An Efficient Algorithm for Computing Attractors of Synchronous And Asynchronous Boolean Networks

PLoS ONE

Volumn 8, Issue 4, 2013, Pages

  Zheng, Desheng ^a,b   Yang, Guowu ^a   Li, Xiaoyu ^a,b   Wang, Zhicai ^a   Liu, Feng ^c   He, Lei ^b  

^a UNIVERSITY OF ELECTRONIC SCIENCE AND TECHNOLOGY OF CHINA   (China)

^b UNIVERSITY OF CALIFORNIA   (United States)

^c UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

T LYMPHOCYTE RECEPTOR;

ARTICLE; ASYNCHRONOUS BOOLEAN NETWORK; ATTRACTOR COMPUTING; BIOINFORMATICS; BIOLOGICAL MODEL; CLASSIFICATION ALGORITHM; COMPARATIVE STUDY; COMPUTER PROGRAM; DENDRITIC CELL; EXPERIMENTAL STUDY; FEASIBILITY STUDY; GENEFATT; GENEYSIS; HELPER CELL; ITERATIVE COMPUTING; MAMMAL CELL; MATHEMATICAL ANALYSIS; MATHEMATICAL MODEL; MATHEMATICAL PARAMETERS; PROTEIN EX MODEL; QUALITY CONTROL; REDUCED ORDER BINARY DECISION DIAGRAM; SYNCHRONOUS BOOLEAN NETWORK; VALIDATION PROCESS;

ALGORITHMS; ANIMALS; COMPUTER SIMULATION; EUKARYOTIC CELLS; GENE EXPRESSION REGULATION; GENE REGULATORY NETWORKS; HUMANS; MODELS, GENETIC; SOFTWARE;

EID: 84876015814     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0060593     Document Type: Article

References (23)

1. Proulx S, Promislow D, Phillips P, (2005) Network thinking in ecology and evolution. Trends in Ecology & Evolution 20: 345-353.
2. Basso K, Margolin A, Stolovitzky G, Klein U, Dalla-Favera R, et al. (2005) Reverse engineering of regulatory networks in human b cells. Nature genetics 37: 382-390.
3. Margolin A, Nemenman I, Basso K, Wiggins C, Stolovitzky G, et al. (2006) Aracne: an algorithm for the reconstruction of gene regulatory networks in a mammalian cellular context. BMC bioinformatics 7: S7.
4. Hirose O, Yoshida R, Imoto S, Yamaguchi R, Higuchi T, et al. (2008) Statistical inference of transcriptional module-based gene networks from time course gene expression profiles by using state space models. Bioinformatics 24: 932-942.
5. Glass L (1985). Boolean and continuous models for the generation of biological rhythms.
6. Kauffman S (1995) At home in the universe. Oxford University Press New York.
7. 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: e124.
8. Remy E, Ruet P, Mendoza L, Thieffry D, Chaouiya C, (2006) From logical regulatory graphs to standard petri nets: dynamical roles and functionality of feedback circuits. Transactions on Computational Systems Biology VII: 56-72.
9. Naldi A, Thieffry D, Chaouiya C (2007) Decision diagrams for the representation and analysis of logical models of genetic networks. In: Proceedings of the 2007 international conference on Computational methods in systems biology. Springer-Verlag, 233-247.
10. Garg A, Di Cara A, Xenarios I, Mendoza L, De Micheli G, (2008) Synchronous versus asynchronous modeling of gene regulatory networks. Bioinformatics 24: 1917.
11. Davidich M, Bornholdt S, (2008) Boolean network model predicts cell cycle sequence of fission yeast. PLoS One 3: e1672.
12. Harvey I, Bossomaier T (1997) Time out of joint: Attractors in asynchronous random boolean networks. In: Proceedings of the Fourth European Conference on Artificial Life. MIT Press, Cambridge, 67-75.
13. Devloo Vea (2003) Identification of all steady states in large biological systems by logical anslysis. Bull Math Biol: 1025-1051.
14. Thomas R, (1991) Regulatory networks seen as asynchronous automata: a logical description. Journal of Theoretical Biology 153: 1-23.
15. Li F, Long T, Lu Y, Ouyang Q, Tang C, (2004) The yeast cell-cycle network is robustly designed. Proceedings of the National Academy of Sciences of the United States of America 101: 4781.
16. Ay F, Xu F, Kahveci T, (2009) Scalable steady state analysis of boolean biological regulatory networks. PloS one 4: e7992.
17. Heidel J, Maloney J, Farrow C, Rogers J, (2003) Finding cycles in synchronous boolean networks with applications to biochemical systems. International Journal of Bifurcation and Chaos in Applied Sciences and Engineering 13: 535-552.
18. Farrow C, Heidel J, Maloney J, Rogers J, (2004) Scalar equations for synchronous boolean networks with biological applications. IEEE Transactions on Neural Networks 15: 348-354.
19. Zhao Q, (2005) A remark on "scalar equations for synchronous boolean networks with biological applications by C. Farrow, J. Heidel, J. Maloney, and J. Rogers". IEEE Transactions on Neural Networks 16: 1715-1716.
20. Dubrova E, Teslenko M, Martinelli A (2005) Kauffman networks: Analysis and applications. In: Proceedings of the 2005 IEEE/ACM International conference on Computer-aided design. IEEE Computer Society, 479-484.
21. Lind-Nielsen J (2000). Bdd package buddy, v. 1.9, august 2000, http://www.itu.dk/research/buddy/index.html.
22. Luis M, Ioannis X (2006) A method for the generation of standardized qualitative dynamical systems of regulatory networks. Theoretical Biology and Medical Modelling 3.
23. Klamt S, Saez-Rodriguez J, Lindquist J, Simeoni L, Gilles E, (2006) A methodology for the structural and functional analysis of signaling and regulatory networks. BMC bioinformatics 7: 56.