Inferring the physical connectivity of complex networks from their functional dynamics

BMC Systems Biology

Volumn 4, Issue , 2010, Pages

  Ta, Hung X ^a   Yoon, Chang N ^b   Holm, Liisa ^a   Han, Seung K ^b  

^a UNIVERSITY OF HELSINKI   (Finland)

^b Chungbuk National University   (South Korea)

Author keywords

[No Author keywords available]

Indexed keywords

ALGORITHM; ARTICLE; COMPUTER SIMULATION; GENE REGULATORY NETWORK; NONLINEAR SYSTEM; OSCILLOMETRY; PROTEIN ANALYSIS; THEORETICAL MODEL;

ALGORITHMS; COMPUTER SIMULATION; GENE REGULATORY NETWORKS; MODELS, THEORETICAL; NONLINEAR DYNAMICS; OSCILLOMETRY; PROTEIN INTERACTION MAPPING;

EID: 77952627808     PISSN: None     EISSN: 17520509     Source Type: Journal    
DOI: 10.1186/1752-0509-4-70     Document Type: Article

References (39)

1. Albert R, Barabási AL. Statistical mechanics of complex networks. Rev Mod Phys 2002, 74:47-97.
2. Dorogovtsev SN, Mendes JF. Evolution of Networks: from Biological Nets to the Internet and WWW 2003, Oxford: Oxford University Press.
3. Erdo{double acute}s P, Rényi A. On the evolution of random graphs. Publ Math Inst Hung Acad Sci 1960, 5:17-61.
4. Albert R, Jeong H, Barabási AL. Internet: Diameter of the World-Wide Web. Nature 1999, 401:130-131.
5. Newman MEJ, Forrest S, Balthrop J. Email networks and the spread of computer viruses. Phys Rev E 2002, 66:035101.
6. Vázquez A, Pastor-Satorras R, Vespignani A. Large-scale topological and dynamical properties of the Internet. Phys Rev E 2002, 65:066130.
7. Uetz P, Giot L, Cagney G, Mansfield TA, Judson RS, Knight JR, Lockshon D, Narayan V, Srinivasan M, Pochart P, Qureshi-Emili A, Li Y, Godwin B, Conover D, Kalbfleisch T, Vijayadamodar G, Yang M, Johnston M, Fields S, Rothberg JM. A comprehensive analysis of protein-protein interactions in Saccharomyces cerevisiae. Nature 2000, 403:623-627. 10.1038/35001009, 10688190.
8. Camacho J, Guimerá R, Amaral LAN. Robust Patterns in Food Web Structure. Phys Rev Lett 2002, 88:228102. 10.1103/PhysRevLett.88.228102, 12059454.
9. Jeong H, Tombor B, Albert R, Oltvai ZN, Barabási AL. The large-scale organization of metabolic networks. Nature 2000, 407:651-654. 10.1038/35036627, 11034217.
10. Newman MEJ. The structure of scientific collaboration networks. Proc Natl Acad Sci USA 2001, 98:404-409. 10.1073/pnas.021544898, 14598, 11149952.
11. Barabási AL, Albert R. Emergence of Scaling in Random Networks. Science 1999, 286:509-512. 10.1126/science.286.5439.509, 10521342.
12. Pikovsky AS, Rosenblum MG, Kurth J. Synchronization: A Universal Concept in Nonlinear Science 2001, Cambrige: Cambrige University Press.
13. Kuramoto Y. Chemical Oscillations, Waves and Turbulence 1984, Berlin: Springer.
14. Watts DJ, Strogatz SH. Collective dynamics of 'small-world' networks. Nature 1998, 393:440-442. 10.1038/30918, 9623998.
15. Glass L. Synchronization and rhythmic processes in physiology. Nature 2001, 410:277-284. 10.1038/35065745, 11258383.
16. Strogatz SH. Exploring complex networks. Nature 2001, 410:268-276. 10.1038/35065725, 11258382.
17. Boccaletti S, Latorab V, Moreno Y, Chavez M, Hwang DU. Complex networks: Structure and dynamics. Physics Reports 2006, 412:175-308.
18. Timme M. Revealing Network Connectivity from Response Dynamics. Phys Rev Lett 2007, 98(22):224101. 10.1103/PhysRevLett.98.224101, 17677845.
19. Barabási AL, Albert R, Jeong H. Mean-field theory for scale-free random networks. Physica A 1999, 272:173-187.
20. Ravasz E, Somera AL, Mongru DA, Oltvai ZN, Barabási AL. Hierarchical Organization of Modularity in Metabolic Networks. Science 2002, 297:1551-1555. 10.1126/science.1073374, 12202830.
21. Fernández LFL, Huerta R, Corbacho F, Sigüenza JA. Fast Response and Temporal Coherent Oscillations in Small-World Networks. Phys Rev Lett 2000, 84:2758-2761. 10.1103/PhysRevLett.84.2758, 11017318.
22. Barahona M, Pecora LM. Synchronization in Small-World Systems. Phys Rev Lett 2002, 89:054101. 10.1103/PhysRevLett.89.054101, 12144443.
23. McGraw PN, Menzinger M. Clustering and the synchronization of oscillator networks. Phys Rev E 2005, 72:015101.
24. Oh E, Rho K, Hong H, Kahng B. Modular synchronization in complex networks. Phys Rev E 2005, 72:047101.
25. Park K, Lai Y, Gupte S, Kim JW. Synchronization in complex networks with a modular structure. Chaos 2006, 16:015105. 10.1063/1.2154881, 16599771.
26. Gómez-Gardeñes J, Moreno Y, Arenas A. Paths to Synchronization on Complex Networks. Phys Rev Lett 2007, 98(3):034101. 10.1103/PhysRevLett.98.034101, 17358685.
27. Gómez-Gardeñes J, Moreno Y, Arenas A. Synchronizability determined by coupling strengths and topology on complex networks. Phys Rev E 2007, 75(6):066106.
28. Acebrón AL, Bonilla LL, Conrad J, Vicente P, Ritort F, Spigler R. The Kuramoto model: A simple paradigm for synchronization phenomena. Rev Mod Phys 2005, 77:137-185.
29. Hong H, Choi MY, Kim BJ. Synchronization on small-world networks. Phys Rev E 2002, 65(2):026139.
30. Kruskal JB. On the shortest spanning subtree of a graph and the travelling salesman problem. Proc Am Math Soc 1956, 7:48-50.
31. Mouraux A, Iannetti GD. Across-trial averaging of event-related responses and beyond. Magnetic Resonance Imaging 2008, 26(7):1041-1054. 10.1016/j.mri.2008.01.011, 18479877.
32. Kudela P, Franaszczuk PJ, Bergey GK. Changing Excitation and Inhibition in Simulated Neural Networks: Effects on Induced Bursting Behavior. Biol Cybern 2003, 88:88-276.
33. Newman MEJ, Strogatz SH, Watts DJ. Random graphs with arbitrary degree distributions and their applications. Phys Rev E 2001, 64:026118.
34. Amaral LAN, Scala A, Barthélémy M, Stanley HE. Classes of small-world networks. Proc Natl Acad Sci USA 2000, 97:11149-11152. 10.1073/pnas.200327197, 17168, 11005838.
35. Moreno Y, Pacheco AF. Synchronization of Kuramoto oscillators in scale-free networks. Europhys Lett 2004, 68:603.
36. Hammond C, Bergman H, Brown P. Pathological synchronization in Parkinson's disease: networks, models and treatments. Trends Neurosci 2007, 30(7):357-364. 10.1016/j.tins.2007.05.004, 17532060.
37. Fisher R, Boas VEW, Blume W, Elger C, Genton P, Lee P, Engel J. Epileptic seizures and epilepsy: definitions proposed by the International League Against Epilepsy (ILAE) and the International Bureau for Epilepsy (IBE). Epilepsia 2005, 46(4):470-472. 10.1111/j.0013-9580.2005.66104.x, 15816939.
38. Moreno Y, Pacheco AF. Synchronization of Kuramoto oscillators in scale-free networks. EPL (Europhysics Letters) 2004, 68(4):603-609.
39. Hanley JA, McNeil BJ. A method of comparing the areas under receiver operating characteristic curves derived from the same cases. Radiology 1983, 148(3):839-843.