Determining the distance to monotonicity of a biological network: A graph-theoretical approach

IET Systems Biology

Volumn 4, Issue 3, 2010, Pages 223-235

  Iacono, G ^a   Ramezani, F ^b   Soranzo, N ^a   Altafini, C ^a  

^a SISSA   (Italy)

^b MAX PLANCK INSTITUTE FOR INFORMATICS   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

BIOLOGICAL NETWORKS; FUNDAMENTAL CYCLES; GRAPH THEORETICAL APPROACH; MONOTONICITY; SIGNED GRAPHS;

GRAPH THEORY;

PROTEOME;

ALGORITHM; ANIMAL; ARTICLE; BIOLOGICAL MODEL; COMPUTER SIMULATION; HUMAN; METABOLISM; PHYSIOLOGY; SIGNAL TRANSDUCTION;

ALGORITHMS; ANIMALS; COMPUTER SIMULATION; HUMANS; MODELS, BIOLOGICAL; PROTEOME; SIGNAL TRANSDUCTION;

EID: 77953264688     PISSN: 17518849     EISSN: None     Source Type: Journal    
DOI: 10.1049/iet-syb.2009.0040     Document Type: Article

References (23)

1. DasGupta, B. Enciso, G.A. Sontag, E. Zhang, Y.: 'Algorithmic and complexity results for decompositions of biological networks into monotone subsystems', Biosystems, 2007, 90, (1), p. 161-178
2. Ma'ayan, A. Lipshtat, A. Iyengar, R. Sontag, E.: 'Proximity of intracellular regulatory networks to monotone', IET Syst. Biol., 2008, 2, p. 103-112
3. SontagE.D.: 'Monotone and near-monotone biochemical networks'Syst. Synth. Biol.20071p. 59-87
4. SontagE. Veliz-CubaA. LaubenbacherR. JarrahA.S.: 'The effect of negative feedback loops on the dynamics of boolean networks'Biophys. J.200895(2)p. 518-5260006-3495
5. SmithH.L.: 'Systems of ordinary differential equations which generate an order preserving flow. A survey of results'SIAM Rev.198830(1)p. 87-1130036-1445
6. AlonU.: 'Network motifs: theory and experimental approaches'Nat. Rev. Genet.20078(6)p. 450-461
7. HirschM. SmithH.L.: 'Monotone dynamical systems,'CanadaA.DrabekP.FondaA. Handbook of differential equationsordinary differential equations(North Holland 2006),Vol. 2Ch. 4)pp. 239-357
8. KirchhoffG.: 'Uμ;ber die Auflösung der Gleichungenauf welche man bei der untersuchung der linearen Verteilung galvanischer strome gefuhrt wird'Ann. Phys. Chem.184772p. 497-508
9. SoléP. ZaslavskyT.: 'A coding approach to signed graphs'SIAM J. Discrete Math.19947(4)p. 544-5530895-4801
10. ZaslavskyT.: 'Signed graphs'Discrete Appl. Math.19824(1) 47-740166-218X
11. HüffnerF. BetzlerN. NiedermeierR.: 'Separator-based data reduction for signed graph balancing''J. Comb. Optim.2009DOI 10.1007/s10878-009-9212-21382-6905
12. DeoN.: 'Graph theory with applications to engineering and computer science'(Prentice-HallEnglewood Cliffs 1974)
13. ToulouseG.: 'Theory of the frustration effect in spin glasses: I'Commun. Phys.19772 1150306-9486
14. GoemansM.X. WilliamsonD.: 'Improved approximation algorithms for maximum cut and satisfiability problems using semi-definite programming'J. ACM199542(6) 1115-11450004-5411
15. ZaslavskyT.: 'A mathematical bibliography of signed and gain graphs and allied areas'Electr. J. Comb.1998DS8
16. Bang-JensenA. GutinG.: 'When the greedy algorithm fails'Discrete Optim.20041 121-127
17. MiloR. Shen-OrrS. ItzkovitzS. KashtanN. ChklovskiiD. AlonU.: 'Network motifs: simple building blocks of complex networks'Science2002298(5594) 824-8270036-8075
18. CapraraA. PanconesiA. RizziR.: 'Packing cycles in undirected graphs'J. Algorithms200348(1) 239-2560196-6774
19. OdaK. MatsuokaY. FunahashiA. KitanoH.: 'A comprehensive pathway map of epidermal growth factor receptor signaling'Mol. Syst. Biol.20051 2005
20. OdaK. KimuraT. MatsuokaY. FunahashiA. MuramatsuM. KitanoH.: 'Molecular inter-action map of a macrophage'AfCS Reports20042(14)
21. SalgadoH. Gama-CastroS. Peralta-GilM.: et al. 'RegulonDB (version 5.0): Escherichia coli K-12 transcriptional regulatory networkoperon organizationand growth conditions'Nucl. Acids Res.200634 D394-D397 (Database issue)
22. Shen-OrrS.S. MiloR. ManganS. AlonU.: 'Network motifs in the transcriptional regulation network of Escherichia coli'Nat. Genet.200231(1) 64-68
23. PrimR.: 'Shortest connection networks and some generalizations'Bell Syst. Tech. J.195736 1389-14010005-8580