{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,10,29]],"date-time":"2025-10-29T19:15:09Z","timestamp":1761765309486},"reference-count":10,"publisher":"Oxford University Press (OUP)","issue":"14","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2010,7,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Summary: Interrogating protein complexes and pathways in an evolutionary context provides insights into the formation of the basic functional components of the cell. We developed two independent Cytoscape plugins that can be cooperatively used to map evolving protein interaction networks at the module level. The APCluster plugin implements a recent affinity propagation (AP) algorithm for graph clustering and can be applied to decompose networks into coherent modules. The NetworkEvolution plugin provides the capability to visualize selected modules in consecutive evolutionary stages.<\/jats:p>\n               <jats:p>Availability: The plugins, input data and usage scenarios are freely available from the project web site: http:\/\/bioputer.mimuw.edu.pl\/modevo. The plugins are also available from the Cytoscape plugin repository.<\/jats:p>\n               <jats:p>Contact: \u00a0janusz@ucsd.edu<\/jats:p>\n               <jats:p>Supplementary information: \u00a0Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btq274","type":"journal-article","created":{"date-parts":[[2010,5,28]],"date-time":"2010-05-28T00:46:57Z","timestamp":1275007617000},"page":"1790-1791","source":"Crossref","is-referenced-by-count":13,"title":["MODEVO: exploring modularity and evolution of protein interaction networks"],"prefix":"10.1093","volume":"26","author":[{"given":"Micha\u0142","family":"Wo\u017aniak","sequence":"first","affiliation":[{"name":"Institute of Informatics, University of Warsaw, Banacha 2, 02-097 Warsaw, Poland"}]},{"given":"Jerzy","family":"Tiuryn","sequence":"additional","affiliation":[{"name":"Institute of Informatics, University of Warsaw, Banacha 2, 02-097 Warsaw, Poland"}]},{"given":"Janusz","family":"Dutkowski","sequence":"additional","affiliation":[{"name":"Institute of Informatics, University of Warsaw, Banacha 2, 02-097 Warsaw, Poland"}]}],"member":"286","published-online":{"date-parts":[[2010,5,27]]},"reference":[{"key":"2023012507574398700_B1","doi-asserted-by":"crossref","first-page":"2","DOI":"10.1186\/1471-2105-4-2","article-title":"An automated method for finding molecular complexes in large protein interaction networks","volume":"4","author":"Bader","year":"2003","journal-title":"BMC Bioinformatics"},{"key":"2023012507574398700_B2","doi-asserted-by":"crossref","first-page":"i149","DOI":"10.1093\/bioinformatics\/btm194","article-title":"Identification of functional modules from conserved ancestral protein-protein interactions","volume":"23","author":"Dutkowski","year":"2007","journal-title":"Bioinformatics"},{"key":"2023012507574398700_B3","doi-asserted-by":"crossref","first-page":"1575","DOI":"10.1093\/nar\/30.7.1575","article-title":"An efficient algorithm for large-scale detection of protein families","volume":"30","author":"Enright","year":"2002","journal-title":"Nucleic Acids Res."},{"key":"2023012507574398700_B4","doi-asserted-by":"crossref","first-page":"972","DOI":"10.1126\/science.1136800","article-title":"Clustering by passing messages between data points","volume":"15","author":"Frey","year":"2007","journal-title":"Science"},{"key":"2023012507574398700_B5","doi-asserted-by":"crossref","first-page":"507","DOI":"10.1098\/rstb.2005.1807","article-title":"The origins and evolution of functional modules: lessons from protein complexes","volume":"361","author":"Pereira-Leal","year":"2006","journal-title":"Phil. Trans. R. Soc. Lond. Ser. B Biol. Sci."},{"key":"2023012507574398700_B6","doi-asserted-by":"crossref","first-page":"R51","DOI":"10.1186\/gb-2007-8-4-r51","article-title":"Evolution of protein complexes by duplication of homomeric interactions","volume":"3","author":"Pereira-Leal","year":"2007","journal-title":"Genome Biol."},{"key":"2023012507574398700_B7","doi-asserted-by":"crossref","first-page":"2498","DOI":"10.1101\/gr.1239303","article-title":"Cytoscape: a software environment for integrated models of biomolecular interaction networks","volume":"13","author":"Shannon","year":"2003","journal-title":"Genome Res."},{"key":"2023012507574398700_B8","doi-asserted-by":"crossref","first-page":"427","DOI":"10.1038\/nbt1196","article-title":"Modeling cellular machinery through biological network comparison","volume":"24","author":"Sharan","year":"2006","journal-title":"Nat. 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