Reference
- Barabasi AL, Oltvai ZN. Network biology: understanding the cell's functional organisation. Nature Rev Genet. 5, 101–113 (2004).
- Bollobas B. Random Graphs. Academic Press, London, UK (1985).
- Albert R, Barabasi AL. Statistical mechanics of complex networks. Rev Mod. Phys. 74, 47–97 (2002).
- Newman MEJ, Strogatz SH, Watts DJ. Random graphs with arbitrary degree distributions and their applications. Phys. Rev E. 64, (2001).
- Watts DJ, Strogatz SH. Collective dynamics of 'small-world' networks. Nature 393,440–442 (1998).
- Barabasi AL, AlbertR. Emergence of scaling in random networks. Science 286,509–512 (1999).
- Wagner A. How the global structure of protein interaction networks evolves. Proc. R. Soc. Lond. 270,457–466 (2003).
- Uetz P A comprehensive analysis of protein—protein interactions in Saccharomyces cerevisiae. Nature 403, 623–627 (2000).
- Grindrod P Range-dependent random graphs and their application to modeling large small-world proteome data sets. Phys. Rev E. 66,1–7 (2002).
- Grindrod P. Modeling proteome networks with range-dependent graphs. Am. .1. Pharmacogenomics3, 1–4 (2003).
- Thomas A, Cannings R, Monk NAM, Cannings C. On the structure of protein—protein interaction networks. Biochem. Soc. Trans. 31,1491–1496 (2003).
- Jeong H, Mason SP, Barabasi AL, Oltvai ZN. Lethality and centrality in protein networks. Nature 411,41— 42 (2001).
- Xenarios I. DIP: the Database of Interacting Proteins. Nucleic Acids Res. 28,289–291 (2000).
- Wagner A. The yeast protein interaction network evolves rapidly and contains few redundant duplicate genes. Mol. Biol. Evol.18,1283–1292 (2001).
- Ito T. A comprehensive two-hybrid analysis to explore the yeast protein interactome. Proc. Natl Acad. Sci. USA 98,4569–4574 (2001).
- Gilchrist MA, Salter LA, Wagner A. A statistical framework for combining and interpreting proteomic datasets. Bioinformatics 20,689–700 (2004).
- Gavin AC. Functional organisation of the yeast proteome by systematic analysis of protein complexes. Nature 415,141–147 (2002).
- Ho Y. Systematic identification of protein complexes in Saccharomyces cerevisiae by mass spectometry. Nature 415,180–183 (2002).
- Joeng H, Tombor B, Albert R, Oltvai ZN, Barabasi AL. The large-scale organisation of metabolic networks. Nature 407,651–654 (2000).
- Overbeek R. WIT: integrated system for high-throughput genome sequence analysis and metabolic reconstruction. Nucleic Acids Res. 28,123–125 (2000).
- Rung J, Schlitt T, Brazma A, Freivalds K, Vile J. Building and analysing genome-wide gene disruption networks. Bioinformatics 18 (Suppl. 2), 5202—S210 (2002).
- Hughes TR. Functional discovery via a compendium of expression profiles. Ce11102, 109–126 (2000).
- Wuchty S. Scale-free behavior in protein domain networks. Mal Biol. Evol. 18, 1694-1702 (2001).
- Albert R, Jeong H, Barabasi AL. Error and attack tolerance of complex networks. Nature 406,378–382 (2000).
- Schwikowski B, Uetz P, Fields S. A network of protein— protein interactions in yeast. Nature BiotechnoL 18,1257–1261 (2000).
- Schlitt T. From gene networks to gene function. Genome Res. 13,2568–2576 (2003).
- Ideker T. Discovering regulatory and signalling circuits in molecular interaction networks. Bioinformatics 18 (Suppl. 1), 5233—S240 (2002).
- Bader GD, Hogue CWV. An automated method for finding molecular complexes in large protein interaction networks. BMC Bioinformatics 4 (2), January (2003).
- Wagner A. How to reconstruct a large genetic network from n gene perturbations in fewer than n2 easy steps. Bioinformatics 17,1183–1197 (2001).
- Higham DJ. Unravelling small world networks. Computational Applied Math. 158,61–74 (2003).
- Higham DJ. Spectral reordering of a range- dependent weighted random graph. University of Strathclyde Mathematics Research Report 14, (2003).
- Kannan N, Vishveshwara S. Identification of side chain clusters in protein structures by a graph spectral method. .1. Moll Biol. 292,441-464 (1999).
- Gardiner EJ, Willett P, Artymiuk PJ. Graph-theoretic techniques for macromolecular docking. .1. Chem. In! Comput. Sci 40,273-279 (2000).
- Hendrickson B. The molecule problem: exploiting structure in global optimization. SIAM J. Opt. 5,835— 857 (1995).
- Tong AHY. A combined experimental and computational strategy to define protein interaction networks for peptide recognition modules. Science 295, 321–324 (2002).
- Bader GD, Hogue CWV. Analyzing yeast protein— protein interaction data obtained from different sources. Nature BiotechnoL 20,991–997 (2002).
- Bollobas B. Graph Theory' An IntroductoryCourse. Springer—Verlag, Berlin, Germany (1979).