{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,10,29]],"date-time":"2025-10-29T13:21:34Z","timestamp":1761744094306},"reference-count":8,"publisher":"Oxford University Press (OUP)","issue":"14","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2015,7,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Summary: Identification of protein interaction subnetworks is an important step to help us understand complex molecular mechanisms in cancer. In this paper, we develop a BMRF-Net package, implemented in Java and C++, to identify protein interaction subnetworks based on a bagging Markov random field (BMRF) framework. By integrating gene expression data and protein\u2013protein interaction data, this software tool can be used to identify biologically meaningful subnetworks. A user friendly graphic user interface is developed as a Cytoscape plugin for the BMRF-Net software to deal with the input\/output interface. The detailed structure of the identified networks can be visualized in Cytoscape conveniently. The BMRF-Net package has been applied to breast cancer data to identify significant subnetworks related to breast cancer recurrence.<\/jats:p>\n               <jats:p>Availability and implementation: The BMRF-Net package is available at http:\/\/sourceforge.net\/projects\/bmrfcjava\/. The package is tested under Ubuntu 12.04 (64-bit), Java 7, glibc 2.15 and Cytoscape 3.1.0.<\/jats:p>\n               <jats:p>Contact: \u00a0xuan@vt.edu<\/jats:p>\n               <jats:p>Supplementary information: Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btv137","type":"journal-article","created":{"date-parts":[[2015,3,10]],"date-time":"2015-03-10T00:22:11Z","timestamp":1425946931000},"page":"2412-2414","source":"Crossref","is-referenced-by-count":9,"title":["BMRF-Net: a software tool for identification of protein interaction subnetworks by a bagging Markov random field-based method"],"prefix":"10.1093","volume":"31","author":[{"given":"Xu","family":"Shi","sequence":"first","affiliation":[{"name":"1 Bradley Department of Electrical and Computer Engineering, Virginia Tech, Arlington, VA 22203, USA,"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Robert O.","family":"Barnes","sequence":"additional","affiliation":[{"name":"1 Bradley Department of Electrical and Computer Engineering, Virginia Tech, Arlington, VA 22203, USA,"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Li","family":"Chen","sequence":"additional","affiliation":[{"name":"2 Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD 21231, USA and"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Ayesha N.","family":"Shajahan-Haq","sequence":"additional","affiliation":[{"name":"3 Lombardi Comprehensive Cancer Center and Department of Oncology, Georgetown University, Washington, DC 20057, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Leena","family":"Hilakivi-Clarke","sequence":"additional","affiliation":[{"name":"3 Lombardi Comprehensive Cancer Center and Department of Oncology, Georgetown University, Washington, DC 20057, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Robert","family":"Clarke","sequence":"additional","affiliation":[{"name":"3 Lombardi Comprehensive Cancer Center and Department of Oncology, Georgetown University, Washington, DC 20057, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Yue","family":"Wang","sequence":"additional","affiliation":[{"name":"1 Bradley Department of Electrical and Computer Engineering, Virginia Tech, Arlington, VA 22203, USA,"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Jianhua","family":"Xuan","sequence":"additional","affiliation":[{"name":"1 Bradley Department of Electrical and Computer Engineering, Virginia Tech, Arlington, VA 22203, USA,"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2015,3,8]]},"reference":[{"key":"2023020202161134000_btv137-B1","doi-asserted-by":"crossref","first-page":"e42","DOI":"10.1093\/nar\/gks951","article-title":"Identifying protein interaction subnetworks by a bagging Markov random field-based method","volume":"41","author":"Chen","year":"2013","journal-title":"Nucleic Acids Res."},{"key":"2023020202161134000_btv137-B2","doi-asserted-by":"crossref","first-page":"140","DOI":"10.1038\/msb4100180","article-title":"Network-based classification of breast cancer metastasis","volume":"3","author":"Chuang","year":"2007","journal-title":"Mol. Syst. Biol."},{"key":"2023020202161134000_btv137-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":"2023020202161134000_btv137-B4","doi-asserted-by":"crossref","first-page":"638","DOI":"10.1038\/nrc1414","article-title":"Integrated global profiling of cancer","volume":"4","author":"Hanash","year":"2004","journal-title":"Nat. Rev. Cancer"},{"key":"2023020202161134000_btv137-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":"2023020202161134000_btv137-B6","doi-asserted-by":"crossref","first-page":"D767","DOI":"10.1093\/nar\/gkn892","article-title":"Human protein reference database\u20142009 update","volume":"37","author":"Keshava Prasad","year":"2009","journal-title":"Nucleic Acids Res."},{"key":"2023020202161134000_btv137-B7","doi-asserted-by":"crossref","first-page":"10208","DOI":"10.1073\/pnas.0907011107","article-title":"PIK3CA mutations associated with gene signature of low mTORC1 signaling and better outcomes in estrogen receptor-positive breast cancer","volume":"107","author":"Loi","year":"2010","journal-title":"Proc. Natl Acad. Sci. USA"},{"key":"2023020202161134000_btv137-B8","doi-asserted-by":"crossref","first-page":"431","DOI":"10.1093\/bioinformatics\/btq675","article-title":"Cytoscape 2.8: new features for data integration and network visualization","volume":"27","author":"Smoot","year":"2011","journal-title":"Bioinformatics"}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/31\/14\/2412\/49035221\/bioinformatics_31_14_2412.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/31\/14\/2412\/49035221\/bioinformatics_31_14_2412.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,2,2]],"date-time":"2023-02-02T03:43:34Z","timestamp":1675309414000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/31\/14\/2412\/254875"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2015,3,8]]},"references-count":8,"journal-issue":{"issue":"14","published-print":{"date-parts":[[2015,7,15]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btv137","relation":{},"ISSN":["1367-4811","1367-4803"],"issn-type":[{"value":"1367-4811","type":"electronic"},{"value":"1367-4803","type":"print"}],"subject":[],"published-other":{"date-parts":[[2015,7,15]]},"published":{"date-parts":[[2015,3,8]]}}}