{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,7,10]],"date-time":"2026-07-10T18:10:49Z","timestamp":1783707049762,"version":"3.55.0"},"reference-count":9,"publisher":"Oxford University Press (OUP)","issue":"8","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2010,4,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Motivation: Increasing quantity and quality of data in transcriptomics and interactomics create the need for integrative approaches to network analysis. Here, we present a comprehensive R-package for the analysis of biological networks including an exact and a heuristic approach to identify functional modules.<\/jats:p>\n               <jats:p>Results: The BioNet package provides an extensive framework for integrated network analysis in R. This includes the statistics for the integration of transcriptomic and functional data with biological networks, the scoring of nodes as well as methods for network search and visualization.<\/jats:p>\n               <jats:p>Availability: The BioNet package and a tutorial are available from http:\/\/bionet.bioapps.biozentrum.uni-wuerzburg.de<\/jats:p>\n               <jats:p>Contact: \u00a0marcus.dittrich@biozentrum.uni-wuerzburg.de; tobias.mueller@biozentrum.uni-wuerzburg.de<\/jats:p>","DOI":"10.1093\/bioinformatics\/btq089","type":"journal-article","created":{"date-parts":[[2010,2,27]],"date-time":"2010-02-27T01:13:51Z","timestamp":1267233231000},"page":"1129-1130","source":"Crossref","is-referenced-by-count":203,"title":["BioNet: an R-Package for the functional analysis of biological networks"],"prefix":"10.1093","volume":"26","author":[{"given":"Daniela","family":"Beisser","sequence":"first","affiliation":[{"name":"1 Department of Bioinformatics, Biocenter, University of W\u00fcrzburg, Am Hubland, 97074 W\u00fcrzburg, Germany and 2 Life Sciences group, CWI, Science Park 123, 1098 XG Amsterdam, The Netherlands"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Gunnar W.","family":"Klau","sequence":"additional","affiliation":[{"name":"1 Department of Bioinformatics, Biocenter, University of W\u00fcrzburg, Am Hubland, 97074 W\u00fcrzburg, Germany and 2 Life Sciences group, CWI, Science Park 123, 1098 XG Amsterdam, The Netherlands"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Thomas","family":"Dandekar","sequence":"additional","affiliation":[{"name":"1 Department of Bioinformatics, Biocenter, University of W\u00fcrzburg, Am Hubland, 97074 W\u00fcrzburg, Germany and 2 Life Sciences group, CWI, Science Park 123, 1098 XG Amsterdam, The Netherlands"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Tobias","family":"M\u00fcller","sequence":"additional","affiliation":[{"name":"1 Department of Bioinformatics, Biocenter, University of W\u00fcrzburg, Am Hubland, 97074 W\u00fcrzburg, Germany and 2 Life Sciences group, CWI, Science Park 123, 1098 XG Amsterdam, The Netherlands"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Marcus T.","family":"Dittrich","sequence":"additional","affiliation":[{"name":"1 Department of Bioinformatics, Biocenter, University of W\u00fcrzburg, Am Hubland, 97074 W\u00fcrzburg, Germany and 2 Life Sciences group, CWI, Science Park 123, 1098 XG Amsterdam, The Netherlands"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2010,2,25]]},"reference":[{"key":"2023012508075760500_B1","doi-asserted-by":"crossref","first-page":"135","DOI":"10.1093\/bioinformatics\/bth458","article-title":"Network structures and algorithms in Bioconductor","volume":"21","author":"Carey","year":"2005","journal-title":"Bioinformatics"},{"key":"2023012508075760500_B2","article-title":"The igraph software package for complex network research","author":"Csardi","year":"2006","journal-title":"InterJournal"},{"key":"2023012508075760500_B3","doi-asserted-by":"crossref","first-page":"i223","DOI":"10.1093\/bioinformatics\/btn161","article-title":"Identifying functional modules in protein-protein interaction networks: an integrated exact approach","volume":"24","author":"Dittrich","year":"2008","journal-title":"Bioinformatics"},{"key":"2023012508075760500_B4","doi-asserted-by":"crossref","first-page":"R80","DOI":"10.1186\/gb-2004-5-10-r80","article-title":"Bioconductor: open software development for computational biology and bioinformatics","volume":"5","author":"Gentleman","year":"2004","journal-title":"Genome Biol."},{"issue":"Suppl. 1","key":"2023012508075760500_B5","doi-asserted-by":"crossref","first-page":"S233","DOI":"10.1093\/bioinformatics\/18.suppl_1.S233","article-title":"Discovering regulatory and signalling circuits in molecular interaction networks","volume":"18","author":"Ideker","year":"2002","journal-title":"Bioinformatics"},{"key":"2023012508075760500_B6","doi-asserted-by":"crossref","first-page":"1236","DOI":"10.1093\/bioinformatics\/btg148","article-title":"Estimating the occurrence of false positives and false negatives in microarray studies by approximating and partitioning the empirical distribution of p-values","volume":"19","author":"Pounds","year":"2003","journal-title":"Bioinformatics"},{"key":"2023012508075760500_B7","doi-asserted-by":"crossref","first-page":"D767","DOI":"10.1093\/nar\/gkn892","article-title":"Human protein reference database\u20132009 update","volume":"37","author":"Prasad","year":"2009","journal-title":"Nucleic Acids Res."},{"key":"2023012508075760500_B8","doi-asserted-by":"crossref","first-page":"1937","DOI":"10.1056\/NEJMoa012914","article-title":"The use of molecular profiling to predict survival after chemotherapy for diffuse large-B-cell lymphoma","volume":"346","author":"Rosenwald","year":"2002","journal-title":"N. 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