Detection of attractors of large Boolean networks via exhaustive enumeration of appropriate subspaces of the state space

BMC Bioinformatics

Volumn 14, Issue 1, 2013, Pages

  Berntenis, Nikolaos ^a   Ebeling, Martin ^a  

^a F HOFFMANN LA ROCHE LTD   (Switzerland)

Author keywords

Attractor; Boolean network; Cycle; Fixed state; Regulatory network; State space

Indexed keywords

ATTRACTOR; BOOLEAN NETWORKS; CYCLE; FIXED STATE; REGULATORY NETWORK;

ALGORITHMS; BOOLEAN ALGEBRA; DYNAMICAL SYSTEMS; PROTEINS; SIGNALING; SOFTWARE PACKAGES; STATE SPACE METHODS;

COMPLEX NETWORKS;

PROTEIN; TRANSCRIPTION FACTOR;

ALGORITHM; ARTICLE; BIOLOGICAL MODEL; COMPARATIVE STUDY; COMPUTER PROGRAM; DATA STORAGE DEVICE; EQUIPMENT; GENE REGULATORY NETWORK; GENE TARGETING; GENETICS; INFORMATION PROCESSING; METHODOLOGY; RNA STABILITY; SIGNAL TRANSDUCTION;

ALGORITHMS; COMPUTER STORAGE DEVICES; DATA COLLECTION; GENE REGULATORY NETWORKS; GENE TARGETING; MODELS, GENETIC; PROTEINS; RNA STABILITY; SIGNAL TRANSDUCTION; SOFTWARE; TRANSCRIPTION FACTORS;

EID: 84889954232     PISSN: None     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-14-361     Document Type: Article

References (19)

1. Kauffman S. Metabolic stability and epigenesis in randomly constructed genetic nets. J Theor Biol 1969, 22:437-467. 10.1016/0022-5193(69)90015-0, 5803332.
2. Glass L, Kauffman SA. The logical analysis of continuous non-linear biochemical control networks. J Theor Biol 1973, 103:103-129.
3. Thomas R. Boolean formalization of genetic control circuits. J Theor Biol 1973, 42:563-585. 10.1016/0022-5193(73)90247-6, 4588055.
4. Thomas R, Thieffry D, Kaufman M. 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 1995, 57:247-276.
5. Thieffry D, Thomas R. Dynamical behaviour of biological regulatory networks--II. Immunity control in bacteriophage lambda. Bull Math Biol 1995, 57:277-295.
6. Thomas R, Richard D. Biological Feedback 1990, Boca Raton: CRC Press.
7. Garg A, Xenarios I, Mendoza L, DeMicheli G. Efficient methods for dynamic analysis of genetic networks and in silico gene perturbation experiments. Lect Notes Comput Sci 2007, 4453:62-76.
8. Di Cara A, Garg A, De Micheli G, Xenarios I, Mendoza L. Dynamic simulation of regulatory networks using SQUAD. BMC Bioinformatics 2007, 8:462. 10.1186/1471-2105-8-462, 2238325, 18039375.
9. Gonzalez AG, Naldi A, Sánchez L, Thieffry D, Chaouiya C. GINsim: a software suite for the qualitative modeling, simulation and analysis of regulatory networks. Biosystems 2006, 84(2):91-100. 10.1016/j.biosystems.2005.10.003, 16434137.
10. Hinkelmann F, Brandon M, Guang B, McNeill R, Blekherman G, Veliz-Cuba A, Laubenbacher R. ADAM: Analysis of Discrete Models of Biological Systems Using Computer Algebra. BMC Bioinformatics 2011, 12:295. 10.1186/1471-2105-12-295, 3154873, 21774817.
11. Helikar T, Rogers JA. ChemChains: a platform for simulation and analysis of biochemical networks aimed to laboratory scientists. BMC Syst Biol 2009, 3:58. 10.1186/1752-0509-3-58, 2705353, 19500393.
12. Müssel C, Hopfensitz M, Kestler HA. BoolNet an R package for generation, reconstruction and analysis of Boolean networks. Bioinformatics 2010, 26(10):1378-1380. 10.1093/bioinformatics/btq124, 20378558.
13. Naldi A, Remy E, Thieffry D, Chaouiya C. Dynamically consistent reduction of logical regulatory graphs. Theor Comput Sci 2011, 412(21):2207-2218.
14. Veliz-Cuba A. Reduction of Boolean network models. J Theor Biol 2011, 289C:167-172.
15. Saadatpour A, Albert I, Albert R. Attractor analysis of asynchronous Boolean models of signal transduction networks. J Theor Biol 2010, 266:641-656. 10.1016/j.jtbi.2010.07.022, 20659480.
16. Saadatpour A, Wang RS, Liao A, Liu X, Loughran TP, Albert I, Albert R. Dynamical and structural analysis of a T cell survival network identifies novel candidate therapeutic targets for large granular lymphocyte leukemia. PLoS Comput Biol 2011, 7(11):e1002267. 10.1371/journal.pcbi.1002267, 3213185, 22102804.
17. Ay F, Fei X, Kahveci T. Scalable Steady State Analysis of Boolean Biological Regulatory Networks. PLoS ONE 2009, 4(12):e7992. 10.1371/journal.pone.0007992, 2779454, 19956604.
18. Hinkelmann F. Algebraic theory for discrete models in systems biology 2011, Virginia Polytechnic Institute, Mathematics Department, PhD thesis.
19. Shu-Qin Z, Morihiro H, Tatsuya A, Wai-Ki C, Michael KN. Algorithms for finding small attractors in Boolean networks. EURASIP Journal on Bioinformatics and Systems Biology 2007, 2007:20180.