{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2024,8,6]],"date-time":"2024-08-06T07:09:43Z","timestamp":1722928183185},"reference-count":24,"publisher":"Oxford University Press (OUP)","issue":"6","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2012,3,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Motivation: Phylogenetic profiling methods can achieve good accuracy in predicting protein\u2013protein interactions, especially in prokaryotes. Recent studies have shown that the choice of reference taxa (RT) is critical for accurate prediction, but with more than 2500 fully sequenced taxa publicly available, identifying the most-informative RT is becoming increasingly difficult. Previous studies on the selection of RT have provided guidelines for manual taxon selection, and for eliminating closely related taxa. However, no general strategy for automatic selection of RT is currently available.<\/jats:p>\n               <jats:p>Results: We present three novel methods for automating the selection of RT, using machine learning based on known protein\u2013protein interaction networks. One of these methods in particular, Tree-Based Search, yields greatly improved prediction accuracies. We further show that different methods for constituting phylogenetic profiles often require very different RT sets to support high prediction accuracy.<\/jats:p>\n               <jats:p>Availability: The datasets and software used in the experiments can be found at http:\/\/users-birc.au.dk\/zxr\/phyloprof\/<\/jats:p>\n               <jats:p>Contact: \u00a0zxr@birc.au.dk; somme89@gmail.com<\/jats:p>\n               <jats:p>Supplementary information: \u00a0Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btr720","type":"journal-article","created":{"date-parts":[[2012,1,5]],"date-time":"2012-01-05T21:07:16Z","timestamp":1325797636000},"page":"851-857","source":"Crossref","is-referenced-by-count":13,"title":["Automatic selection of reference taxa for protein\u2013protein interaction prediction with phylogenetic profiling"],"prefix":"10.1093","volume":"28","author":[{"given":"Martin","family":"Simonsen","sequence":"first","affiliation":[{"name":"1 Bioinformatics Research Centre, Aarhus University, Aarhus 8000, Denmark, 2Australian Research Council Centre of Excellence in Bioinformatics and 3The University of Queensland, Institute for Molecular Bioscience, Brisbane, QLD 4072, Australia"},{"name":"1 Bioinformatics Research Centre, Aarhus University, Aarhus 8000, Denmark, 2Australian Research Council Centre of Excellence in Bioinformatics and 3The University of Queensland, Institute for Molecular Bioscience, Brisbane, QLD 4072, Australia"}]},{"given":"Stefan R.","family":"Maetschke","sequence":"additional","affiliation":[{"name":"1 Bioinformatics Research Centre, Aarhus University, Aarhus 8000, Denmark, 2Australian Research Council Centre of Excellence in Bioinformatics and 3The University of Queensland, Institute for Molecular Bioscience, Brisbane, QLD 4072, Australia"},{"name":"1 Bioinformatics Research Centre, Aarhus University, Aarhus 8000, Denmark, 2Australian Research Council Centre of Excellence in Bioinformatics and 3The University of Queensland, Institute for Molecular Bioscience, Brisbane, QLD 4072, Australia"}]},{"given":"Mark A.","family":"Ragan","sequence":"additional","affiliation":[{"name":"1 Bioinformatics Research Centre, Aarhus University, Aarhus 8000, Denmark, 2Australian Research Council Centre of Excellence in Bioinformatics and 3The University of Queensland, Institute for Molecular Bioscience, Brisbane, QLD 4072, Australia"},{"name":"1 Bioinformatics Research Centre, Aarhus University, Aarhus 8000, Denmark, 2Australian Research Council Centre of Excellence in Bioinformatics and 3The University of Queensland, Institute for Molecular Bioscience, Brisbane, QLD 4072, Australia"}]}],"member":"286","published-online":{"date-parts":[[2012,1,4]]},"reference":[{"key":"2023012512201713800_B1","doi-asserted-by":"crossref","first-page":"154","DOI":"10.1093\/nar\/gki070","article-title":"The universal protein resource (UniProt)","volume":"33","author":"Bairoch","year":"2005","journal-title":"Nucleic Acids Res."},{"issue":"Suppl. 1","key":"2023012512201713800_B2","doi-asserted-by":"crossref","first-page":"S2","DOI":"10.1186\/1471-2105-7-S1-S2","article-title":"Choosing negative examples for the prediction of protein-protein interactions","volume":"7","author":"Ben-Hur","year":"2006","journal-title":"BMC Bioinformatics"},{"issue":"Suppl. 4","key":"2023012512201713800_B3","doi-asserted-by":"crossref","first-page":"S7","DOI":"10.1186\/1471-2105-8-S4-S7","article-title":"An improved method for identifying functionally linked proteins using phylogenetic profiles","volume":"8","author":"Cokus","year":"2007","journal-title":"BMC Bioinformatics"},{"key":"2023012512201713800_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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