{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,9]],"date-time":"2026-03-09T10:03:57Z","timestamp":1773050637077,"version":"3.50.1"},"reference-count":16,"publisher":"Oxford University Press (OUP)","issue":"7","license":[{"start":{"date-parts":[[2016,10,28]],"date-time":"2016-10-28T00:00:00Z","timestamp":1477612800000},"content-version":"vor","delay-in-days":337,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"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: A successful approach for predicting functional associations between non-homologous genes is to compare their phylogenetic distributions. We have devised a phylogenetic profiling algorithm, SVD-Phy, which uses truncated singular value decomposition to address the problem of uninformative profiles giving rise to false positive predictions. Benchmarking the algorithm against the KEGG pathway database, we found that it has substantially improved performance over existing phylogenetic profiling methods.<\/jats:p>\n               <jats:p>Availability and implementation: The software is available under the open-source BSD license at https:\/\/bitbucket.org\/andrea\/svd-phy<\/jats:p>\n               <jats:p>Contact: \u00a0lars.juhl.jensen@cpr.ku.dk<\/jats:p>\n               <jats:p>Supplementary information: \u00a0Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btv696","type":"journal-article","created":{"date-parts":[[2015,11,28]],"date-time":"2015-11-28T01:48:27Z","timestamp":1448675307000},"page":"1085-1087","source":"Crossref","is-referenced-by-count":98,"title":["SVD-phy: improved prediction of protein functional associations through singular value decomposition of phylogenetic profiles"],"prefix":"10.1093","volume":"32","author":[{"given":"Andrea","family":"Franceschini","sequence":"first","affiliation":[{"name":"1 Institute of Molecular Life Sciences, University of Zurich, Winterthurerstrasse 190, Zurich, 8057, Switzerland,"},{"name":"2 Swiss Institute of Bioinformatics, Quartier Sorge, B\u00e2timent G\u00e9nopode, Lausanne, 1015, Switzerland,"}]},{"given":"Jianyi","family":"Lin","sequence":"additional","affiliation":[{"name":"3 Department of Computer Science, University of Milan, via Comelico 39, Milan, 20135, Italy and"}]},{"given":"Christian","family":"von Mering","sequence":"additional","affiliation":[{"name":"1 Institute of Molecular Life Sciences, University of Zurich, Winterthurerstrasse 190, Zurich, 8057, Switzerland,"},{"name":"2 Swiss Institute of Bioinformatics, Quartier Sorge, B\u00e2timent G\u00e9nopode, Lausanne, 1015, Switzerland,"}]},{"given":"Lars Juhl","family":"Jensen","sequence":"additional","affiliation":[{"name":"4 Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Copenhagen N, 2200, Denmark"}]}],"member":"286","published-online":{"date-parts":[[2015,11,26]]},"reference":[{"key":"2023020111595153400_btv696-B1","doi-asserted-by":"crossref","first-page":"D279","DOI":"10.1093\/nar\/gkt970","article-title":"SIMAP\u2014the database of all-against-all protein sequence similarities and annotations with new interfaces and increased coverage","volume":"42","author":"Arnold","year":"2014","journal-title":"Nucleic Acids Res"},{"key":"2023020111595153400_btv696-B2","doi-asserted-by":"crossref","first-page":"W160","DOI":"10.1093\/nar\/gkv455","article-title":"ProtPhylo: identification of protein\u2013phenotype and protein\u2013protein functional associations via phylogenetic profiling","volume":"43","author":"Cheng","year":"2015","journal-title":"Nucleic Acids Res"},{"key":"2023020111595153400_btv696-B3","doi-asserted-by":"crossref","first-page":"D472","DOI":"10.1093\/nar\/gkt1102","article-title":"The Reactome pathway knowledgebase","volume":"42","author":"Croft","year":"2014","journal-title":"Nucleic Acids Res"},{"key":"2023020111595153400_btv696-B4","doi-asserted-by":"crossref","first-page":"1055","DOI":"10.1038\/nbt861","article-title":"Discovery of uncharacterized cellular systems by genome-wide analysis of functional linkages","volume":"21","author":"Date","year":"2003","journal-title":"Nat. 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