{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,14]],"date-time":"2026-02-14T02:59:59Z","timestamp":1771037999492,"version":"3.50.1"},"reference-count":6,"publisher":"Oxford University Press (OUP)","issue":"23","license":[{"start":{"date-parts":[[2016,10,2]],"date-time":"2016-10-02T00:00:00Z","timestamp":1475366400000},"content-version":"vor","delay-in-days":776,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc\/4.0\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2014,12,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>We introduce Pepper (Protein complex Expansion using Protein\u2013Protein intERactions), a Cytoscape app designed to identify protein complexes as densely connected subnetworks from seed lists of proteins derived from proteomic studies. Pepper identifies connected subgraph by using multi-objective optimization involving two functions: (i) the coverage, a solution must contain as many proteins from the seed as possible, (ii) the density, the proteins of a solution must be as connected as possible, using only interactions from a proteome-wide interaction network. Comparisons based on gold standard yeast and human datasets showed Pepper\u2019s integrative approach as superior to standard protein complex discovery methods. The visualization and interpretation of the results are facilitated by an automated post-processing pipeline based on topological analysis and data integration about the predicted complex proteins. Pepper is a user-friendly tool that can be used to analyse any list of proteins.<\/jats:p>\n               <jats:p>Availability: Pepper is available from the Cytoscape plug-in manager or online (http:\/\/apps.cytoscape.org\/apps\/pepper) and released under GNU General Public License version 3.<\/jats:p>\n               <jats:p>Contact: mohamed.elati@issb.genopole.fr<\/jats:p>\n               <jats:p>Supplementary information: \u00a0Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btu517","type":"journal-article","created":{"date-parts":[[2014,8,20]],"date-time":"2014-08-20T05:11:29Z","timestamp":1408511489000},"page":"3419-3420","source":"Crossref","is-referenced-by-count":7,"title":["P<scp>epper<\/scp>: cytoscape app for protein complex expansion using protein\u2013protein interaction networks"],"prefix":"10.1093","volume":"30","author":[{"given":"C.","family":"Winterhalter","sequence":"first","affiliation":[{"name":"1 iSSB, CNRS, University of Evry, Genopole, 5 rue H. Desbru\u00e8res, 91030 Evry Cedex, France, 2School of Computing Science, Newcastle University, Newcastle NE1 7RU, UK and 3UMR 144 CNRS\/Institut Curie, 26 rue d\u2019Ulm, Paris, 75248 cedex 05, France"},{"name":"1 iSSB, CNRS, University of Evry, Genopole, 5 rue H. Desbru\u00e8res, 91030 Evry Cedex, France, 2School of Computing Science, Newcastle University, Newcastle NE1 7RU, UK and 3UMR 144 CNRS\/Institut Curie, 26 rue d\u2019Ulm, Paris, 75248 cedex 05, France"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"R.","family":"Nicolle","sequence":"additional","affiliation":[{"name":"1 iSSB, CNRS, University of Evry, Genopole, 5 rue H. Desbru\u00e8res, 91030 Evry Cedex, France, 2School of Computing Science, Newcastle University, Newcastle NE1 7RU, UK and 3UMR 144 CNRS\/Institut Curie, 26 rue d\u2019Ulm, Paris, 75248 cedex 05, France"},{"name":"1 iSSB, CNRS, University of Evry, Genopole, 5 rue H. Desbru\u00e8res, 91030 Evry Cedex, France, 2School of Computing Science, Newcastle University, Newcastle NE1 7RU, UK and 3UMR 144 CNRS\/Institut Curie, 26 rue d\u2019Ulm, Paris, 75248 cedex 05, France"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"A.","family":"Louis","sequence":"additional","affiliation":[{"name":"1 iSSB, CNRS, University of Evry, Genopole, 5 rue H. Desbru\u00e8res, 91030 Evry Cedex, France, 2School of Computing Science, Newcastle University, Newcastle NE1 7RU, UK and 3UMR 144 CNRS\/Institut Curie, 26 rue d\u2019Ulm, Paris, 75248 cedex 05, France"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"C.","family":"To","sequence":"additional","affiliation":[{"name":"1 iSSB, CNRS, University of Evry, Genopole, 5 rue H. Desbru\u00e8res, 91030 Evry Cedex, France, 2School of Computing Science, Newcastle University, Newcastle NE1 7RU, UK and 3UMR 144 CNRS\/Institut Curie, 26 rue d\u2019Ulm, Paris, 75248 cedex 05, France"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"F.","family":"Radvanyi","sequence":"additional","affiliation":[{"name":"1 iSSB, CNRS, University of Evry, Genopole, 5 rue H. Desbru\u00e8res, 91030 Evry Cedex, France, 2School of Computing Science, Newcastle University, Newcastle NE1 7RU, UK and 3UMR 144 CNRS\/Institut Curie, 26 rue d\u2019Ulm, Paris, 75248 cedex 05, France"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"M.","family":"Elati","sequence":"additional","affiliation":[{"name":"1 iSSB, CNRS, University of Evry, Genopole, 5 rue H. Desbru\u00e8res, 91030 Evry Cedex, France, 2School of Computing Science, Newcastle University, Newcastle NE1 7RU, UK and 3UMR 144 CNRS\/Institut Curie, 26 rue d\u2019Ulm, Paris, 75248 cedex 05, France"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2014,8,18]]},"reference":[{"key":"2023012712041783600_btu517-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":"2023012712041783600_btu517-B2","doi-asserted-by":"crossref","first-page":"70","DOI":"10.1038\/nmeth.1541","article-title":"Saint: probabilistic scoring of affinity purification-mass spectrometry data","volume":"8","author":"Choi","year":"2010","journal-title":"Nat. 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