Scalable steady state analysis of boolean biological regulatory networks

PLoS ONE

Volumn 4, Issue 12, 2009, Pages

  Ay, Ferhat ^a   Xu, Fei ^a   Kahveci, Tamer ^a  

^a University of Florida   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

SONIC HEDGEHOG PROTEIN;

ALGORITHM; ARTICLE; BUDDING; CELL CYCLE; CELL CYCLE G1 PHASE; CELL CYCLE S PHASE; CELL DIVISION; GENE EXPRESSION; GENE IDENTIFICATION; GENE REGULATORY NETWORK; HUMAN; INFORMATION SCIENCE; MATHEMATICAL MODEL; NONHUMAN; ONLINE SYSTEM; SCHIZOSACCHAROMYCES POMBE; STEADY STATE; YEAST CELL;

ALGORITHMS; CELL CYCLE; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION; GENE REGULATORY NETWORKS; HEDGEHOG PROTEINS; HUMANS; MODELS, GENETIC; SACCHAROMYCETALES; SCHIZOSACCHAROMYCES;

ERINACEIDAE; SCHIZOSACCHAROMYCETACEAE;

EID: 77949511910     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0007992     Document Type: Article

References (46)

1. Ay F, Kahveci T, de Crecy-Lagard V (2008) Consistent alignment of metabolic pathways without abstraction. In: Comput Syst Bioinformatics Conf volume 7: 237-248.
2. Ay F, Kahveci T, de Crecy-Lagard V (2009) A fast and accurate algorithm for comparative analysis of metabolic pathways. J Bioinform Comput Biol 7(3): 389-428.
3. Karlebach G, Shamir R (2008) Modelling and analysis of gene regulatory networks. Nat Rev Mol Cell Biol 9: 770-780.
4. Basso K, Margolin A, Stolovitzky G, Klein U, Dalla-Favera R, et al. (2005) Reverse engineering of regulatory networks in human B cells. Nat Genet 4: 382-390.
5. 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(Suppl 1): S7.
6. Tatsuya A, Satoru M, Satoru K (1999) Identification of genetic networks from a small number of gene expression patterns under the Boolean network model. In: Conf Proc Pac Symp Biocomp volume 4: 17-28.
7. Osamu H, Naoki N, Yoshinori T, Hideo B, Seiya I, et al. (2005) Estimating gene networks from expression data and binding location data via Boolean networks. Lect Notes Comput Sci 3482: 349-356.
8. Tatsuya A, Satoru K, Osamu M, Satoru M (2003) Identification of genetic networks by strategic gene disruptions and gene overexpressions under a Boolean model. Theor Comput Sci 298: 235-251.
9. Satoru M (2003) Inference, modeling and simulation of gene networks. In: Conf Proc Comp Met Sys Biol. pp 207-211.
10. Osamu H, Ryo Y, Seiya I, Rui Y, Tomoyuki H, 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.
11. Wong S, Zhang L, Tong A, Li Z, Goldberg D, et al. (2004) Combining biological networks to predict genetic interactions. Proc Natl Acad Sci USA 101: 15682-15687.
12. Hupp T, Lane D, Ball K (2000) Strategies for manipulating the p53 pathway in the treatment of human cancer. Biochem J 352: 1-17.
13. Lane D (1999) Exploiting the p53 pathway for cancer diagnosis and therapy. Br J Cancer 80: 1-5.
14. Ostergaard S, Olsson L, Johnston M, Nielsen J (2000) Increasing galactose consumption by Saccharomyces cerevisiae through metabolic engineering of the GAL gene regulatory network. Nat Biotechnol 18: 1283-1286.
15. Mendoza L, Thieffry D, Alvarez-Buylla E (1999) Genetic control of flower morphogenesis in Arabidopsis thaliana: A logical analysis. Bioinformatics 15: 593-606.
16. Demongeot J, Morvan M, Sene S (2008) Impact of fixed boundary conditions on the basins of attraction in the flower's morphogenesis of Arabidopsis thaliana. In: Conf Proc Adv Info Net App. pp 782-789.
17. Álvarez Buylla E, Chaos, Aldana M, Benítez M, Cortes-Poza Y, et al. (2008) Floral morphogenesis: stochastic explorations of a gene network epigenetic landscape. PLoS ONE 3: e3626.
18. 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. In: Conf Proc Res Comput Mol Biol. pp 62-76.
19. Garg A, Di Cara A, Xenarios I, Mendoza L, De Micheli G (2008) Synchronous versus asynchronous modeling of gene regulatory networks. Bioinformatics 24: 1917-1925.
20. Mendoza L (2006) A network model for the control of the differentiation process in Th cells. Biosystems 84: 101-114.
21. Saez-Rodriguez J, Simeoni L, Lindquist J, Hemenway R, Bommhardt U, et al. (2007) A logical model provides insights into T cell receptor signaling. PLoS Comput Biol 3: 1580-1590.
22. Davidich M, Bornholdt S (2008) Boolean network model predicts cell cycle sequence of fission yeast. PLoS ONE 3: e1672.
23. Fangting L, Tao L, Ying L, Qi O, Chao T (2004) The yeast cell-cycle network is robustly designed. Proc Natl Acad Sci USA 101: 4781-4786.
24. Garg A, Mendoza L, Xenarios I, DeMicheli G (2007) Modeling of multiple valued gene regulatory networks. In: Conf Proc IEEE Eng Med Biol Soc. pp 1398-1404.
25. Mendoza L, Xenarios I (2006) A method for the generation of standardized qualitative dynamical systems of regulatory networks. Theor Biol Med Model 3: 13.
26. Hachtel G, Macii E, Pardo A, Somenzi F (1996) Markovian analysis of large finite state machines. IEEE Trans Comp-Aided Des 15: 1479-1493.
27. Devloo V, Hansen P, Labbé M (2003) Identification of all steady states in large networks by logical analysis. Bull Math Biol 65: 1025-1051.
28. Shmulevich I, Dougherty E, Kim S, Zhang W (2002) Probabilistic Boolean Networks: A rule-based uncertainty model for gene regulatory networks. Bioinformatics 18: 261-274.
29. Shlomi T, Berkman O, Ruppin E (2005) Regulatory on/off minimization of metabolic flux changes after genetic perturbations. Proc Natl Acad Sci USA 102: 7695-7700.
30. Schaub M, Henzinger T, Fisher J (2007) Qualitative networks: A symbolic approach to analyze biological signaling networks. BMC Syst Biol 1: 4.
31. Segal E, Pe'er D, Regev A, Koller D, Friedman N (2005) Learning module networks. J Mach Learn Res 6: 557-588.
32. Segal E, Michael S, Regev A, Pe'er D, David B, et al. (2003) Module Networks: Discovering regulatory modules and their condition specific regulators from gene expression data. Nat Genet 34: 166-176.
33. Albert I, Thakar J, Li S, Zhang R, Albert R (2008) Boolean network simulations for life scientists. Source Code Biol Med 3: 16.
34. Albert R, Othmer H (2003) The topology of the regulatory interactions predicts the expression pattern of the segment polarity genes in Drosophila melanogaster. J Theor Biol 223: 1-18.
35. Kauffman S (1969) Homeostasis and differentiation in random genetic control networks. Nature 224: 177-178.
36. Nielsen J (2006) BUDDY - A Binary Decision Diagram Package. Tech Report Technical University of Denmark, http://www.itu.dk/research/buddy.
37. Tyson J, Csikasz-Nagy A, Novak B (2002) The dynamics of cell cycle regulation. Bioessays 24: 1095-1109.
38. Tyson J, Chen K, Novak B (2001) Network dynamics and cell physiology. Nat Rev Mol Cell Biol 2: 908-916.
39. Bornholdt S (2008) Boolean network models of cellular regulation: Prospects and limitations. J R Soc Interface 5(Suppl 1): 85-94.
40. Wu Y, Zhang X, Yu J, Ouyang Q (2009) Identification of a topological characteristic responsible for the biological robustness of regulatory networks. PLoS Comput Biol 5: e1000442.
41. Schaefer C, Anthony K, Krupa S, Buchoff J, Day M, et al. (2009) PID: The Pathway Interaction Database. Nucleic Acids Res 37: 674-679.
42. Stuart J, Segal E, Koller D, Kim S (2003) A gene-coexpression network for global discovery of conserved genetic modules. Science 302: 240-241.
43. Zotenko E, Guimaraes K, Jothi R, Przytycka T (2005) Decomposition of overlapping protein complexes: A graph theoretical method for analyzing static and dynamic protein associations. Algorithms Mol Biol 1: 7.
44. Oldham M, Horvath S, Geschwind D (2006) Conservation and evolution of gene coexpression networks in human and chimpanzee brains. Proc Natl Acad Sci USA 103: 17973-17978.
45. Obayashi T, Hayashi S, Shibaoka M, Saeki M, Ohta H, et al. (2008) COXPRESdb: A database of coexpressed gene networks in mammals. Nucleic Acids Res 36(Database issue): 77-82.
46. Ogata H, Goto S, Sato K, Fujibuchi W, Bono H, et al. (1999) KEGG: Kyoto Encyclopedia of Genes and Genomes. Nucleic Acids Res 27: 29-34.