Effects of feedback and feedforward loops on dynamics of transcriptional regulatory model networks

Proceedings of the 13th International Symposium on Artificial Life and Robotics, AROB 13th'08

Volumn , Issue , 2008, Pages 885-890

  Oosawa, Chikoo ^a   Takemoto, Kazuhiro ^b   Savageau, Michael A ^c  

^a KYUSHU INSTITUTE OF TECHNOLOGY   (Japan)

^b KYOTO UNIVERSITY   (Japan)

^c University of California Davis   (United States)

Author keywords

Boolean networks; Entropy; Feedback loop; Feedforward loop; Mutual information; Transcriptional regulatory networks

Indexed keywords

BOOLEAN NETWORKS; FEEDBACK LOOP; FEEDFORWARD LOOPS; MUTUAL INFORMATIONS; TRANSCRIPTIONAL REGULATORY NETWORKS;

BOOLEAN ALGEBRA; DYNAMICAL SYSTEMS; ENTROPY; GENE EXPRESSION; MATHEMATICAL MODELS; ROBOTICS; STRUCTURED PROGRAMMING;

NEURAL NETWORKS;

EID: 53949119078     PISSN: None     EISSN: None     Source Type: Conference Proceeding    
DOI: None     Document Type: Conference Paper

References (25)

1. A. A. Moreira, L. A. N. Amaral, "Canalizing Kauffman Networks: Nonergodicity and Its Effect on Their Critical Behavior", Phys. Rev. Lett., 94, 218702, 2005.
2. A.-L. Barabási, Z. N. Oltvai, "Network biology: Understanding the cell's functional organization", Nature Gnenetics, 5, 101-112, 2004.
3. C. G. Langton, "Computation at the edge of chaos: Phase transitions and emergent computation", Physica D, 42, 12-37, 1990.
4. C. Oosawa, "Roles of hubs in Boolean networks", Proceedings of the 15th IEEE International Workshop on Nonlinear Dynamics of Electrical Systems, 245-248, 2007.
5. C. Oosawa, K. Takemoto, S. Matsumoto, M. A. Savageau, "Local cause of coherence in Boolean networks", Proceedings of the 12th International Symposium on Artificial Life and Robotics, 621-627, 2007.
6. C. Oosawa, M. A. Savageau, "Effects of alternaltive connectivity on behavior of randomly constructed Boolean networks", Physica D, 170, 143-161, 2002.
7. C. Y. Huang, C.-T. Sun, C-.Y. Cheng, J.-L. Hsieh, "Bridge and brick motifs in complex networks", Physica A, 377, 340-350, 2007.
8. D. J. Watts, S. H. Strogatz,"Collective dynamics of 'small-world' networks", Nature, 393, 440-442, 1998.
9. H. Jeong, B. Tombor, R. Albert, Z.N. Oltvai, A.-L. Barabási, "The Large-scale organization of metabolic networks", Nature, 407, 651-654, 2000.
10. K. Takemoto, C. Oosawa, "Evolving networks by merging cliques", Physical Review E, 72, 046116, 2005.
11. K. Takemoto, C. Oosawa, "Modeling for evolving biological networks with scale-free connectivity, hierarchical modularity, and disassortativity", Mathematical Biosciences, 208, 454-468, 2007.
12. K. Takemoto, C. Oosawa, T. Akutsu, "Structure of n-clique networks embedded in a complex network", Physica A, 380, 665-672, 2007.
13. K. Klemm, S. Bornholdt, "Topology of biological networks and reliability of information processing", Proc. Natl. Acad. Sci., 102, 18414-18419, 2005.
14. L. Raeymakers, "Dynamics of Boolean Networks Controlled by Biologically Meaningful Functions", J. Theor. Biol., 218, 331-341, 2002.
15. M. Aldana, P. Cluzel, "A natural class of robust networks", Proc. Natl. Acad. Sci., 100, 8710-8714, 2003.
16. M. B. Elowitz, S. Leibler, "A synthetic oscillatory network of transcriptional regulators", Nature, 403, 335-338, 2000.
17. M. Newman, A.-L. Barabási, D. J. Watts, The Structure and Dynamics of Networks, Princeton University Press, 2006.
18. N. Kashtan, S. Itzkovitz, R. Milo, U. Alon, "Topological generalizations of network motifs", Phys. Rev. E, 70, 031909, 2004.
19. P. Krawitz, I. Shmulevich, "Basin Entropy in Boolean Ensembles", Phys. Rev. Lett., 98, 158701, 2007.
20. R. Milo, S. Shen-Orr, S. Itzkovitz, N. Kashtan, D. Chklovskii, U. Alon, "Network motifs: simple building blocks of complex networks", Science, 298, 824-827 2002.
21. S. A. Kauffman, The Origins of Order, Oxford University Press, 1993.
22. S. Ishihara, K. Fujimoto, T. Shibata, "Cross talking of network motifs in gene regulation that generate temporal pulses and spatial stripes", Gene to Cells, 10, 1025-1038, 2005.
23. T. S. Gardner, C. R. Cantor, J. J. Collins, "Construction of a genetic toggle switch in Escherichia coli", Nature, 403, 339-342, 2000.
24. U. Alon, An Introduction to Systems Biology, Chapman & Hall/CRC (2006).
25. Y. Setty, A. E. Mayo, M. G. Surette, U. Alon, "Detailed map of cis-regulatory input function", Proc. Natl. Acad. Sci., 100, 7702-7707, 2003.