Petri net representation of multi-valued logical regulatory graphs
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
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