{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,14]],"date-time":"2026-04-14T21:49:32Z","timestamp":1776203372119,"version":"3.50.1"},"reference-count":9,"publisher":"Oxford University Press (OUP)","issue":"3","license":[{"start":{"date-parts":[[2016,10,6]],"date-time":"2016-10-06T00:00:00Z","timestamp":1475712000000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/journals\/pages\/about_us\/legal\/notices"}],"funder":[{"name":"Ghent University; iMinds; a PhD fellowship of the Research Foundation \u2013 Flanders to MH and the Multidisciplinary Research Partnership \u2018Bioinformatics","award":["01MR0310W"],"award-info":[{"award-number":["01MR0310W"]}]},{"name":"Ghent University"},{"DOI":"10.13039\/100011102","name":"European Union Seventh Framework Programme","doi-asserted-by":"crossref","award":["FP7\/2007-2013"],"award-info":[{"award-number":["FP7\/2007-2013"]}],"id":[{"id":"10.13039\/100011102","id-type":"DOI","asserted-by":"crossref"}]},{"name":"European Research Council Advanced Grant Agreement","award":["322739-DOUBLEUP"],"award-info":[{"award-number":["322739-DOUBLEUP"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2017,2,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Summary<\/jats:title>\n                  <jats:p>We present a Cytoscape app for the ISMAGS algorithm, which can enumerate all instances of a motif in a graph, making optimal use of the motif\u2019s symmetries to make the search more efficient. The Cytoscape app provides a handy interface for this algorithm, which allows more efficient network analysis.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and Implementation<\/jats:title>\n                  <jats:p>The Cytoscape app for ISMAGS can be freely downloaded from the Cytoscape App store http:\/\/apps.cytoscape.org\/apps\/ismags. Source code and documentation for ISMAGS are available at https:\/\/github.com\/biointec\/ismags. Source code and documentation for the Cytoscape app are available at https:\/\/gitlab.psb.ugent.be\/thpar\/ISMAGS_Cytoscape.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Supplementary information<\/jats:title>\n                  <jats:p>Supplementary data are available at Bioinformatics online.<\/jats:p>\n               <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btw626","type":"journal-article","created":{"date-parts":[[2016,10,3]],"date-time":"2016-10-03T19:05:37Z","timestamp":1475521537000},"page":"461-463","source":"Crossref","is-referenced-by-count":28,"title":["A Cytoscape app for motif enumeration with ISMAGS"],"prefix":"10.1093","volume":"33","author":[{"given":"Thomas","family":"Van Parys","sequence":"first","affiliation":[{"name":"Department of Plant Systems Biology, VIB, Ghent, Belgium"},{"name":"Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium"},{"name":"Bioinformatics Institute Ghent, Ghent University, Ghent, Belgium"}]},{"given":"Ine","family":"Melckenbeeck","sequence":"additional","affiliation":[{"name":"Department of Information Technology (INTEC), Ghent University \u2013 iMinds, Ghent, Belgium"}]},{"given":"Maarten","family":"Houbraken","sequence":"additional","affiliation":[{"name":"Department of Information Technology (INTEC), Ghent University \u2013 iMinds, Ghent, Belgium"}]},{"given":"Pieter","family":"Audenaert","sequence":"additional","affiliation":[{"name":"Bioinformatics Institute Ghent, Ghent University, Ghent, Belgium"},{"name":"Department of Information Technology (INTEC), Ghent University \u2013 iMinds, Ghent, Belgium"}]},{"given":"Didier","family":"Colle","sequence":"additional","affiliation":[{"name":"Bioinformatics Institute Ghent, Ghent University, Ghent, Belgium"},{"name":"Department of Information Technology (INTEC), Ghent University \u2013 iMinds, Ghent, Belgium"}]},{"given":"Mario","family":"Pickavet","sequence":"additional","affiliation":[{"name":"Bioinformatics Institute Ghent, Ghent University, Ghent, Belgium"},{"name":"Department of Information Technology (INTEC), Ghent University \u2013 iMinds, Ghent, Belgium"}]},{"given":"Piet","family":"Demeester","sequence":"additional","affiliation":[{"name":"Bioinformatics Institute Ghent, Ghent University, Ghent, Belgium"},{"name":"Department of Information Technology (INTEC), Ghent University \u2013 iMinds, Ghent, Belgium"}]},{"given":"Yves","family":"Van de Peer","sequence":"additional","affiliation":[{"name":"Department of Plant Systems Biology, VIB, Ghent, Belgium"},{"name":"Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium"},{"name":"Bioinformatics Institute Ghent, Ghent University, Ghent, Belgium"},{"name":"Genomics Research Institute, University of Pretoria, Pretoria, South Africa"}]}],"member":"286","published-online":{"date-parts":[[2016,10,6]]},"reference":[{"key":"2023020204402946500_btw626-B1","doi-asserted-by":"crossref","first-page":"163","DOI":"10.1126\/science.aad9029","article-title":"Higher-order organization of complex networks","volume":"353","author":"Benson","year":"2016","journal-title":"Science"},{"key":"2023020204402946500_btw626-B2","doi-asserted-by":"crossref","first-page":"e61183.","DOI":"10.1371\/journal.pone.0061183","article-title":"The index-based subgraph matching algorithm (ISMA): fast subgraph enumeration in large networks using optimized search trees","volume":"8","author":"Demeyer","year":"2013","journal-title":"PloS One"},{"key":"2023020204402946500_btw626-B3","doi-asserted-by":"crossref","first-page":"92","DOI":"10.1007\/978-3-540-71681-5_7","volume-title":"Research in Computational Molecular Biology: 11th Annual International Conference, RECOMB 2007","author":"Grochow","year":"2007"},{"key":"2023020204402946500_btw626-B4","doi-asserted-by":"crossref","first-page":"e97896.","DOI":"10.1371\/journal.pone.0097896","article-title":"The Index-based Subgraph Matching Algorithm with General Symmetries (ISMAGS): exploiting symmetry for faster subgraph enumeration","volume":"9","author":"Houbraken","year":"2014","journal-title":"PloS One"},{"key":"2023020204402946500_btw626-B5","doi-asserted-by":"crossref","first-page":"831","DOI":"10.1109\/ICDE.2015.7113337","volume-title":"2015 IEEE 31st International Conference on Data Engineering","author":"Lin","year":"2015"},{"key":"2023020204402946500_btw626-B6","doi-asserted-by":"crossref","first-page":"824","DOI":"10.1126\/science.298.5594.824","article-title":"Network motifs: simple building blocks of complex networks","volume":"298","author":"Milo","year":"2002","journal-title":"Science"},{"key":"2023020204402946500_btw626-B7","doi-asserted-by":"crossref","first-page":"385","DOI":"10.1266\/ggs.84.385","article-title":"MODA: an efficient algorithm for network motif","volume":"84","author":"Omidi","year":"2009","journal-title":"Genes Genet. 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