Alberts B: The cell as a collection of protein machines: preparing the next generation of molecular biologists. Cell. 1998, 92 (3): 291-294. 10.1016/S0092-8674(00)80922-8.
Article
CAS
PubMed
Google Scholar
Dezso Z, Oltvai ZN, Barabasi AL: Bioinformatics analysis of experimentally determined protein complexes in the yeast Saccharomyces cerevisiae. Genome Res. 2003, 13 (11): 2450-2454. 10.1101/gr.1073603.
Article
PubMed Central
PubMed
Google Scholar
Gavin AC, Aloy P, Grandi P, Krause R, Boesche M, Marzioch M, Rau C, Jensen LJ, Bastuck S, Dumpelfeld B: Proteome survey reveals modularity of the yeast cell machinery. Nature. 2006, 440 (7084): 631-636. 10.1038/nature04532.
Article
CAS
PubMed
Google Scholar
Pang CN, Krycer JR, Lek A, Wilkins MR: Are protein complexes made of cores, modules and attachments?. Proteomics. 2008, 8 (3): 425-434. 10.1002/pmic.200700801.
Article
CAS
PubMed
Google Scholar
Ishihama A: Functional modulation of Escherichia coli RNA polymerase. AnnuRevMicrobiol. 2000, 54: 499-518.
CAS
Google Scholar
Snel B, Huynen MA: Quantifying modularity in the evolution of biomolecular systems. Genome Res. 2004, 14 (3): 391-397. 10.1101/gr.1969504.
Article
CAS
PubMed Central
PubMed
Google Scholar
Suthram S, Sittler T, Ideker T: The Plasmodium protein network diverges from those of other eukaryotes. Nature. 2005, 438 (7064): 108-112. 10.1038/nature04135.
Article
CAS
PubMed Central
PubMed
Google Scholar
Mika S, Rost B: Protein-protein interactions more conserved within species than across species. PLoSComputBiol. 2006, 2 (7): e79-
Google Scholar
van Dam TJ, Snel B: Protein complex evolution does not involve extensive network rewiring. PLoSComputBiol. 2008, 4 (7): e1000132-
Google Scholar
Ranea JA, Sillero A, Thornton JM, Orengo CA: Protein superfamily evolution and the last universal common ancestor (LUCA). JMolEvol. 2006, 63 (4): 513-525.
CAS
Google Scholar
Monahan BJ, Villen J, Marguerat S, Bahler J, Gygi SP, Winston F: Fission yeast SWI/SNF and RSC complexes show compositional and functional differences from budding yeast. NatStructMolBiol. 2008, 15 (8): 873-880.
CAS
Google Scholar
Friedrich T: Complex I: a chimaera of a redox and conformation-driven proton pump?. Journal of Bioenergetics and Biomembranes. 2001, 33: 169-177. 10.1023/A:1010722717257.
Article
CAS
PubMed
Google Scholar
Gabaldon T, Rainey D, Huynen MA: Tracing the evolution of a large protein complex in the eukaryotes, NADH:ubiquinone oxidoreductase (Complex I). JMolBiol. 2005, 348 (4): 857-870.
CAS
Google Scholar
Levy ED, Pereira-Leal JB, Chothia C, Teichmann SA: 3D complex: a structural classification of protein complexes. PLoSComputBiol. 2006, 2 (11): e155-
Google Scholar
Pereira-Leal JB, Levy ED, Kamp C, Teichmann SA: Evolution of protein complexes by duplication of homomeric interactions. Genome Biol. 2007, 8 (4): R51-10.1186/gb-2007-8-4-r51.
Article
PubMed Central
PubMed
Google Scholar
Szklarczyk R, Huynen MA, Snel B: Complex fate of paralogs. BMC Evol Biol. 2008, 8: 337-10.1186/1471-2148-8-337.
Article
PubMed Central
PubMed
Google Scholar
Yu X, Egelman EH: The RecA hexamer is a structural homologue of ring helicases. NatStructBiol. 1997, 4 (2): 101-104.
CAS
Google Scholar
Wapinski I, Pfeffer A, Friedman N, Regev A: Natural history and evolutionary principles of gene duplication in fungi. Nature. 2007, 449 (7158): 54-61. 10.1038/nature06107.
Article
CAS
PubMed
Google Scholar
Pereira-Leal JB, Teichmann SA: Novel specificities emerge by stepwise duplication of functional modules. Genome Res. 2005, 15 (4): 552-559. 10.1101/gr.3102105.
Article
CAS
PubMed Central
PubMed
Google Scholar
Mewes HW, Dietmann S, Frishman D, Gregory R, Mannhaupt G, Mayer KF, Munsterkotter M, Ruepp A, Spannagl M, Stumpflen V: MIPS: analysis and annotation of genome information in 2007. Nucleic Acids Res. 2008, 36 (36 Database): D196-D201.
CAS
PubMed Central
PubMed
Google Scholar
Karp PD, Keseler IM, Shearer A, Latendresse M, Krummenacker M, Paley SM, Paulsen I, Collado-Vides J, Gama-Castro S, Peralta-Gil M: Multidimensional annotation of the Escherichia coli K-12 genome. Nucleic Acids Res. 2007, 35 (22): 7577-7590. 10.1093/nar/gkm740.
Article
CAS
PubMed Central
PubMed
Google Scholar
Henrick K, Thornton JM: PQS: a protein quaternary structure file server. Trends BiochemSci. 1998, 23 (9): 358-361. 10.1016/S0968-0004(98)01253-5.
Article
CAS
Google Scholar
Krogan NJ, Cagney G, Yu H, Zhong G, Guo X, Ignatchenko A, Li J, Pu S, Datta N, Tikuisis AP: Global landscape of protein complexes in the yeast Saccharomyces cerevisiae. Nature. 2006, 440 (7084): 637-643. 10.1038/nature04670.
Article
CAS
PubMed
Google Scholar
Butland G, Peregrin-Alvarez JM, Li J, Yang W, Yang X, Canadien V, Starostine A, Richards D, Beattie B, Krogan N: Interaction network containing conserved and essential protein complexes in Escherichia coli. Nature. 2005, 433 (7025): 531-537. 10.1038/nature03239.
Article
CAS
PubMed
Google Scholar
Arifuzzaman M, Maeda M, Itoh A, Nishikata K, Takita C, Saito R, Ara T, Nakahigashi K, Huang HC, Hirai A: Large-scale identification of protein-protein interaction of Escherichia coli K-12. Genome Res. 2006, 16 (5): 686-691. 10.1101/gr.4527806.
Article
CAS
PubMed Central
PubMed
Google Scholar
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
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
Bader GD, Betel D, Hogue CW: BIND: the Biomolecular Interaction Network Database. Nucleic Acids Res. 2003, 31 (1): 248-250. 10.1093/nar/gkg056.
Article
CAS
PubMed Central
PubMed
Google Scholar
Brohee S, van Helden J: Evaluation of clustering algorithms for protein-protein interaction networks. BMCBioinformatics. 2006, 7 (488):
Bandyopadhyay S, Kelley R, Krogan NJ, Ideker T: Functional maps of protein complexes from quantitative genetic interaction data. PLoSComputBiol. 2008, 4 (4): e1000065-
Google Scholar
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
von Mering C, Zdobnov EM, Tsoka S, Ciccarelli FD, Pereira-Leal JB, Ouzounis CA, Bork P: Genome evolution reveals biochemical networks and functional modules. ProcNatlAcadSciUSA. 2003, 100 (26): 15428-15433.
Article
CAS
Google Scholar
Tamames J, Moya A, Valencia A: Modular organization in the reductive evolution of protein-protein interaction networks. Genome Biol. 2007, 8 (5): R94-10.1186/gb-2007-8-5-r94.
Article
PubMed Central
PubMed
Google Scholar
Pereira-Leal JB, Enright AJ, Ouzounis CA: Detection of functional modules from protein interaction networks. Proteins. 2004, 54 (1): 49-57. 10.1002/prot.10505.
Article
CAS
PubMed
Google Scholar
Bader GD, Hogue CW: An automated method for finding molecular complexes in large protein interaction networks. BMCBioinformatics. 2003, 4 (2):
Enright AJ, Van Dongen S, Ouzounis CA: An efficient algorithm for large-scale detection of protein families. Nucleic Acids Res. 2002, 30 (7): 1575-1584. 10.1093/nar/30.7.1575.
Article
CAS
PubMed Central
PubMed
Google Scholar
Guimera R, Nunes Amaral LA: Functional cartography of complex metabolic networks. Nature. 2005, 433 (7028): 895-900. 10.1038/nature03288.
Article
CAS
PubMed Central
PubMed
Google Scholar
King AD, Przulj N, Jurisica I: Protein complex prediction via cost-based clustering. Bioinformatics. 2004, 20 (17): 3013-3020. 10.1093/bioinformatics/bth351.
Article
CAS
PubMed
Google Scholar
Blatt M, Wiseman S, Domany E: Superparamagnetic clustering of data. PhysRevLett. 1996, 76 (18): 3251-3254.
CAS
Google Scholar
Lubovac Z, Gamalielsson J, Olsson B: Combining functional and topological properties to identify core modules in protein interaction networks. Proteins. 2006, 64 (4): 948-959. 10.1002/prot.21071.
Article
CAS
PubMed
Google Scholar
Zheng H, Wang H, Glass DH: Integration of genomic data for inferring protein complexes from global protein-protein interaction networks. IEEE TransSystManCybernB Cybern. 2008, 38 (1): 5-16. 10.1109/TSMCB.2007.908912.
Article
Google Scholar
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
Wagner A: The yeast protein interaction network evolves rapidly and contains few redundant duplicate genes. MolBiolEvol. 2001, 18 (7): 1283-1292.
CAS
Google Scholar
Baudot A, Jacq B, Brun C: A scale of functional divergence for yeast duplicated genes revealed from analysis of the protein-protein interaction network. Genome Biol. 2004, 5 (10): R76-10.1186/gb-2004-5-10-r76.
Article
PubMed Central
PubMed
Google Scholar
Gavin AC, Bosche M, Krause R, Grandi P, Marzioch M, Bauer A, Schultz J, Rick JM, Michon AM, Cruciat CM: Functional organization of the yeast proteome by systematic analysis of protein complexes. Nature. 2002, 415 (6868): 141-147. 10.1038/415141a.
Article
CAS
PubMed
Google Scholar
Ho Y, Gruhler A, Heilbut A, Bader GD, Moore L, Adams SL, Millar A, Taylor P, Bennett K, Boutilier K: Systematic identification of protein complexes in Saccharomyces cerevisiae by mass spectrometry. Nature. 2002, 415 (6868): 180-183. 10.1038/415180a.
Article
CAS
PubMed
Google Scholar
Betel D, Isserlin R, Hogue CW: Analysis of domain correlations in yeast protein complexes. Bioinformatics. 2004, 20 (Suppl 1): i55-i62. 10.1093/bioinformatics/bth903.
Article
CAS
PubMed
Google Scholar
Staley JP, Guthrie C: Mechanical devices of the spliceosome: motors, clocks, springs, and things. Cell. 1998, 92 (3): 315-326. 10.1016/S0092-8674(00)80925-3.
Article
CAS
PubMed
Google Scholar
Rubin DM, Finley D: Proteolysis. The proteasome: a protein-degrading organelle?. CurrBiol. 1995, 5 (8): 854-858.
Article
CAS
Google Scholar
Hu P, Janga SC, Babu M, Diaz-Mejia JJ, Butland G, Yang W, Pogoutse O, Guo X, Phanse S, Wong P: Global functional atlas of Escherichia coli encompassing previously uncharacterized proteins. PLoS Biol. 2009, 7 (4): e96-10.1371/journal.pbio.1000096.
Article
PubMed
Google Scholar
Pu S, Wong J, Turner B, Cho E, Wodak SJ: Up-to-date catalogues of yeast protein complexes. Nucleic Acids Res. 2009, 37 (3): 825-831. 10.1093/nar/gkn1005.
Article
CAS
PubMed Central
PubMed
Google Scholar
Teichmann SA, Rison SC, Thornton JM, Riley M, Gough J, Chothia C: The evolution and structural anatomy of the small molecule metabolic pathways in Escherichia coli. JMolBiol. 2001, 311 (4): 693-708.
CAS
Google Scholar
Ranea JA, Yeats C, Grant A, Orengo CA: Predicting protein function with hierarchical phylogenetic profiles: the Gene3D Phylo-Tuner method applied to eukaryotic genomes. PLoSComputBiol. 2007, 3 (11): e237-
Google Scholar
Ranea JA: Genome evolution: micro(be)-economics. Heredity. 2006, 96 (5): 337-338. 10.1038/sj.hdy.6800766.
Article
CAS
PubMed
Google Scholar
Kellis M, Birren BW, Lander ES: Proof and evolutionary analysis of ancient genome duplication in the yeast Saccharomyces cerevisiae. Nature. 2004, 428 (6983): 617-624. 10.1038/nature02424.
Article
CAS
PubMed
Google Scholar
Ochman H, Daubin V, Lerat E: A bunch of fun-guys: the whole-genome view of yeast evolution. Trends Genet. 2005, 21 (1): 1-3. 10.1016/j.tig.2004.11.006.
Article
CAS
PubMed
Google Scholar
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
Resnik P: Semantic similarity in a taxonomy: An information-based measure and its application to problems of ambiguity in natural language. Journal of Artificial Intelligence Research. 1999, 11: 95-130.
Google Scholar
Lord PW, Stevens RD, Brass A, Goble CA: Investigating semantic similarity measures across the Gene Ontology: the relationship between sequence and annotation. Bioinformatics. 2003, 19 (10): 1275-1283. 10.1093/bioinformatics/btg153.
Article
CAS
PubMed
Google Scholar
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
Gene Ontology C: The Gene Ontology (GO) project in 2006. Nucleic Acids Res. 2006, D322-D326. 10.1093/nar/gkj021. 34 Database
Ruepp A, Zollner A, Maier D, Albermann K, Hani J, Mokrejs M, Tetko I, Guldener U, Mannhaupt G, Munsterkotter M: The FunCat, a functional annotation scheme for systematic classification of proteins from whole genomes. Nucleic Acids Res. 2004, 32 (18): 5539-5545. 10.1093/nar/gkh894.
Article
CAS
PubMed Central
PubMed
Google Scholar
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
Vogel C, Berzuini C, Bashton M, Gough J, Teichmann SA: Supra-domains: evolutionary units larger than single protein domains. JMolBiol. 2004, 336 (3): 809-823.
CAS
Google Scholar
Ispolatov I, Yuryev A, Mazo I, Maslov S: Binding properties and evolution of homodimers in protein-protein interaction networks. Nucleic Acids Res. 2005, 33 (11): 3629-3635. 10.1093/nar/gki678.
Article
CAS
PubMed Central
PubMed
Google Scholar
Baldauf SL: The deep roots of eukaryotes. Science. 2003, 300 (5626): 1703-1706. 10.1126/science.1085544.
Article
CAS
PubMed
Google Scholar