TY - JOUR AU - Alberts, B. PY - 1998 DA - 1998// TI - The cell as a collection of protein machines: preparing the next generation of molecular biologists JO - Cell VL - 92 UR - https://doi.org/10.1016/S0092-8674(00)80922-8 DO - 10.1016/S0092-8674(00)80922-8 ID - Alberts1998 ER - TY - JOUR AU - Dezso, Z. AU - Oltvai, Z. N. AU - Barabasi, A. L. PY - 2003 DA - 2003// TI - Bioinformatics analysis of experimentally determined protein complexes in the yeast Saccharomyces cerevisiae JO - Genome Res VL - 13 UR - https://doi.org/10.1101/gr.1073603 DO - 10.1101/gr.1073603 ID - Dezso2003 ER - TY - JOUR AU - Gavin, A. C. AU - Aloy, P. AU - Grandi, P. AU - Krause, R. AU - Boesche, M. AU - Marzioch, M. AU - Rau, C. AU - Jensen, L. J. AU - Bastuck, S. AU - Dumpelfeld, B. PY - 2006 DA - 2006// TI - Proteome survey reveals modularity of the yeast cell machinery JO - Nature VL - 440 UR - https://doi.org/10.1038/nature04532 DO - 10.1038/nature04532 ID - Gavin2006 ER - TY - JOUR AU - Pang, C. N. AU - Krycer, J. R. AU - Lek, A. AU - Wilkins, M. R. PY - 2008 DA - 2008// TI - Are protein complexes made of cores, modules and attachments? JO - Proteomics VL - 8 UR - https://doi.org/10.1002/pmic.200700801 DO - 10.1002/pmic.200700801 ID - Pang2008 ER - TY - JOUR AU - Ishihama, A. PY - 2000 DA - 2000// TI - Functional modulation of Escherichia coli RNA polymerase JO - AnnuRevMicrobiol VL - 54 ID - Ishihama2000 ER - TY - JOUR AU - Snel, B. AU - Huynen, M. A. PY - 2004 DA - 2004// TI - Quantifying modularity in the evolution of biomolecular systems JO - Genome Res VL - 14 UR - https://doi.org/10.1101/gr.1969504 DO - 10.1101/gr.1969504 ID - Snel2004 ER - TY - JOUR AU - Suthram, S. AU - Sittler, T. AU - Ideker, T. PY - 2005 DA - 2005// TI - The Plasmodium protein network diverges from those of other eukaryotes JO - Nature VL - 438 UR - https://doi.org/10.1038/nature04135 DO - 10.1038/nature04135 ID - Suthram2005 ER - TY - JOUR AU - Mika, S. AU - Rost, B. PY - 2006 DA - 2006// TI - Protein-protein interactions more conserved within species than across species JO - PLoSComputBiol VL - 2 ID - Mika2006 ER - TY - JOUR AU - van Dam, T. J. AU - Snel, B. PY - 2008 DA - 2008// TI - Protein complex evolution does not involve extensive network rewiring JO - PLoSComputBiol VL - 4 ID - van Dam2008 ER - TY - JOUR AU - Ranea, J. A. AU - Sillero, A. AU - Thornton, J. M. AU - Orengo, C. A. PY - 2006 DA - 2006// TI - Protein superfamily evolution and the last universal common ancestor (LUCA) JO - JMolEvol VL - 63 ID - Ranea2006 ER - TY - JOUR AU - Monahan, B. J. AU - Villen, J. AU - Marguerat, S. AU - Bahler, J. AU - Gygi, S. P. AU - Winston, F. PY - 2008 DA - 2008// TI - Fission yeast SWI/SNF and RSC complexes show compositional and functional differences from budding yeast JO - NatStructMolBiol VL - 15 ID - Monahan2008 ER - TY - JOUR AU - Friedrich, T. PY - 2001 DA - 2001// TI - Complex I: a chimaera of a redox and conformation-driven proton pump? JO - Journal of Bioenergetics and Biomembranes VL - 33 UR - https://doi.org/10.1023/A:1010722717257 DO - 10.1023/A:1010722717257 ID - Friedrich2001 ER - TY - JOUR AU - Gabaldon, T. AU - Rainey, D. AU - Huynen, M. A. PY - 2005 DA - 2005// TI - Tracing the evolution of a large protein complex in the eukaryotes, NADH:ubiquinone oxidoreductase (Complex I) JO - JMolBiol VL - 348 ID - Gabaldon2005 ER - TY - JOUR AU - Levy, E. D. AU - Pereira-Leal, J. B. AU - Chothia, C. AU - Teichmann, S. A. PY - 2006 DA - 2006// TI - 3D complex: a structural classification of protein complexes JO - PLoSComputBiol VL - 2 ID - Levy2006 ER - TY - JOUR AU - Pereira-Leal, J. B. AU - Levy, E. D. AU - Kamp, C. AU - Teichmann, S. A. PY - 2007 DA - 2007// TI - Evolution of protein complexes by duplication of homomeric interactions JO - Genome Biol VL - 8 UR - https://doi.org/10.1186/gb-2007-8-4-r51 DO - 10.1186/gb-2007-8-4-r51 ID - Pereira-Leal2007 ER - TY - JOUR AU - Szklarczyk, R. AU - Huynen, M. A. AU - Snel, B. PY - 2008 DA - 2008// TI - Complex fate of paralogs JO - BMC Evol Biol VL - 8 UR - https://doi.org/10.1186/1471-2148-8-337 DO - 10.1186/1471-2148-8-337 ID - Szklarczyk2008 ER - TY - JOUR AU - Yu, X. AU - Egelman, E. H. PY - 1997 DA - 1997// TI - The RecA hexamer is a structural homologue of ring helicases JO - NatStructBiol VL - 4 ID - Yu1997 ER - TY - JOUR AU - Wapinski, I. AU - Pfeffer, A. AU - Friedman, N. AU - Regev, A. PY - 2007 DA - 2007// TI - Natural history and evolutionary principles of gene duplication in fungi JO - Nature VL - 449 UR - https://doi.org/10.1038/nature06107 DO - 10.1038/nature06107 ID - Wapinski2007 ER - TY - JOUR AU - Pereira-Leal, J. B. AU - Teichmann, S. A. PY - 2005 DA - 2005// TI - Novel specificities emerge by stepwise duplication of functional modules JO - Genome Res VL - 15 UR - https://doi.org/10.1101/gr.3102105 DO - 10.1101/gr.3102105 ID - Pereira-Leal2005 ER - TY - JOUR AU - Mewes, H. W. AU - Dietmann, S. AU - Frishman, D. AU - Gregory, R. AU - Mannhaupt, G. AU - Mayer, K. F. AU - Munsterkotter, M. AU - Ruepp, A. AU - Spannagl, M. AU - Stumpflen, V. PY - 2008 DA - 2008// TI - MIPS: analysis and annotation of genome information in 2007 JO - Nucleic Acids Res VL - 36 ID - Mewes2008 ER - TY - JOUR AU - Karp, P. D. AU - Keseler, I. M. AU - Shearer, A. AU - Latendresse, M. AU - Krummenacker, M. AU - Paley, S. M. AU - Paulsen, I. AU - Collado-Vides, J. AU - Gama-Castro, S. AU - Peralta-Gil, M. PY - 2007 DA - 2007// TI - Multidimensional annotation of the Escherichia coli K-12 genome JO - Nucleic Acids Res VL - 35 UR - https://doi.org/10.1093/nar/gkm740 DO - 10.1093/nar/gkm740 ID - Karp2007 ER - TY - JOUR AU - Henrick, K. AU - Thornton, J. M. PY - 1998 DA - 1998// TI - PQS: a protein quaternary structure file server JO - Trends BiochemSci VL - 23 UR - https://doi.org/10.1016/S0968-0004(98)01253-5 DO - 10.1016/S0968-0004(98)01253-5 ID - Henrick1998 ER - TY - JOUR AU - Krogan, N. J. AU - Cagney, G. AU - Yu, H. AU - Zhong, G. AU - Guo, X. AU - Ignatchenko, A. AU - Li, J. AU - Pu, S. AU - Datta, N. AU - Tikuisis, A. P. PY - 2006 DA - 2006// TI - Global landscape of protein complexes in the yeast Saccharomyces cerevisiae JO - Nature VL - 440 UR - https://doi.org/10.1038/nature04670 DO - 10.1038/nature04670 ID - Krogan2006 ER - TY - JOUR AU - Butland, G. AU - Peregrin-Alvarez, J. M. AU - Li, J. AU - Yang, W. AU - Yang, X. AU - Canadien, V. AU - Starostine, A. AU - Richards, D. AU - Beattie, B. AU - Krogan, N. PY - 2005 DA - 2005// TI - Interaction network containing conserved and essential protein complexes in Escherichia coli JO - Nature VL - 433 UR - https://doi.org/10.1038/nature03239 DO - 10.1038/nature03239 ID - Butland2005 ER - TY - JOUR AU - Arifuzzaman, M. AU - Maeda, M. AU - Itoh, A. AU - Nishikata, K. AU - Takita, C. AU - Saito, R. AU - Ara, T. AU - Nakahigashi, K. AU - Huang, H. C. AU - Hirai, A. PY - 2006 DA - 2006// TI - Large-scale identification of protein-protein interaction of Escherichia coli K-12 JO - Genome Res VL - 16 UR - https://doi.org/10.1101/gr.4527806 DO - 10.1101/gr.4527806 ID - Arifuzzaman2006 ER - TY - STD TI - Kerrien S, Alam-Faruque Y, Aranda B, Bancarz I, Bridge A, Derow C, Dimmer E, Feuermann M, Friedrichsen A, Huntley R: IntAct--open source resource for molecular interaction data. Nucleic Acids Res. 2007, D561-D565. 10.1093/nar/gkl958. 35 Database ID - ref26 ER - TY - STD TI - Chatr-aryamontri A, Ceol A, Palazzi LM, Nardelli G, Schneider MV, Castagnoli L, Cesareni G: MINT: the Molecular INTeraction database. Nucleic Acids Res. 2007, D572-D574. 10.1093/nar/gkl950. 35 Database ID - ref27 ER - TY - JOUR AU - Bader, G. D. AU - Betel, D. AU - Hogue, C. W. PY - 2003 DA - 2003// TI - BIND: the Biomolecular Interaction Network Database JO - Nucleic Acids Res VL - 31 UR - https://doi.org/10.1093/nar/gkg056 DO - 10.1093/nar/gkg056 ID - Bader2003 ER - TY - STD TI - Brohee S, van Helden J: Evaluation of clustering algorithms for protein-protein interaction networks. BMCBioinformatics. 2006, 7 (488): ID - ref29 ER - TY - JOUR AU - Bandyopadhyay, S. AU - Kelley, R. AU - Krogan, N. J. AU - Ideker, T. PY - 2008 DA - 2008// TI - Functional maps of protein complexes from quantitative genetic interaction data JO - PLoSComputBiol VL - 4 ID - Bandyopadhyay2008 ER - TY - STD TI - von Mering C, Jensen LJ, Kuhn M, Chaffron S, Doerks T, Kruger B, Snel B, Bork P: STRING 7--recent developments in the integration and prediction of protein interactions. Nucleic Acids Res. 2007, D358-D362. 10.1093/nar/gkl825. 35 Database ID - ref31 ER - TY - JOUR AU - von Mering, C. AU - Zdobnov, E. M. AU - Tsoka, S. AU - Ciccarelli, F. D. AU - Pereira-Leal, J. B. AU - Ouzounis, C. A. AU - Bork, P. PY - 2003 DA - 2003// TI - Genome evolution reveals biochemical networks and functional modules JO - ProcNatlAcadSciUSA VL - 100 UR - https://doi.org/10.1073/pnas.2136809100 DO - 10.1073/pnas.2136809100 ID - von Mering2003 ER - TY - JOUR AU - Tamames, J. AU - Moya, A. AU - Valencia, A. PY - 2007 DA - 2007// TI - Modular organization in the reductive evolution of protein-protein interaction networks JO - Genome Biol VL - 8 UR - https://doi.org/10.1186/gb-2007-8-5-r94 DO - 10.1186/gb-2007-8-5-r94 ID - Tamames2007 ER - TY - JOUR AU - Pereira-Leal, J. B. AU - Enright, A. J. AU - Ouzounis, C. A. PY - 2004 DA - 2004// TI - Detection of functional modules from protein interaction networks JO - Proteins VL - 54 UR - https://doi.org/10.1002/prot.10505 DO - 10.1002/prot.10505 ID - Pereira-Leal2004 ER - TY - STD TI - Bader GD, Hogue CW: An automated method for finding molecular complexes in large protein interaction networks. BMCBioinformatics. 2003, 4 (2): ID - ref35 ER - TY - JOUR AU - Enright, A. J. AU - Van Dongen, S. AU - Ouzounis, C. A. PY - 2002 DA - 2002// TI - An efficient algorithm for large-scale detection of protein families JO - Nucleic Acids Res VL - 30 UR - https://doi.org/10.1093/nar/30.7.1575 DO - 10.1093/nar/30.7.1575 ID - Enright2002 ER - TY - JOUR AU - Guimera, R. AU - Nunes Amaral, L. A. PY - 2005 DA - 2005// TI - Functional cartography of complex metabolic networks JO - Nature VL - 433 UR - https://doi.org/10.1038/nature03288 DO - 10.1038/nature03288 ID - Guimera2005 ER - TY - JOUR AU - King, A. D. AU - Przulj, N. AU - Jurisica, I. PY - 2004 DA - 2004// TI - Protein complex prediction via cost-based clustering JO - Bioinformatics VL - 20 UR - https://doi.org/10.1093/bioinformatics/bth351 DO - 10.1093/bioinformatics/bth351 ID - King2004 ER - TY - JOUR AU - Blatt, M. AU - Wiseman, S. AU - Domany, E. PY - 1996 DA - 1996// TI - Superparamagnetic clustering of data JO - PhysRevLett VL - 76 ID - Blatt1996 ER - TY - JOUR AU - Lubovac, Z. AU - Gamalielsson, J. AU - Olsson, B. PY - 2006 DA - 2006// TI - Combining functional and topological properties to identify core modules in protein interaction networks JO - Proteins VL - 64 UR - https://doi.org/10.1002/prot.21071 DO - 10.1002/prot.21071 ID - Lubovac2006 ER - TY - JOUR AU - Zheng, H. AU - Wang, H. AU - Glass, D. H. PY - 2008 DA - 2008// TI - Integration of genomic data for inferring protein complexes from global protein-protein interaction networks JO - IEEE TransSystManCybernB Cybern VL - 38 UR - https://doi.org/10.1109/TSMCB.2007.908912 DO - 10.1109/TSMCB.2007.908912 ID - Zheng2008 ER - TY - STD TI - Kersey P, Bower L, Morris L, Horne A, Petryszak R, Kanz C, Kanapin A, Das U, Michoud K, Phan I: Integr8 and Genome Reviews: integrated views of complete genomes and proteomes. Nucleic Acids Res. 2005, D297-D302. 33 Database ID - ref42 ER - TY - JOUR AU - Wagner, A. PY - 2001 DA - 2001// TI - The yeast protein interaction network evolves rapidly and contains few redundant duplicate genes JO - MolBiolEvol VL - 18 ID - Wagner2001 ER - TY - JOUR AU - Baudot, A. AU - Jacq, B. AU - Brun, C. PY - 2004 DA - 2004// TI - A scale of functional divergence for yeast duplicated genes revealed from analysis of the protein-protein interaction network JO - Genome Biol VL - 5 UR - https://doi.org/10.1186/gb-2004-5-10-r76 DO - 10.1186/gb-2004-5-10-r76 ID - Baudot2004 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 cerevisiae by mass spectrometry JO - Nature VL - 415 UR - https://doi.org/10.1038/415180a DO - 10.1038/415180a ID - Ho2002 ER - TY - JOUR AU - Betel, D. AU - Isserlin, R. AU - Hogue, C. W. PY - 2004 DA - 2004// TI - Analysis of domain correlations in yeast protein complexes JO - Bioinformatics VL - 20 UR - https://doi.org/10.1093/bioinformatics/bth903 DO - 10.1093/bioinformatics/bth903 ID - Betel2004 ER - TY - JOUR AU - Staley, J. P. AU - Guthrie, C. PY - 1998 DA - 1998// TI - Mechanical devices of the spliceosome: motors, clocks, springs, and things JO - Cell VL - 92 UR - https://doi.org/10.1016/S0092-8674(00)80925-3 DO - 10.1016/S0092-8674(00)80925-3 ID - Staley1998 ER - TY - JOUR AU - Rubin, D. M. AU - Finley, D. PY - 1995 DA - 1995// TI - Proteolysis. The proteasome: a protein-degrading organelle? JO - CurrBiol VL - 5 UR - https://doi.org/10.1016/S0960-9822(95)00172-2 DO - 10.1016/S0960-9822(95)00172-2 ID - Rubin1995 ER - TY - JOUR AU - Hu, P. AU - Janga, S. C. AU - Babu, M. AU - Diaz-Mejia, J. J. AU - Butland, G. AU - Yang, W. AU - Pogoutse, O. AU - Guo, X. AU - Phanse, S. AU - Wong, P. PY - 2009 DA - 2009// TI - Global functional atlas of Escherichia coli encompassing previously uncharacterized proteins JO - PLoS Biol VL - 7 UR - https://doi.org/10.1371/journal.pbio.1000096 DO - 10.1371/journal.pbio.1000096 ID - Hu2009 ER - TY - JOUR AU - Pu, S. AU - Wong, J. AU - Turner, B. AU - Cho, E. AU - Wodak, S. J. PY - 2009 DA - 2009// TI - Up-to-date catalogues of yeast protein complexes JO - Nucleic Acids Res VL - 37 UR - https://doi.org/10.1093/nar/gkn1005 DO - 10.1093/nar/gkn1005 ID - Pu2009 ER - TY - JOUR AU - Teichmann, S. A. AU - Rison, S. C. AU - Thornton, J. M. AU - Riley, M. AU - Gough, J. AU - Chothia, C. PY - 2001 DA - 2001// TI - The evolution and structural anatomy of the small molecule metabolic pathways in Escherichia coli JO - JMolBiol VL - 311 ID - Teichmann2001 ER - TY - JOUR AU - Ranea, J. A. AU - Yeats, C. AU - Grant, A. AU - Orengo, C. A. PY - 2007 DA - 2007// TI - Predicting protein function with hierarchical phylogenetic profiles: the Gene3D Phylo-Tuner method applied to eukaryotic genomes JO - PLoSComputBiol VL - 3 ID - Ranea2007 ER - TY - JOUR AU - Ranea, J. A. PY - 2006 DA - 2006// TI - Genome evolution: micro(be)-economics JO - Heredity VL - 96 UR - https://doi.org/10.1038/sj.hdy.6800766 DO - 10.1038/sj.hdy.6800766 ID - Ranea2006 ER - TY - JOUR AU - Kellis, M. AU - Birren, B. W. AU - Lander, E. S. PY - 2004 DA - 2004// TI - Proof and evolutionary analysis of ancient genome duplication in the yeast Saccharomyces cerevisiae JO - Nature VL - 428 UR - https://doi.org/10.1038/nature02424 DO - 10.1038/nature02424 ID - Kellis2004 ER - TY - JOUR AU - Ochman, H. AU - Daubin, V. AU - Lerat, E. PY - 2005 DA - 2005// TI - A bunch of fun-guys: the whole-genome view of yeast evolution JO - Trends Genet VL - 21 UR - https://doi.org/10.1016/j.tig.2004.11.006 DO - 10.1016/j.tig.2004.11.006 ID - Ochman2005 ER - TY - STD TI - Yeats C, Lees J, Reid A, Kellam P, Martin N, Liu X, Orengo C: Gene3D: comprehensive structural and functional annotation of genomes. Nucleic Acids Res. 2008, D414-D418. 36 Database ID - ref57 ER - TY - JOUR AU - Resnik, P. PY - 1999 DA - 1999// TI - Semantic similarity in a taxonomy: An information-based measure and its application to problems of ambiguity in natural language JO - Journal of Artificial Intelligence Research VL - 11 ID - Resnik1999 ER - TY - JOUR AU - Lord, P. W. AU - Stevens, R. D. AU - Brass, A. AU - Goble, C. A. PY - 2003 DA - 2003// TI - Investigating semantic similarity measures across the Gene Ontology: the relationship between sequence and annotation JO - Bioinformatics VL - 19 UR - https://doi.org/10.1093/bioinformatics/btg153 DO - 10.1093/bioinformatics/btg153 ID - Lord2003 ER - TY - STD TI - Greene LH, Lewis TE, Addou S, Cuff A, Dallman T, Dibley M, Redfern O, Pearl F, Nambudiry R, Reid A: The CATH domain structure database: new protocols and classification levels give a more comprehensive resource for exploring evolution. Nucleic Acids Res. 2007, D291-D297. 10.1093/nar/gkl959. 35 Database ID - ref60 ER - TY - STD TI - Gene Ontology C: The Gene Ontology (GO) project in 2006. Nucleic Acids Res. 2006, D322-D326. 10.1093/nar/gkj021. 34 Database ID - ref61 ER - TY - JOUR AU - Ruepp, A. AU - Zollner, A. AU - Maier, D. AU - Albermann, K. AU - Hani, J. AU - Mokrejs, M. AU - Tetko, I. AU - Guldener, U. AU - Mannhaupt, G. AU - Munsterkotter, M. PY - 2004 DA - 2004// TI - The FunCat, a functional annotation scheme for systematic classification of proteins from whole genomes JO - Nucleic Acids Res VL - 32 UR - https://doi.org/10.1093/nar/gkh894 DO - 10.1093/nar/gkh894 ID - Ruepp2004 ER - TY - STD TI - Stark C, Breitkreutz BJ, Reguly T, Boucher L, Breitkreutz A, Tyers M: BioGRID: a general repository for interaction datasets. Nucleic Acids Res. 2006, D535-D539. 10.1093/nar/gkj109. 34 Database ID - ref63 ER - TY - JOUR AU - Vogel, C. AU - Berzuini, C. AU - Bashton, M. AU - Gough, J. AU - Teichmann, S. A. PY - 2004 DA - 2004// TI - Supra-domains: evolutionary units larger than single protein domains JO - JMolBiol VL - 336 ID - Vogel2004 ER - TY - JOUR AU - Ispolatov, I. AU - Yuryev, A. AU - Mazo, I. AU - Maslov, S. PY - 2005 DA - 2005// TI - Binding properties and evolution of homodimers in protein-protein interaction networks JO - Nucleic Acids Res VL - 33 UR - https://doi.org/10.1093/nar/gki678 DO - 10.1093/nar/gki678 ID - Ispolatov2005 ER - TY - JOUR AU - Baldauf, S. L. PY - 2003 DA - 2003// TI - The deep roots of eukaryotes JO - Science VL - 300 UR - https://doi.org/10.1126/science.1085544 DO - 10.1126/science.1085544 ID - Baldauf2003 ER -