TY - BOOK AU - Bar-Yam, Y. PY - 1997 DA - 1997// TI - Dynamics of Complex Systems PB - Addison Wesley Longman CY - London ID - Bar-Yam1997 ER - TY - JOUR AU - Watts, D. J. AU - Strogatz, S. H. PY - 1998 DA - 1998// TI - Collective dynamics of 'small-world' networks. JO - Nature VL - 393 UR - https://doi.org/10.1038/30918 DO - 10.1038/30918 ID - Watts1998 ER - TY - JOUR AU - Barabasi, A. L. AU - Albert, R. PY - 1999 DA - 1999// TI - Emergence of scaling in random networks. JO - Science VL - 286 UR - https://doi.org/10.1126/science.286.5439.509 DO - 10.1126/science.286.5439.509 ID - Barabasi1999 ER - TY - JOUR AU - Uetz, P. AU - Giot, L. AU - Cagney, G. AU - Mansfield, T. A. AU - Judson, R. S. AU - Knight, J. R. AU - Lockshon, D. AU - Narayan, V. AU - Srinivasan, M. AU - Pochart, P. PY - 2000 DA - 2000// TI - A comprehensive analysis of protein-protein interactions in Saccharomyces cerevisiae. JO - Nature VL - 403 UR - https://doi.org/10.1038/35001009 DO - 10.1038/35001009 ID - Uetz2000 ER - TY - JOUR AU - Ito, T. AU - Chiba, T. AU - Ozawa, R. AU - Yoshida, M. AU - Hattori, M. AU - Sakaki, Y. PY - 2001 DA - 2001// TI - A comprehensive two-hybrid analysis to explore the yeast protein interactome. JO - Proc Natl Acad Sci USA VL - 98 UR - https://doi.org/10.1073/pnas.061034498 DO - 10.1073/pnas.061034498 ID - Ito2001 ER - TY - JOUR AU - Gavin, A. C. AU - Bosche, M. AU - Krause, R. AU - Grandi, P. AU - Marzioch, M. AU - Bauer, A. AU - Schultz, J. AU - Rick, J. M. AU - Michon, A. M. AU - Cruciat, C. M. PY - 2002 DA - 2002// TI - Functional organization of the yeast proteome by systematic analysis of protein complexes. JO - Nature VL - 415 UR - https://doi.org/10.1038/415141a DO - 10.1038/415141a ID - Gavin2002 ER - TY - JOUR AU - Ho, Y. AU - Gruhler, A. AU - Heilbut, A. AU - Bader, G. D. AU - Moore, L. AU - Adams, S. L. AU - Millar, A. AU - Taylor, P. AU - Bennett, K. AU - Boutilier, K. PY - 2002 DA - 2002// TI - Systematic identification of protein complexes in Saccharomyces cerevisiaeby mass spectrometry. JO - Nature VL - 415 UR - https://doi.org/10.1038/415180a DO - 10.1038/415180a ID - Ho2002 ER - TY - JOUR AU - Galperin, M. Y. AU - Koonin, E. V. PY - 2000 DA - 2000// TI - Who's your neighbor? New computational approaches for functional genomics. JO - Nat Biotechnol VL - 18 UR - https://doi.org/10.1038/76443 DO - 10.1038/76443 ID - Galperin2000 ER - TY - JOUR AU - Huynen, M. AU - Snel, B. AU - Lathe, W. AU - Bork, P. PY - 2000 DA - 2000// TI - Exploitation of gene context. JO - Curr Opin Struct Biol VL - 10 UR - https://doi.org/10.1016/S0959-440X(00)00098-1 DO - 10.1016/S0959-440X(00)00098-1 ID - Huynen2000 ER - TY - JOUR AU - Eisenberg, D. AU - Marcotte, E. M. AU - Xenarios, I. AU - Yeates, T. O. PY - 2000 DA - 2000// TI - Protein function in the post-genomic era. JO - Nature VL - 405 UR - https://doi.org/10.1038/35015694 DO - 10.1038/35015694 ID - Eisenberg2000 ER - TY - JOUR AU - Marcotte, E. M. PY - 2000 DA - 2000// TI - Computational genetics: finding protein function by nonhomology methods. JO - Curr Opin Struct Biol VL - 10 UR - https://doi.org/10.1016/S0959-440X(00)00097-X DO - 10.1016/S0959-440X(00)00097-X ID - Marcotte2000 ER - TY - JOUR AU - Tatusov, R. L. AU - Koonin, E. V. AU - Lipman, D. J. PY - 1997 DA - 1997// TI - A genomic perspective on protein families. JO - Science VL - 278 UR - https://doi.org/10.1126/science.278.5338.631 DO - 10.1126/science.278.5338.631 ID - Tatusov1997 ER - TY - JOUR AU - Gaasterland, T. AU - Ragan, M. A. PY - 1998 DA - 1998// TI - Constructing multigenome views of whole microbial genomes. JO - Microb Comp Genomics VL - 3 UR - https://doi.org/10.1089/omi.1.1998.3.177 DO - 10.1089/omi.1.1998.3.177 ID - Gaasterland1998 ER - TY - JOUR AU - Pellegrini, M. AU - Marcotte, E. M. AU - Thompson, M. J. AU - Eisenberg, D. AU - Yeates, T. O. PY - 1999 DA - 1999// TI - Assigning protein functions by comparative genome analysis: protein phylogenetic profiles. JO - Proc Natl Acad Sci USA VL - 96 UR - https://doi.org/10.1073/pnas.96.8.4285 DO - 10.1073/pnas.96.8.4285 ID - Pellegrini1999 ER - TY - JOUR AU - Lawrence, J. G. PY - 1997 DA - 1997// TI - Selfish operons and speciation by gene transfer. JO - Trends Microbiol VL - 5 UR - https://doi.org/10.1016/S0966-842X(97)01110-4 DO - 10.1016/S0966-842X(97)01110-4 ID - Lawrence1997 ER - TY - JOUR AU - Overbeek, R. AU - Fonstein, M. AU - D'Souza, M. AU - Pusch, G. D. AU - Maltsev, N. PY - 1999 DA - 1999// TI - The use of gene clusters to infer functional coupling. JO - Proc Natl Acad Sci USA VL - 96 UR - https://doi.org/10.1073/pnas.96.6.2896 DO - 10.1073/pnas.96.6.2896 ID - Overbeek1999 ER - TY - JOUR AU - Dandekar, T. AU - Snel, B. AU - Huynen, M. AU - Bork, P. PY - 1998 DA - 1998// TI - Conservation of gene order: a fingerprint of proteins that physically interact. JO - Trends Biochem Sci VL - 23 UR - https://doi.org/10.1016/S0968-0004(98)01274-2 DO - 10.1016/S0968-0004(98)01274-2 ID - Dandekar1998 ER - TY - JOUR AU - Fujibuchi, W. AU - Ogata, H. AU - Matsuda, H. AU - Kanehisa, M. PY - 2000 DA - 2000// TI - Automatic detection of conserved gene clusters in multiple genomes by graph comparison and P-quasi grouping. JO - Nucleic Acids Res VL - 28 UR - https://doi.org/10.1093/nar/28.20.4029 DO - 10.1093/nar/28.20.4029 ID - Fujibuchi2000 ER - TY - JOUR AU - Yanai, I. AU - Mellor, J. C. AU - DeLisi, C. PY - 2002 DA - 2002// TI - Identifying functional links between genes using conserved chromosomal proximity. JO - Trends Genet VL - 18 UR - https://doi.org/10.1016/S0168-9525(01)02621-X DO - 10.1016/S0168-9525(01)02621-X ID - Yanai2002 ER - TY - JOUR AU - Marcotte, E. M. AU - Pellegrini, M. AU - Ng, H. L. AU - Rice, D. W. AU - Yeates, T. O. AU - Eisenberg, D. PY - 1999 DA - 1999// TI - Detecting protein function and protein-protein interactions from genome sequences. JO - Science VL - 285 UR - https://doi.org/10.1126/science.285.5428.751 DO - 10.1126/science.285.5428.751 ID - Marcotte1999 ER - TY - JOUR AU - Enright, A. J. AU - Iliopoulos, I. AU - Kyrpides, N. C. AU - Ouzounis, C. A. PY - 1999 DA - 1999// TI - Protein interaction maps for complete genomes based on gene fusion events. JO - Nature VL - 402 UR - https://doi.org/10.1038/47056 DO - 10.1038/47056 ID - Enright1999 ER - TY - JOUR AU - Yanai, I. AU - Derti, A. AU - DeLisi, C. PY - 2001 DA - 2001// TI - Genes linked by fusion events are generally of the same functional category: a systematic analysis of 30 microbial genomes. JO - Proc Natl Acad Sci USA VL - 98 UR - https://doi.org/10.1073/pnas.141236298 DO - 10.1073/pnas.141236298 ID - Yanai2001 ER - TY - JOUR AU - Enright, A. J. AU - Ouzounis, C. A. PY - 2001 DA - 2001// TI - Functional associations of proteins in entire genomes by means of exhaustive detection of gene fusions. JO - Genome Biol VL - 2 UR - https://doi.org/10.1186/gb-2001-2-9-research0034 DO - 10.1186/gb-2001-2-9-research0034 ID - Enright2001 ER - TY - JOUR AU - Mellor, J. C. AU - Yanai, I. AU - Clodfelter, K. H. AU - Mintseris, J. AU - DeLisi, C. PY - 2002 DA - 2002// TI - Predictome: a database of putative functional links between proteins. JO - Nucleic Acids Res VL - 30 UR - https://doi.org/10.1093/nar/30.1.306 DO - 10.1093/nar/30.1.306 ID - Mellor2002 ER - TY - JOUR AU - Wuchty, S. PY - 2001 DA - 2001// TI - Scale-free behavior in protein domain networks. JO - Mol Biol Evol VL - 18 UR - https://doi.org/10.1093/oxfordjournals.molbev.a003957 DO - 10.1093/oxfordjournals.molbev.a003957 ID - Wuchty2001 ER - TY - JOUR AU - Apic, G. AU - Gough, J. AU - Teichmann, S. A. PY - 2001 DA - 2001// TI - Domain combinations in archaeal, eubacterial and eukaryotic proteomes. JO - J Mol Biol VL - 310 UR - https://doi.org/10.1006/jmbi.2001.4776 DO - 10.1006/jmbi.2001.4776 ID - Apic2001 ER - TY - JOUR AU - Apic, G. AU - Gough, J. AU - Teichmann, S. A. PY - 2001 DA - 2001// TI - An insight into domain combinations. JO - Bioinformatics VL - 17 UR - https://doi.org/10.1093/bioinformatics/17.suppl_1.S83 DO - 10.1093/bioinformatics/17.suppl_1.S83 ID - Apic2001 ER - TY - JOUR AU - Huynen, M. AU - Snel, B. AU - Lathe, W. AU - Bork, P. PY - 2000 DA - 2000// TI - Predicting protein function by genomic context: quantitative evaluation and qualitative inferences. JO - Genome Res VL - 10 UR - https://doi.org/10.1101/gr.10.8.1204 DO - 10.1101/gr.10.8.1204 ID - Huynen2000 ER - TY - JOUR AU - Marcotte, E. M. AU - Pellegrini, M. AU - Thompson, M. J. AU - Yeates, T. O. AU - Eisenberg, D. PY - 1999 DA - 1999// TI - A combined algorithm for genome-wide prediction of protein function. JO - Nature VL - 402 UR - https://doi.org/10.1038/47048 DO - 10.1038/47048 ID - Marcotte1999 ER - TY - JOUR AU - Snel, B. AU - Bork, P. AU - Huynen, M. A. PY - 2002 DA - 2002// TI - The identification of functional modules from the genomic association of genes. JO - Proc Natl Acad Sci USA VL - 99 UR - https://doi.org/10.1073/pnas.092632599 DO - 10.1073/pnas.092632599 ID - Snel2002 ER - TY - JOUR AU - Amaral, L. A. AU - Scala, A. AU - Barthelemy, M. AU - Stanley, H. E. PY - 2000 DA - 2000// TI - Classes of small-world networks. JO - Proc Natl Acad Sci USA VL - 97 UR - https://doi.org/10.1073/pnas.200327197 DO - 10.1073/pnas.200327197 ID - Amaral2000 ER - TY - JOUR AU - Rain, J. C. AU - Selig, L. AU - De Reuse, H. AU - Battaglia, V. AU - Reverdy, C. AU - Simon, S. AU - Lenzen, G. AU - Petel, F. AU - Wojcik, J. AU - Schachter, V. PY - 2001 DA - 2001// TI - The protein-protein interaction map of Helicobacter pylori. JO - Nature VL - 409 UR - https://doi.org/10.1038/35051615 DO - 10.1038/35051615 ID - Rain2001 ER - TY - JOUR AU - Hazbun, T. R. AU - Fields, S. PY - 2001 DA - 2001// TI - Networking proteins in yeast. JO - Proc Natl Acad Sci USA VL - 98 UR - https://doi.org/10.1073/pnas.091096398 DO - 10.1073/pnas.091096398 ID - Hazbun2001 ER - TY - JOUR AU - Tucker, C. L. AU - Gera, J. F. AU - Uetz, P. PY - 2001 DA - 2001// TI - Towards an understanding of complex protein networks. JO - Trends Cell Biol VL - 11 UR - https://doi.org/10.1016/S0962-8924(00)01902-4 DO - 10.1016/S0962-8924(00)01902-4 ID - Tucker2001 ER - TY - JOUR AU - von Mering, C. AU - Krause, R. AU - Snel, B. AU - Cornell, M. AU - Oliver, S. G. AU - Fields, S. AU - Bork, P. PY - 2002 DA - 2002// TI - Comparative assessment of large-scale data sets of protein-protein interactions. JO - Nature VL - 417 UR - https://doi.org/10.1038/nature750 DO - 10.1038/nature750 ID - von Mering2002 ER - TY - STD TI - Predictome. [http://predictome.bu.edu] UR - http://predictome.bu.edu ID - ref36 ER - TY - JOUR AU - Tatusov, R. L. AU - Natale, D. A. AU - Garkavtsev, I. V. AU - Tatusova, T. A. AU - Shankavaram, U. T. AU - Rao, B. S. AU - Kiryutin, B. AU - Galperin, M. Y. AU - Fedorova, N. D. AU - Koonin, E. V. PY - 2001 DA - 2001// TI - The COG database: new developments in phylogenetic classification of proteins from complete genomes. JO - Nucleic Acids Res VL - 29 UR - https://doi.org/10.1093/nar/29.1.22 DO - 10.1093/nar/29.1.22 ID - Tatusov2001 ER - TY - JOUR AU - Altschul, S. F. AU - Madden, T. L. AU - Schaffer, A. A. AU - Zhang, J. AU - Zhang, Z. AU - Miller, W. AU - Lipman, D. J. PY - 1997 DA - 1997// TI - Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. JO - Nucleic Acids Res VL - 25 UR - https://doi.org/10.1093/nar/25.17.3389 DO - 10.1093/nar/25.17.3389 ID - Altschul1997 ER - TY - JOUR AU - Holm, L. AU - Sander, C. PY - 1998 DA - 1998// TI - Removing near-neighbour redundancy from large protein sequence collections. JO - Bioinformatics VL - 14 UR - https://doi.org/10.1093/bioinformatics/14.5.423 DO - 10.1093/bioinformatics/14.5.423 ID - Holm1998 ER - TY - JOUR AU - Kanehisa, M. AU - Goto, S. PY - 2000 DA - 2000// TI - KEGG: Kyoto encyclopedia of genes and genomes. JO - Nucleic Acids Res VL - 28 UR - https://doi.org/10.1093/nar/28.1.27 DO - 10.1093/nar/28.1.27 ID - Kanehisa2000 ER - TY - JOUR AU - Newman, M. E. AU - Strogatz, S. H. AU - Watts, D. J. PY - 2001 DA - 2001// TI - Random graphs with arbitrary degree distributions and their applications. JO - Phys Rev E Stat Phys Plasmas Fluids Relat Interdiscip Topics VL - 64 ID - Newman2001 ER - TY - STD TI - Pajek: package for large network analysis. [http://vlado.fmf.uni-lj.si/pub/networks/pajek/] UR - http://vlado.fmf.uni-lj.si/pub/networks/pajek/ ID - ref42 ER -