Discrete dynamic modeling of signal transduction networks

Methods in Molecular Biology

Volumn 880, Issue , 2012, Pages 255-272

  Saadatpour, Assieh ^a   Albert, Réka ^a  

^a PENNSYLVANIA STATE UNIVERSITY   (United States)

Author keywords

Asynchronous method; Boolean dynamic modeling; Signal transduction; Synchronous method

Indexed keywords

ABSCISIC ACID;

CELL SURVIVAL; HUMAN; SIGNAL TRANSDUCTION; T LYMPHOCYTE; BIOLOGICAL MODEL; GENETICS; KINETICS; METABOLISM; METHODOLOGY; MOLECULAR DYNAMICS; PHYSIOLOGY; REVIEW; SYSTEMS BIOLOGY;

ABSCISIC ACID; HUMANS; KINETICS; MODELS, BIOLOGICAL; MOLECULAR DYNAMICS SIMULATION; SIGNAL TRANSDUCTION; SYSTEMS BIOLOGY; T-LYMPHOCYTES;

EID: 84887345645     PISSN: 10643745     EISSN: None     Source Type: Book Series    
DOI: 10.1007/978-1-61779-833-7_12     Document Type: Chapter

References (35)

1. Marks F, Klingmuller U, Muller-Decker K (2009) Cellular signal processing: an introduction to the molecular mechanisms of signal transduction: Garland sciences. Taylor and Francis Group, LLC, Philadelphia, PA
2. Chen KC, Csikasz-Nagy A, Gyorffy B, Val J, Novak B et al (2000) Kinetic analysis of a molecular model of the budding yeast cell cycle. Mol Biol Cell 11:369–391
3. Kauffman SA (1969) Metabolic stability and epigenesis in randomly constructed genetic nets. J Theor Biol 22:437–467
4. Thomas R (1973) Boolean formalization of genetic control circuits. J Theor Biol 42:563–585
5. Mendoza L, Alvarez-Buylla ER (2000) Genetic regulation of root hair development in Arabidopsis thaliana: a network model. J Theor Biol 204:311–326
6. Sanchez L, Thieffry D (2001) A logical analysis of the Drosophila gap-gene system. J Theor Biol 211:115–141
7. Sanchez L, van Helden J, Thieffry D (1997) Establishement of the dorso-ventral pattern during embryonic development of Drosophila melanogasater: a logical analysis. J Theor Biol 189:377–389
8. May RM (1976) Simple mathematical models with very complicated dynamics. Nature 261:459–467
9. Song M, Ouyang Z, Liu ZL (2009) Discrete dynamical system modelling for gene regulatory networks of 5-hydroxymethylfurfural tolerance for ethanologenic yeast. IET Syst Biol 3:203–218
10. Chaouiya C (2007) Petri net modelling of biological networks. Brief Bioinform 8:210–219
11. Peterson JL (1981) Petri Net Theory and the modeling of systems. Prentice Hall PTR, Upper Saddle River, NJ
12. Sackmann A, Heiner M, Koch I (2006) Application of Petri net based analysis techniques to signal transduction pathways. BMC Bioinformatics 7:482
13. Kauffman S (1993) Origins of order: selforganization and selection in evolution. Oxford University Press, Oxford
14. Papin JA, Hunter T, Palsson BO, Subramaniam S (2005) Reconstruction of cellular signalling networks and analysis of their properties. Nat Rev Mol Cell Biol 6:99–111
15. Li S, Assmann SM, Albert R (2006) Predicting essential components of signal transduction networks: a dynamic model of guard cell abscisic acid signaling. PLoS Biol 4:e312
16. Thakar J, Pilione M, Kirimanjeswara G, Harvill ET, Albert R (2007) Modeling systems-level regulation of host immune responses. PLoS Comput Biol 3:e109
17. Zhang R, Shah MV, Yang J, Nyland SB, Liu X et al (2008) Network model of survival signaling in large granular lymphocyte leukemia. Proc Natl Acad Sci USA 105:16308–16313
18. Albert R, DasGupta B, Dondi R, Kachalo S, Sontag E et al (2007) A novel method for signal transduction network inference from indirect experimental evidence. J Comput Biol 14:927–949
19. Kachalo S, Zhang R, Sontag E, Albert R, Das- Gupta B (2008) NET-SYNTHESIS: a software for synthesis, inference and simplification of signal transduction networks. Bioinformatics 24:293–295
20. Albert R, Barabasi AL (2002) Statistical mechanics of complex networks. Rev Mod Phys 74:47–97
21. Chaves M, Albert R, Sontag ED (2005) Robustness and fragility of Boolean models for genetic regulatory networks. J Theor Biol 235:431–449
22. Harvey I, Bossomaier T (1997) Time out of joint: attractors in asynchronous random Boolean networks. In: Husbands P, Harvey I, editors; Proceedings of the Fourth European Conference on Artificial Life, MIT Press; Cambridge, pp 67–75
23. Chaves M, Sontag ED, Albert R (2006) Methods of robustness analysis for Boolean models of gene control networks. Syst Biol (Stevenage) 153:154–167
24. Albert I, Thakar J, Li S, Zhang R, Albert R (2008) Boolean network simulations for life scientists. Source Code Biol Med 3:16
25. Mussel C, Hopfensitz M, Kestler HA (2010) BoolNet – an R package for generation, reconstruction, and analysis of Boolean networks. Bioinformatics 26:1378–1380
26. Faure 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:e124–e131
27. Mochizuki A (2005) An analytical study of the number of steady states in gene regulatory networks. J Theor Biol 236:291–310
28. Saez-Rodriguez J, Simeoni L, Lindquist JA, Hemenway R, Bommhardt U et al (2007) A logical model provides insights into T cell receptor signaling. PLoS Comput Biol 3:e163
29. Gupta S, Bisht SS, Kukreti R, Jain S, Brahmachari SK (2007) Boolean network analysis of a neurotransmitter signaling pathway. J Theor Biol 244:463–469
30. Kervizic G, Corcos L (2008) Dynamical modeling of the cholesterol regulatory pathway with Boolean networks. BMC Syst Biol 2:99
31. Christensen TS, Oliveira AP, Nielsen J (2009) Reconstruction and logical modeling of glucose repression signaling pathways in Saccharomyces cerevisiae. BMC Syst Biol 3:7
32. Saadatpour A, Albert I, Albert R (2010) Attractor analysis of asynchronous Boolean models of signal transduction networks. J Theor Biol 266:641–656
33. Glass L, Kauffman SA (1973) The logical analysis of continuous, non-linear biochemical control networks. J Theor Biol 39:103–129
34. Glass L (1975) Classification of biological networks by their qualitative dynamics. J Theor Biol 54:85–107
35. Thakar J, Saadatpour-Moghaddam A, Harvill ET, Albert R (2009) Constraint-based network model of pathogen–immune system interactions. J R Soc Interface 6:599–612