{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,8,7]],"date-time":"2026-08-07T04:30:32Z","timestamp":1786077032928,"version":"3.56.0"},"reference-count":14,"publisher":"Oxford University Press (OUP)","issue":"7","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2016,4,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Summary: Breast cancer is one of the most frequent cancers among women. Extensive studies into the molecular heterogeneity of breast cancer have produced a plethora of molecular subtype classification and prognosis prediction algorithms, as well as numerous gene expression signatures. However, reimplementation of these algorithms is a tedious but important task to enable comparison of existing signatures and classification models between each other and with new models. Here, we present the genefu R\/Bioconductor package, a multi-tiered compendium of bioinformatics algorithms and gene signatures for molecular subtyping and prognostication in breast cancer.<\/jats:p>\n               <jats:p>Availability and implementation: The genefu package is available from Bioconductor. http:\/\/www.bioconductor.org\/packages\/devel\/bioc\/html\/genefu.html. Source code is also available on Github https:\/\/github.com\/bhklab\/genefu.<\/jats:p>\n               <jats:p>Contact: \u00a0bhaibeka@uhnresearch.ca<\/jats:p>\n               <jats:p>Supplementary information: \u00a0Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btv693","type":"journal-article","created":{"date-parts":[[2015,11,26]],"date-time":"2015-11-26T02:03:25Z","timestamp":1448503405000},"page":"1097-1099","source":"Crossref","is-referenced-by-count":342,"title":["Genefu: an R\/Bioconductor package for computation of gene expression-based signatures in breast cancer"],"prefix":"10.1093","volume":"32","author":[{"given":"Deena M. A.","family":"Gendoo","sequence":"first","affiliation":[{"name":"1 Bioinformatics and Computational Laboratory, Princess Margaret Cancer Centre, University Health Network and"},{"name":"2 Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada,"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Natchar","family":"Ratanasirigulchai","sequence":"additional","affiliation":[{"name":"1 Bioinformatics and Computational Laboratory, Princess Margaret Cancer Centre, University Health Network and"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Markus S.","family":"Schr\u00f6der","sequence":"additional","affiliation":[{"name":"3 UCD School of Biomolecular and Biomedical Science, Conway Institute, University College Dublin, Dublin, UK,"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Laia","family":"Par\u00e9","sequence":"additional","affiliation":[{"name":"4 Translational Genomics and Targeted Therapeutics in Solid Tumors, August Pi i Sunyer Biomedical Research Institute (IDIBAPS), 08036 Barcelona, Spain,"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Joel S.","family":"Parker","sequence":"additional","affiliation":[{"name":"5 Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC 27599, USA,"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Aleix","family":"Prat","sequence":"additional","affiliation":[{"name":"4 Translational Genomics and Targeted Therapeutics in Solid Tumors, August Pi i Sunyer Biomedical Research Institute (IDIBAPS), 08036 Barcelona, Spain,"},{"name":"6 Translational Genomics Group, Vall d\u2019Hebron Institute of Oncology (VHIO), 08035 Barcelona, Spain and"},{"name":"7 Department of Medical Oncology, Hospital Cl\u00ednic of Barcelona, 08036 Barcelona, Spain"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Benjamin","family":"Haibe-Kains","sequence":"additional","affiliation":[{"name":"1 Bioinformatics and Computational Laboratory, Princess Margaret Cancer Centre, University Health Network and"},{"name":"2 Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada,"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2015,11,24]]},"reference":[{"key":"2023020112012982900_btv693-B1","doi-asserted-by":"crossref","first-page":"346","DOI":"10.1038\/nature10983","article-title":"The genomic and transcriptomic architecture of 2\u2009000 breast tumours reveals novel subgroups","volume":"486","author":"Curtis","year":"2012","journal-title":"Nature"},{"key":"2023020112012982900_btv693-B2","doi-asserted-by":"crossref","first-page":"5158","DOI":"10.1158\/1078-0432.CCR-07-4756","article-title":"Biological processes associated with breast cancer clinical outcome depend on the molecular subtypes","volume":"14","author":"Desmedt","year":"2008","journal-title":"Clin. 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