Control of complex networks requires both structure and dynamics

Scientific Reports

Volumn 6, Issue , 2016, Pages

  Gates, Alexander J ^a,b   Rocha, Luis M ^a,b,c  

^a INDIANA UNIVERSITY   (United States)

^b INDIANA UNIVERSITY   (United States)

^c INSTITUTO GULBENKIAN DE CIÊNCIA   (Portugal)

Author keywords

[No Author keywords available]

Indexed keywords

ARABIDOPSIS THALIANA; BUDDING; CELL CYCLE; DROSOPHILA MELANOGASTER; LOGIC; MODEL; ORGAN; SACCHAROMYCES CEREVISIAE; STATISTICAL MODEL; ANATOMY AND HISTOLOGY; ANIMAL; ARABIDOPSIS; BIOLOGICAL MODEL; CYTOLOGY; FLOWER; GENETICS; NONLINEAR SYSTEM; PROTEIN MOTIF;

AMINO ACID MOTIFS; ANIMALS; ARABIDOPSIS; CELL CYCLE; DROSOPHILA MELANOGASTER; FLOWERS; MODELS, BIOLOGICAL; NONLINEAR DYNAMICS; SACCHAROMYCES CEREVISIAE;

EID: 84964221875     PISSN: None     EISSN: 20452322     Source Type: Journal    
DOI: 10.1038/srep24456     Document Type: Article

References (60)

1. Kauffman, S. A. The Origins of Order: self-organization and selection in evolution (Oxford University Press, New York, 1993).
2. Newman, M. The structure and function of complex networks. SIAM Rev. 167-256 (2003).
3. Huang, S. Gene expression profiling, genetic networks, and cellular states: an integrating concept for tumorigenesis and drug discovery. J. Mol. Med. 77, 469-480 (1999).
4. Barabási, A.-L. & Oltvai, Z. N. Network biology: understanding the cell's functional organization. Nat. Rev. Genet. 5, 101-113 (2004).
5. Zhu, X., Gerstein, M. & Snyder, M. Getting connected: analysis and principles of biological networks. Genes Dev. 21, 1010-1024 (2007).
6. Assmann, S. M. & Albert, R. Discrete dynamic modeling with asynchronous update, or how to model complex systems in the absence of quantitative information. In Belostotsky, D. A. (ed.) Plant Systems Biology vol. 553 of Methods in Molecular Biology 207-225 (Humana Press, 2009).
7. Marques-Pita, M. & Rocha, L. M. Canalization and control in automata networks: body segmentation in Drosophila melanogaster. Plos One 8, e55946 (2013).
8. Wang, R.-S. & Albert, R. Elementary signaling modes predict the essentiality of signal transduction network components. BMC systems biology 5 (2011).
9. Strogatz, S. H. Exploring complex networks. Nature 410, 268-276 (2001).
10. Klemm, K. & Bornholdt, S. Topology of biological networks and reliability of information processing. Proc. Natl. Acad. Sci. USA 102, 18414-18419 (2005).
11. Shmulevich, I., Kauffman, S. A. & Aldana, M. Eukaryotic cells are dynamically ordered or critical but not chaotic. Proc. Natl. Acad. Sci. USA 102, 13439-13444 (2005).
12. Nykter, M. et al. Gene expression dynamics in the macrophage exhibit criticality. Proc. Natl. Acad. Sci. USA 105, 1897-1900 (2008).
13. Hossein, S., Reichl, M. D. & Bassler, K. E. Symmetry in critical random boolean network dynamics. Phys. Rev. E 89, 042808 (2014).
14. Marques-Pita, M., Manicka, S., Teuscher, C. & Rocha, L. M. Effective Connectivity as an Order Parameter in Random Boolean Networks Submitted (2016).
15. Shmulevich, I., Lähdesmäki, H., Dougherty, E. R., Astola, J. & Zhang, W. The role of certain Post classes in Boolean network models of genetic networks. Proc. Natl. Acad. Sci. USA 100, 10734-10739 (2003).
16. Kauffman, S., Peterson, C., Samuelsson, B. & Troein, C. Genetic networks with canalyzing Boolean rules are always stable. Proc. Natl. Acad. Sci. USA 101, 17102-17107 (2004).
17. Li, F., Long, T., Lu, Y., Ouyang, Q. & Tang, C. The yeast cell-cycle network is robustly designed. Proc. Natl. Acad. Sci. USA 101, 4781-4786 (2004).
18. Gershenson, C., Kauffman, S. A. & Shmulevich, I. The role of redundancy in the robustness of random boolean networks. In Artificial Life X (MIT Press, 2006).
19. Lin, C. Structural controllability. IEEE Trans. Automat. Contr. 19, 201-208 (1974).
20. Liu, Y.-Y., Slotine, J.-J. & Barabási, A.-L. Controllability of complex networks. Nature 473, 167-173 (2011).
21. Nacher, J. C. & Akutsu, T. Dominating scale-free networks with variable scaling exponent: heterogeneous networks are not difficult to control. New J. Phys. 14, 073005 (2012).
22. Nacher, J. C. & Akutsu, T. Structural controllability of unidirectional bipartite networks. Scientific Reports 3 (2013).
23. Valente, T. Network Interventions. Science 337, 49-53 (2012).
24. Egerstedt, M. Complex networks: Degrees of control. Nature 473, 158-159 (2011).
25. Ruths, J. & Ruths, D. Control profiles of complex networks. Science 343, 1373-1376 (2014).
26. Delpini, D. et al. Evolution of controllability in interbank networks. Scientific Reports 3 (2013).
27. Österlund, T., Bordel, S. & Nielsen, J. Controllability analysis of transcriptional regulatory networks reveals circular control patterns among transcription factors. Integrative Biology 7, 560-568 (2015).
28. Liu, Y.-Y., Slotine, J.-J. & Barabási, A.-L. Observability of complex systems. Proc. Natl. Acad. Sci. USA 110, 2460-2465 (2013).
29. Müller, F.-J. & Schuppert, A. Few inputs can reprogram biological networks. Nature 478, E4-E5 (2011).
30. Cowan, N. J., Chastain, E. J., Vilhena, D. A., Freudenberg, J. S. & Bergstrom, C. T. Nodal Dynamics, Not Degree Distributions, Determine the Structural Controllability of Complex Networks. Plos One 7, e38398 (2012).
31. Sun, J. & Motter, A. E. Controllability Transition and Nonlocality in Network Control. Phys. Rev. Lett. 110, 208701 (2013).
32. Wuchty, S. Controllability in protein interaction networks. Proc. Natl. Acad. Sci. USA 111, 7156-7160 (2014).
33. Wang, B. et al. Diversified control paths: A significant way disease genes perturb the human regulatory network. PLos One 10 (2015).
34. Bornholdt, S. Boolean network models of cellular regulation: prospects and limitations. J. R. Soc. Interface 5, S85-S94 (2008).
35. Akutsu, T., Hayashida, M., Ching, W.-K. & Ng, M. K. Control of Boolean networks: hardness results and algorithms for tree structured networks. J. Theor. Biol. 244, 670-679 (2007).
36. Langmead, C. J. & Jha, S. K. Symbolic approaches for finding control strategies in boolean networks. J. Bioinform. Comput. Biol. 7, 323-338 (2009).
37. Cheng, D. & Qi, H. Controllability and observability of Boolean control networks. Automatica 45, 1659-1667 (2009).
38. Srihari, S., Raman, V., Leong, H. W. & Ragan, M. A. Evolution and Controllability of Cancer Networks: A Boolean Perspective. IEEE Trans. Control Netw. Syst. 11, 83-94 (2013).
39. Jia, T. & Barabási, A.-L. Control Capacity and A Random Sampling Method in Exploring Controllability of Complex Networks. Scientific Reports 3 (2013).
40. Li, R., Yang, M. & Chu, T. Controllability and observability of boolean networks arising from biology. Chaos 25, 023104 (2015).
41. Lu, W., Tamura, T., Song, J. & Akutsu, T. Computing smallest intervention strategies for multiple metabolic networks in a boolean model. J. Comp. Biol. 22, 85-110 (2015).
42. Motter, A. E. Networkcontrology. Chaos 25, 097621 (2015).
43. Wuensche, A. Discrete dynamical networks and their attractor basins. In Standish, R. et al. (eds) Complex Systems'98 (University of New South Wales, Sydney, Australia, 1998).
44. Willadsen, K. & Wiles, J. Robustness and state-space structure of Boolean gene regulatory models. J. Theor. Biol. 249, 749-765 (2007).
45. Sontag, E. D. Mathematical control theory: deterministic finite dimensional systems. Springer, New York (1998).
46. Kauffman, S. A. Metabolic stability and epigenesis in randomly constructed genetic nets. J. Theor. Biol. 22, 437-467 (1969).
47. Zhang, R. et al. Network model of survival signaling in large granular lymphocyte leukemia. Proc. Natl. Acad. Sci. USA 105, 16308-16313 (2008).
48. Kauffman, S. A., Peterson, C., Samuelsson, B. & Troein, C. Random Boolean network models and the yeast transcriptional network. Proc. Natl. Acad. Sci. USA 100, 14796-14799 (2003).
49. Ciliberti, S., Martin, O. C. & Wagner, A. Innovation and robustness in complex regulatory gene networks. Proc. Natl. Acad. Sci. USA 104, 13591-13596 (2007).
50. Reichhardt, C. J. O. & Bassler, K. Canalization and symmetry in boolean models for genetic regulatory networks. Physica A 40, 4339-4350 (2007).
51. Shen-Orr, S. S., Milo, R., Mangan, S. & Alon, U. Network motifs in the transcriptional regulation network of Escherichia coli. Nature Genetics 31, 64-68 (2002).
52. Ingram, P. J., Stumpf, M. P. & Stark, J. Network motifs: structure does not determine function. BMC Genomics 7, 108 (2006).
53. Prill, R. J., Iglesias, P. A. & Levchenko, A. Dynamic Properties of Network Motifs Contribute to Biological Network Organization. PLos Biology 3, e343 (2005).
54. Mangan, S. & Alon, U. Structure and function of the feed-forward loop network motif. Proc. Natl. Acad. Sci. USA 100, 11980-11985 (2003).
55. Albert, R. & Othmer, H. G. The topology of the regulatory interactions predicts the expression pattern of the segment polarity genes in Drosophila melanogaster. J. Theor. Biol. 223, 1-18 (2003).
56. Chaves, M., Sontag, E. D. & Albert, R. Methods of robustness analysis for boolean models of gene control networks. IEE P. Syst. Biol. 153, 154-167 (2006).
57. Whalen, A. J., Brennan, S. N., Sauer, T. D. & Schiff, S. J. Observability and controllability of nonlinear networks: The role of symmetry. Phys. Rev. X 5, 011005 (2015).
58. Angeli, D. & Sontag, E. D. Monotone control systems. IEEE Trans. Automat. Contr. 48, 1684-1698 (2003).
59. Gutiérrez, R., Sendiña-Nadal, I., Zanin, M., Papo, D. & Boccaletti, S. Targeting the dynamics of complex networks. Scientific Reports 2 (2012).
60. Zañudo, J. G. & Albert, R. Cell fate reprogramming by control of intracellular network dynamics. PLos Comput. Biol. 11, e1004193 (2015).