Evidence for dynamically organized modularity in the yeast protein–protein interaction network

Jeong, H., Mason, S. P., Barabasi, A. L. & Oltvai, Z. N. Lethality and centrality in protein networks. Nature 411, 41–42 (2001)

Li, S. et al. A map of the interactome network of the metazoan C. elegans. Science 303, 540–543 (2004)

Wagner, A. Robustness against mutations in genetic networks of yeast. Nature Genet. 24, 355–361 (2000)

Gu, Z. et al. Role of duplicate genes in genetic robustness against null mutations. Nature 421, 63–66 (2003)

Winzeler, E. A. et al. Functional characterization of the S. cerevisiae genome by gene deletion and parallel analysis. Science 285, 901–906 (1999)

Giaever, G. et al. Functional profiling of the Saccharomyces cerevisiae genome. Nature 418, 387–391 (2002)

Hartwell, L. H., Hopfield, J. J., Leibler, S. & Murray, A. W. From molecular to modular cell biology. Nature 402, C47–C52 (1999)

Papin, J. A., Price, N. D., Wiback, S. J., Fell, D. A. & Palsson, B. O. Metabolic pathways in the post-genome era. Trends Biochem. Sci. 28, 250–258 (2003)

Kemmeren, P. et al. Protein interaction verification and functional annotation by integrated analysis of genome-scale data. Mol. Cell 9, 1133–1143 (2002)

von Mering, C. et al. Comparative assessment of large-scale data sets of protein–protein interactions. Nature 417, 399–403 (2002)

Ge, H., Liu, Z., Church, G. M. & Vidal, M. Correlation between transcriptome and interactome mapping data from Saccharomyces cerevisiae. Nature Genet. 29, 482–486 (2001)

Huh, W. K. et al. Global analysis of protein localization in budding yeast. Nature 425, 686–691 (2003)

Albert, R., Jeong, H. & Barabasi, A. L. Error and attack tolerance of complex networks. Nature 406, 378–382 (2000)

Mewes, H. W. et al. MIPS: a database for genomes and protein sequences. Nucleic Acids Res. 30, 31–34 (2002)

Ideker, T. & Lauffenburger, D. Building with a scaffold: emerging strategies for high- to low-level cellular modeling. Trends Biotechnol. 21, 255–262 (2003)

Giot, L. et al. A protein interaction map of Drosophila melanogaster. Science 302, 1727–1736 (2003)

Le Pont, F. et al. A new scale for measuring dynamic patterns of sexual partnership and concurrency: application to three French Caribbean regions. Sex. Transm. Dis. 30, 6–9 (2003)

Uetz, P. et al. A comprehensive analysis of protein–protein interactions in Saccharomyces cerevisiae. Nature 403, 623–627 (2000)

Ito, T. et al. A comprehensive two-hybrid analysis to explore the yeast protein interactome. Proc. Natl Acad. Sci. USA 98, 4569–4574 (2001)

Fromont-Racine, M., Rain, J. C. & Legrain, P. Toward a functional analysis of the yeast genome through exhaustive two-hybrid screens. Nature Genet. 16, 277–282 (1997)

Fromont-Racine, M. et al. Genome-wide protein interaction screens reveal functional networks involving Sm-like proteins. Yeast 17, 95–110 (2000)

Ho, Y. et al. Systematic identification of protein complexes in Saccharomyces cerevisiae by mass spectrometry. Nature 415, 180–183 (2002)

Gavin, A. C. et al. Functional organization of the yeast proteome by systematic analysis of protein complexes. Nature 415, 141–147 (2002)

Bader, G. D., Betel, D. & Hogue, C. W. BIND: the Biomolecular Interaction Network Database. Nucleic Acids Res. 31, 248–250 (2003)

Marcotte, E. M., Pellegrini, M., Thompson, M. J., Yeates, T. O. & Eisenberg, D. A combined algorithm for genome-wide prediction of protein function. Nature 402, 83–86 (1999)

Dandekar, T., Snel, B., Huynen, M. & Bork, P. Conservation of gene order: a fingerprint of proteins that physically interact. Trends Biochem. Sci. 23, 324–328 (1998)

Watts, D. J. & Strogatz, S. H. Collective dynamics of ‘small-world’ networks. Nature 393, 440–442 (1998)

Snel, B., Bork, P. & Huynen, M. A. The identification of functional modules from the genomic association of genes. Proc. Natl Acad. Sci. USA 99, 5890–5895 (2002)