Predicting effects of structural stress in a genome-reduced model bacterial metabolism

Scientific Reports

Volumn 2, Issue , 2012, Pages

  Güell, Oriol ^a   Sagués, Francesc ^a   Serrano, M Ángeles ^a  

^a UNIVERSITY OF BARCELONA   (Spain)

Author keywords

[No Author keywords available]

Indexed keywords

EID: 84866138656     PISSN: None     EISSN: 20452322     Source Type: Journal    
DOI: 10.1038/srep00621     Document Type: Article

References (30)

1. Albert, R. & Barabási, A.-L. Statistical mechanics of complex networks. Rev. Mod. Phys. 74, 47-97 (2002).
2. Dorogovtsev, S. N., Goltsev, A. V. & Mendes, J. F. F. Critical phenomena in complex networks. Rev. Mod. Phys. 80, 12751335 (2008).
3. Barrat, A., Barthélemy, M. & Vespignani, A. Dynamical Processes on Complex Networks. Cambridge University Press, Cambridge, (2008).
4. Cohen, R., Erez, K., ben Avraham, D. & Havlin, S. Resilience of the internet to random breakdown. Phys. Rev. Lett. 85(21), 4626 (2000).
5. Albert, R., Jeong, H. & Barabási, A.-L. Error and attack tolerance of complex networks. Nature 406, 378 (2000).
6. Watts, D. J. A simple model of global cascades on random networks. Proc. Natl. Acad. Sci. U.S.A. 99, 5766-5771 (2002). (Pubitemid 34493213)
7. Moreno, Y., Gómez, J. B. & Pacheco, A. F. Instability of scale-free networks under nodebreaking avalanches. Europhys. Lett. 58, 630-636 (2002).
8. Motter, A. Error and attack tolerance of complex networks. Phys. Rev. E 66, 065102(R) (2002).
9. Buldyrev, S. V., Parshani, R., Paul, G., Stanley, H. E. & Havlin, S. Catastrophic cascade of failures in interdependent networks. Nature 464, 1025-1028 (2010).
10. Barabási, A.-L. & Oltvai, Z. N. Network biology: understanding the cells functional organization. Nature Reviews Genetics 5, 101-113 (2004). (Pubitemid 38160277)
11. Szalay, M. S., Kovacs, I. A., Korcsmaros, T., Bode, C. & Csermely, P. Stressinduced rearrangements of cellular networks: Consequences for protection and drug design. FEBS Leters 581, 3675-3680 (2007). (Pubitemid 47080997)
12. Motter, A. E., Gulbahce, N., Almaas, E. & Barabási, A.-L. Predicting synthetic rescues in metabolic networks. Molecular Systems Biology 4, 168 (2008).
13. Palsson, B. O. Systems Biology: Properties of Reconstructed Networks (Cambridge University Press, Cambridge, 2006).
14. Jeong, H., Tombor, B., Albert, R., Oltvai, Z. N. & Barabási, A.-L. The large-scale organization of metabolic networks. Nature 407, 651-654 (2000).
15. Ma, H. & Zeng, A.-P. Reconstruction of metabolic networks from genome data and analysis of their global structure for various organisms. Bioinformatics 19, 270-277 (2003). (Pubitemid 36181913)
16. Guimera, R. & Amaral, L. A. N. Functional cartography of complex metabolic networks. Nature 433, 895-900 (2005). (Pubitemid 40314902)
17. Serrano, M. A. & Sagués, F. Network-based confidence scoring system for genome-scale metabolic reconstructions. BMC Systems Biology 5, 76 (2011).
18. Serrano, M. A., Boguná,M. & Sagués, F. Uncovering the hidden geometry behind metabolic networks. Molecular BioSystems 8, 843-850 (2012).
19. Smart, A. G., Amaral, L. A. N. & Ottino, J. Cascading failure and robustness in metabolic networks. Proc. Natl. Acad. Sci. USA 105, 13223-13228 (2008).
20. Edwards, J. S. & d Palsson, B. O. Robustness analysis of the escherichia coli metabolic network. Biotechnol. Prog. 16, 927-939 (2000). (Pubitemid 32044843)
21. Segre, D., Vitkup, D. & Church, G. M. Analysis of optimality in natural and perturbedmetabolic networks. Proc. Natl. Acad. Sci. USA 99, 15112-15117 (2002). (Pubitemid 35334618)
22. Folger, O., Jerby, L., Frezza, C., Gottlieb, E., Ruppin, E. & Shlomi, T. Predicting selective drug targets in cancer through metabolic networks. Molecular Systems Biology 7, 501 (2011).
23. Yus, E. et al. Impact of genome reduction on bacterial metabolism and its regulation. Science 326, 1263-1268 (2009).
24. Kuhner, S. et al. Proteome organization in a genome-reduced bacterium. Science 326, 1235-1240 (2009).
25. Guell, M. et al. Transcriptome complexity in a genome-reduced bacterium. Science 326, 1268-1271 (2009).
26. Smirnov, N. V. Tables for estimating the goodness of fit of empirical distributions. Annals of Mathematical Statistics, 19, 279 (1948).
27. Rosvall, M. & Bergstrom, C. T.Maps of random walks on complex networks reveal community structure. Proc. Natl. Acad. Sci. USA 105, 1118-1123 (2008). (Pubitemid 351397014)
28. Lee, S. H. et al. Neutral theory of chemical reaction networks. New Journal of Physics 14, 033032 (2012).
29. Feist, A. et al. A genome-scale metabolic reconstruction for escherichia coli k-12 mg1655 that accounts for 1260 orfs and thermodynamic information. Molecular Systems Biology 3, 121 (2007).
30. Rozenfeld, A. F., Arnaud-Haond, S., Hernández-García, E., Eguíluz, V. M., Serrão, E. A. S. & Duarte, C. M. Network analysis identifies weak and strong links in a metapopulation system. Proc. Natl. Acad. Sci. USA 105, 18824-18829 (2008).