{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,6,16]],"date-time":"2026-06-16T15:11:20Z","timestamp":1781622680480,"version":"3.54.5"},"reference-count":25,"publisher":"Oxford University Press (OUP)","issue":"22","license":[{"start":{"date-parts":[[2016,7,27]],"date-time":"2016-07-27T00:00:00Z","timestamp":1469577600000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc\/4.0\/"}],"funder":[{"DOI":"10.13039\/100009619","name":"Japan Agency for Medical Research and Development","doi-asserted-by":"crossref","award":["15H02773"],"award-info":[{"award-number":["15H02773"]}],"id":[{"id":"10.13039\/100009619","id-type":"DOI","asserted-by":"crossref"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2016,11,15]]},"abstract":"<jats:p>Motivation: The identification of functional modules from protein\u2013protein interaction (PPI) networks is an important step toward understanding the biological features of PPI networks. The detection of functional modules in PPI networks is often performed by identifying internally densely connected subnetworks, and often produces modules with \u201ccore\u201d and \u201cperipheral\u201d proteins. The core proteins are the ones having dense connections to each other in a module. The difference between core and peripheral proteins is important to understand the functional roles of proteins in modules, but there are few methods to explicitly elucidate the internal structure of functional modules at gene level.<\/jats:p>\n               <jats:p>Results: We propose NCMine, which is a novel network clustering method and visualization tool for the core-peripheral structure of functional modules. It extracts near-complete subgraphs from networks based on a node-weighting scheme using degree centrality, and reports subgroups as functional modules. We implemented this method as a plugin of Cytoscape, which is widely used to visualize and analyze biological networks. The plugin allows users to extract functional modules from PPI networks and interactively filter modules of interest. We applied the method to human PPI networks, and found several examples with the core-peripheral structure of modules that may be related to cancer development.<\/jats:p>\n               <jats:p>Availability and Implementation: The Cytoscape plugin and tutorial are available at Cytoscape AppStore. (http:\/\/apps.cytoscape.org\/apps\/ncmine).<\/jats:p>\n               <jats:p>Contact: \u00a0kengo@ecei.tohoku.ac.jp<\/jats:p>\n               <jats:p>Supplementary information: \u00a0Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btw488","type":"journal-article","created":{"date-parts":[[2016,7,28]],"date-time":"2016-07-28T02:29:14Z","timestamp":1469672954000},"page":"3454-3460","source":"Crossref","is-referenced-by-count":37,"title":["NCMine: Core-peripheral based functional module detection using near-clique mining"],"prefix":"10.1093","volume":"32","author":[{"given":"Shu","family":"Tadaka","sequence":"first","affiliation":[{"name":"1Graduate School of Information Sciences, Tohoku University, Sendai, Japan"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Kengo","family":"Kinoshita","sequence":"additional","affiliation":[{"name":"1Graduate School of Information Sciences, Tohoku University, Sendai, Japan"},{"name":"2Institute of Development, Aging and Cancer, Tohoku University, Sendai, Japan"},{"name":"3Tohoku Medical Megabank Organization, Sendai, Japan"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2016,7,27]]},"reference":[{"key":"2023020113523523500_btw488-B1","doi-asserted-by":"crossref","first-page":"1021","DOI":"10.1093\/bioinformatics\/btl039","article-title":"CFinder: locating cliques and overlapping modules in biological networks","volume":"22","author":"Adamcsek","year":"2006","journal-title":"Bioinformatics"},{"key":"2023020113523523500_btw488-B2","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1145\/2856030","article-title":"Almost optimal local graph clustering using evolving sets","volume":"63","author":"Andersen","year":"2016","journal-title":"J. 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