J Theor Biol 153(1):1–23

Thomas R, D’Ari R (1990) Biological feedback. CRC Press, Boca Raton

Thomas R, Thieffry D, Kaufman M (1995) Dynamical behaviour of biological regulatory networks—I. Biological role of feedback loops and practical use of the concept of the loop-characteristic state. Bull Math Biol 57(2):247–276