Hierarchical structure and the prediction of missing links in networks (original) (raw)

References

  1. Wasserman, S. & Faust, K. Social Network Analysis (Cambridge Univ. Press, Cambridge, 1994)
    Book Google Scholar
  2. Albert, R. & Barabási, A.-L. Statistical mechanics of complex networks. Rev. Mod. Phys. 74, 47–97 (2002)
    Article ADS MathSciNet Google Scholar
  3. Newman, M. E. J. The structure and function of complex networks. SIAM Rev. 45, 167–256 (2003)
    Article ADS MathSciNet Google Scholar
  4. Ravasz, E., Somera, A. L., Mongru, D. A., Oltvai, Z. N. & Barabási, A.-L. Hierarchical organization of modularity in metabolic networks. Science 30, 1551–1555 (2002)
    Article ADS Google Scholar
  5. Clauset, A., Newman, M. E. J. & Moore, C. Finding community structure in very large networks. Phys. Rev. E 70, 066111 (2004)
    Article ADS Google Scholar
  6. Guimera, R. & Amaral, L. A. N. Functional cartography of complex metabolic networks. Nature 433, 895–900 (2005)
    Article ADS CAS Google Scholar
  7. Lagomarsino, M. C., Jona, P., Bassetti, B. & Isambert, H. Hierarchy and feedback in the evolution of the Escherichia coli transcription network. Proc. Natl Acad. Sci. USA 104, 5516–5520 (2001)
    Article Google Scholar
  8. Liben-Nowell, D. & Kleinberg, J. M. The link-prediction problem for social networks. J. Am. Soc. Inform. Sci. Technol. 58, 1019–1031 (2007)
    Article Google Scholar
  9. Girvan, M. & Newman, M. E. J. Community structure in social and biological networks. Proc. Natl Acad. Sci. USA 99, 7821–7826 (2002)
    Article ADS MathSciNet CAS Google Scholar
  10. Krause, A. E., Frank, K. A., Mason, D. M., Ulanowicz, R. E. & Taylor, W. W. Compartments revealed in food-web structure. Nature 426, 282–285 (2003)
    Article ADS CAS Google Scholar
  11. Radicchi, F., Castellano, C., Cecconi, F., Loreto, V. & Parisi, D. Defining and identifying communities in networks. Proc. Natl Acad. Sci. USA 101, 2658–2663 (2004)
    Article ADS CAS Google Scholar
  12. Watts, D. J., Dodds, P. S. & Newman, M. E. J. Identity and search in social networks. Science 296, 1302–1305 (2002)
    Article ADS CAS Google Scholar
  13. Kleinberg, J. in Proc. 2001 Neural Inform. Processing Systems Conf. (eds Dietterich, T. G., Becker, S. & Ghahramani, Z.) 431–438 (MIT Press, Cambridge, MA, 2002)
    Google Scholar
  14. Palla, G., Derényi, I., Farkas, I. & Vicsek, T. Uncovering the overlapping community structure of complex networks in nature and society. Nature 435, 814–818 (2005)
    Article ADS CAS Google Scholar
  15. Casella, G. & Berger, R. L. Statistical Inference (Duxbury, Belmont, 2001)
    MATH Google Scholar
  16. Newman, M. E. J. & Barkema, G. T. Monte Carlo Methods in Statistical Physics (Clarendon, Oxford, 1999)
    MATH Google Scholar
  17. Newman, M. E. J. Assortative mixing in networks. Phys. Rev. Lett. 89, 208701 (2002)
    Article ADS CAS Google Scholar
  18. Huss, M. & Holme, P. Currency and commodity metabolites: Their identification and relation to the modularity of metabolic networks. IET Syst. Biol. 1, 280–285 (2007)
    Article CAS Google Scholar
  19. Krebs, V. Mapping networks of terrorist cells. Connections 24, 43–52 (2002)
    Google Scholar
  20. Dawah, H. A., Hawkins, B. A. & Claridge, M. F. Structure of the parasitoid communities of grass-feeding chalcid wasps. J. Anim. Ecol. 64, 708–720 (1995)
    Article Google Scholar
  21. Bryant, D. in BioConsensus (eds Janowitz, M., Lapointe, F.-J., McMorris, F. R., Mirkin, B. & Roberts, F.) pp. 163–184 (Series in Discrete Mathematics and Theoretical Computer Science, Vol. 61, American Mathematical Society-DIMACS, Providence, RI, 2003)
    Book Google Scholar
  22. Dunne, J. A., Williams, R. J. & Martinez, N. D. Food-web structure and network theroy: The role of connectance and size. Proc. Natl Acad. Sci. USA 99, 12917–12922 (2002)
    Article ADS CAS Google Scholar
  23. Szilágyi, A., Grimm, V., Arakaki, A. K. & Skolnick, J. Prediction of physical protein–protein interactions. Phys. Biol. 2, S1–S16 (2005)
    Article ADS Google Scholar
  24. Sprinzak, E., Sattath, S. & Margalit, H. How reliable are experimental protein-protein interaction data? J. Mol. Biol. 327, 919–923 (2003)
    Article CAS Google Scholar
  25. Ito, T. et al. A comprehensive two-hybrid analysis to explore the yeast protein interactome. Proc. Natl Acad. Sci. USA 98, 4569–4574 (2001)
    Article ADS CAS Google Scholar
  26. Lakhina, A., Byers, J. W., Crovella, M. & Xie, P. in INFOCOM 2003: Twenty-Second Annual Joint Conf. IEEE Computer and Communications Societies (ed. Bauer, F.) Vol. 1 332–341 (IEEE, Piscataway, New Jersey, 2003)
    Google Scholar
  27. Clauset, A. & Moore, C. Accuracy and scaling phenomena in Internet mapping. Phys. Rev. Lett. 94, 018701 (2005)
    Article ADS Google Scholar
  28. Martinez, N. D., Hawkins, B. A., Dawah, H. A. & Feifarek, B. P. Effects of sampling effort on characterization of food-web structure. Ecology 80, 1044–1055 (1999)
    Article Google Scholar
  29. Hanely, J. A. & McNeil, B. J. The meaning and use of the area under a receiver operating characteristic (ROC) curve. Radiology 143, 29–36 (1982)
    Article Google Scholar
  30. Sales-Pardo, M., Guimerá, R., Moreira, A. A. & Amaral, L. A. N. Extracting the hierarchical organization of complex systems. Proc. Natl Acad. Sci. USA 104, 15224–15229 (2007)
    Article ADS CAS Google Scholar

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