{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2024,7,2]],"date-time":"2024-07-02T20:31:53Z","timestamp":1719952313528},"reference-count":11,"publisher":"Oxford University Press (OUP)","issue":"6","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2011,3,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Summary: With increasing numbers of eukaryotic genome sequences, phylogenetic profiles of eukaryotic genes are becoming increasingly informative. Here, we introduce a new web-tool Phylopro (http:\/\/compsysbio.org\/phylopro\/), which uses the 120 available eukaryotic genome sequences to visualize the evolutionary trajectories of user-defined subsets of model organism genes. Applied to pathways or complexes, PhyloPro allows the user to rapidly identify core conserved elements of biological processes together with those that may represent lineage-specific innovations. PhyloPro thus provides a valuable resource for the evolutionary and comparative studies of biological systems.<\/jats:p>\n               <jats:p>Contact: \u00a0jparkin@sickkids.ca<\/jats:p>","DOI":"10.1093\/bioinformatics\/btr023","type":"journal-article","created":{"date-parts":[[2011,1,21]],"date-time":"2011-01-21T01:28:28Z","timestamp":1295573308000},"page":"877-878","source":"Crossref","is-referenced-by-count":10,"title":["PhyloPro: a web-based tool for the generation and visualization of phylogenetic profiles across Eukarya"],"prefix":"10.1093","volume":"27","author":[{"given":"Xuejian","family":"Xiong","sequence":"first","affiliation":[{"name":"1 Program in Molecular Structure and Function, Hospital for Sick Children, 2Department of Molecular Genetics, 3Department of Cell and Systems Biology, 4Centre for the Analysis of Genome Evolution and Function and 5Department of Biochemistry, University of Toronto, Toronto, Canada"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Hongyan","family":"Song","sequence":"additional","affiliation":[{"name":"1 Program in Molecular Structure and Function, Hospital for Sick Children, 2Department of Molecular Genetics, 3Department of Cell and Systems Biology, 4Centre for the Analysis of Genome Evolution and Function and 5Department of Biochemistry, University of Toronto, Toronto, Canada"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Tuan","family":"On","sequence":"additional","affiliation":[{"name":"1 Program in Molecular Structure and Function, Hospital for Sick Children, 2Department of Molecular Genetics, 3Department of Cell and Systems Biology, 4Centre for the Analysis of Genome Evolution and Function and 5Department of Biochemistry, University of Toronto, Toronto, Canada"},{"name":"1 Program in Molecular Structure and Function, Hospital for Sick Children, 2Department of Molecular Genetics, 3Department of Cell and Systems Biology, 4Centre for the Analysis of Genome Evolution and Function and 5Department of Biochemistry, University of Toronto, Toronto, Canada"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Lucas","family":"Lochovsky","sequence":"additional","affiliation":[{"name":"1 Program in Molecular Structure and Function, Hospital for Sick Children, 2Department of Molecular Genetics, 3Department of Cell and Systems Biology, 4Centre for the Analysis of Genome Evolution and Function and 5Department of Biochemistry, University of Toronto, Toronto, Canada"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Nicholas J.","family":"Provart","sequence":"additional","affiliation":[{"name":"1 Program in Molecular Structure and Function, Hospital for Sick Children, 2Department of Molecular Genetics, 3Department of Cell and Systems Biology, 4Centre for the Analysis of Genome Evolution and Function and 5Department of Biochemistry, University of Toronto, Toronto, Canada"},{"name":"1 Program in Molecular Structure and Function, Hospital for Sick Children, 2Department of Molecular Genetics, 3Department of Cell and Systems Biology, 4Centre for the Analysis of Genome Evolution and Function and 5Department of Biochemistry, University of Toronto, Toronto, Canada"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"John","family":"Parkinson","sequence":"additional","affiliation":[{"name":"1 Program in Molecular Structure and Function, Hospital for Sick Children, 2Department of Molecular Genetics, 3Department of Cell and Systems Biology, 4Centre for the Analysis of Genome Evolution and Function and 5Department of Biochemistry, University of Toronto, Toronto, Canada"},{"name":"1 Program in Molecular Structure and Function, Hospital for Sick Children, 2Department of Molecular Genetics, 3Department of Cell and Systems Biology, 4Centre for the Analysis of Genome Evolution and Function and 5Department of Biochemistry, University of Toronto, Toronto, Canada"},{"name":"1 Program in Molecular Structure and Function, Hospital for Sick Children, 2Department of Molecular Genetics, 3Department of Cell and Systems Biology, 4Centre for the Analysis of Genome Evolution and Function and 5Department of Biochemistry, University of Toronto, Toronto, Canada"},{"name":"1 Program in Molecular Structure and Function, Hospital for Sick Children, 2Department of Molecular Genetics, 3Department of Cell and Systems Biology, 4Centre for the Analysis of Genome Evolution and Function and 5Department of Biochemistry, University of Toronto, Toronto, Canada"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2011,1,19]]},"reference":[{"key":"2023012511553317900_B1","doi-asserted-by":"crossref","first-page":"2558","DOI":"10.1093\/bioinformatics\/bti313","article-title":"Protein function prediction using the Protein Link EXplorer (PLEX)","volume":"21","author":"Date","year":"2005","journal-title":"Bioinformatics"},{"key":"2023012511553317900_B2","doi-asserted-by":"crossref","first-page":"14863","DOI":"10.1073\/pnas.95.25.14863","article-title":"Cluster analysis and display of genome-wide expression patterns","volume":"95","author":"Eisen","year":"1998","journal-title":"Proc. Natl Acad. Sci. USA"},{"key":"2023012511553317900_B3","doi-asserted-by":"crossref","first-page":"387","DOI":"10.1007\/978-1-59745-188-8_26","article-title":"Comparative genomics-based prediction of protein function","volume":"439","author":"Gabaldon","year":"2008","journal-title":"Methods Mol. Biol."},{"key":"2023012511553317900_B4","doi-asserted-by":"crossref","first-page":"D731","DOI":"10.1093\/nar\/gkn645","article-title":"PhyloPat: an updated version of the phylogenetic pattern database contains gene neighborhood","volume":"37","author":"Hulsen","year":"2009","journal-title":"Nucleic Acids Res."},{"key":"2023012511553317900_B5","doi-asserted-by":"crossref","first-page":"2178","DOI":"10.1101\/gr.1224503","article-title":"OrthoMCL: identification of ortholog groups for eukaryotic genomes","volume":"13","author":"Li","year":"2003","journal-title":"Genome Res."},{"key":"2023012511553317900_B6","doi-asserted-by":"crossref","first-page":"2075","DOI":"10.1002\/prot.22723","article-title":"The evolutionary landscape of the chromatin modification machinery reveals lineage specific gains, expansions, and losses","volume":"78","author":"On","year":"2010","journal-title":"Proteins"},{"key":"2023012511553317900_B7","doi-asserted-by":"crossref","first-page":"333","DOI":"10.1038\/msb.2009.85","article-title":"Comparison of substrate specificity of the ubiquitin ligases Nedd4 and Nedd4-2 using proteome arrays","volume":"5","author":"Persaud","year":"2009","journal-title":"Mol. Syst. Biol."},{"key":"2023012511553317900_B8","doi-asserted-by":"crossref","first-page":"1041","DOI":"10.1006\/jmbi.2000.5197","article-title":"Automatic clustering of orthologs and in-paralogs from pairwise species comparisons","volume":"314","author":"Remm","year":"2001","journal-title":"J. Mol. Biol."},{"key":"2023012511553317900_B9","doi-asserted-by":"crossref","first-page":"D735","DOI":"10.1093\/nar\/gkm1005","article-title":"TreeFam: 2008 update","volume":"36","author":"Ruan","year":"2008","journal-title":"Nucleic Acids Res."},{"key":"2023012511553317900_B10","doi-asserted-by":"crossref","first-page":"383","DOI":"10.1186\/1471-2105-10-383","article-title":"Comparison of eukaryotic phylogenetic profiling approaches using species tree aware methods","volume":"10","author":"Ruano-Rubio","year":"2009","journal-title":"BMC Bioinformatics"},{"key":"2023012511553317900_B11","doi-asserted-by":"crossref","first-page":"D358","DOI":"10.1093\/nar\/gkl825","article-title":"STRING 7\u2013recent developments in the integration and prediction of protein interactions","volume":"35","author":"von Mering","year":"2007","journal-title":"Nucleic Acids Res."}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/27\/6\/877\/48866308\/bioinformatics_27_6_877.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/27\/6\/877\/48866308\/bioinformatics_27_6_877.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,1,25]],"date-time":"2023-01-25T12:18:25Z","timestamp":1674649105000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/27\/6\/877\/236023"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2011,1,19]]},"references-count":11,"journal-issue":{"issue":"6","published-print":{"date-parts":[[2011,3,15]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btr023","relation":{},"ISSN":["1367-4811","1367-4803"],"issn-type":[{"value":"1367-4811","type":"electronic"},{"value":"1367-4803","type":"print"}],"subject":[],"published-other":{"date-parts":[[2011,3,15]]},"published":{"date-parts":[[2011,1,19]]}}}