{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,5,15]],"date-time":"2026-05-15T06:42:16Z","timestamp":1778827336159,"version":"3.51.4"},"reference-count":20,"publisher":"Oxford University Press (OUP)","issue":"D1","license":[{"start":{"date-parts":[[2016,11,9]],"date-time":"2016-11-09T00:00:00Z","timestamp":1478649600000},"content-version":"vor","delay-in-days":713,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc\/4.0\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2015,1,28]]},"DOI":"10.1093\/nar\/gku1203","type":"journal-article","created":{"date-parts":[[2014,11,28]],"date-time":"2014-11-28T15:52:11Z","timestamp":1417189931000},"page":"D234-D239","source":"Crossref","is-referenced-by-count":443,"title":["InParanoid 8: orthology analysis between 273 proteomes, mostly eukaryotic"],"prefix":"10.1093","volume":"43","author":[{"given":"Erik L.L.","family":"Sonnhammer","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Gabriel","family":"\u00d6stlund","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2014,11,27]]},"reference":[{"key":"key\n\t\t\t\t20171011204855_B1","doi-asserted-by":"crossref","first-page":"99","DOI":"10.2307\/2412448","article-title":"Distinguishing homologous from analogous proteins","volume":"19","author":"Fitch","year":"1970","journal-title":"Syst. Zoolog."},{"key":"key\n\t\t\t\t20171011204855_B2","doi-asserted-by":"crossref","first-page":"619","DOI":"10.1016\/S0168-9525(02)02793-2","article-title":"Orthology, paralogy and proposed classification for paralog subtypes","volume":"18","author":"Sonnhammer","year":"2002","journal-title":"Trends Genet."},{"key":"key\n\t\t\t\t20171011204855_B3","doi-asserted-by":"crossref","first-page":"2993","DOI":"10.1093\/bioinformatics\/btu492","article-title":"Big data and other challenges in the quest for orthologs","volume":"30","author":"Sonnhammer","year":"2014","journal-title":"Bioinformatics"},{"key":"key\n\t\t\t\t20171011204855_B4","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":"key\n\t\t\t\t20171011204855_B5","doi-asserted-by":"crossref","first-page":"R31","DOI":"10.1186\/gb-2006-7-4-r31","article-title":"Benchmarking ortholog identification methods using functional genomics data","volume":"7","author":"Hulsen","year":"2006","journal-title":"Genome Biol."},{"key":"key\n\t\t\t\t20171011204855_B6","doi-asserted-by":"crossref","first-page":"e383","DOI":"10.1371\/journal.pone.0000383","article-title":"Assessing performance of orthology detection strategies applied to eukaryotic genomes","volume":"2","author":"Chen","year":"2007","journal-title":"PloS One"},{"key":"key\n\t\t\t\t20171011204855_B7","doi-asserted-by":"crossref","first-page":"e1000262","DOI":"10.1371\/journal.pcbi.1000262","article-title":"Phylogenetic and functional assessment of orthologs inference projects and methods","volume":"5","author":"Altenhoff","year":"2009","journal-title":"PLoS Comput. Biol."},{"key":"key\n\t\t\t\t20171011204855_B8","doi-asserted-by":"crossref","first-page":"D196","DOI":"10.1093\/nar\/gkp931","article-title":"InParanoid 7: new algorithms and tools for eukaryotic orthology analysis","volume":"38","author":"Ostlund","year":"2010","journal-title":"Nucleic Acids Res."},{"key":"key\n\t\t\t\t20171011204855_B9","doi-asserted-by":"crossref","first-page":"403","DOI":"10.1016\/S0022-2836(05)80360-2","article-title":"Basic local alignment search tool","volume":"215","author":"Altschul","year":"1990","journal-title":"J. Mol. Biol."},{"key":"key\n\t\t\t\t20171011204855_B10","doi-asserted-by":"crossref","first-page":"902","DOI":"10.1093\/bioinformatics\/bti070","article-title":"The construction of amino acid substitution matrices for the comparison of proteins with non-standard compositions","volume":"21","author":"Yu","year":"2005","journal-title":"Bioinformatics"},{"key":"key\n\t\t\t\t20171011204855_B11","doi-asserted-by":"crossref","first-page":"D43","DOI":"10.1093\/nar\/gks1068","article-title":"Update on activities at the Universal Protein Resource (UniProt) in 2013","volume":"41","author":"The UniProt Consortium","year":"2013","journal-title":"Nucleic Acids Res."},{"key":"key\n\t\t\t\t20171011204855_B12","doi-asserted-by":"crossref","first-page":"D263","DOI":"10.1093\/nar\/gkm1020","article-title":"InParanoid 6: eukaryotic ortholog clusters with inparalogs","volume":"36","author":"Berglund","year":"2008","journal-title":"Nucleic Acids Res."},{"key":"key\n\t\t\t\t20171011204855_B13","doi-asserted-by":"crossref","first-page":"485","DOI":"10.1093\/bib\/bbr025","article-title":"Letter to the editor: SeqXML and OrthoXML: standards for sequence and orthology information","volume":"12","author":"Schmitt","year":"2011","journal-title":"Brief. Bioinform."},{"key":"key\n\t\t\t\t20171011204855_B14","doi-asserted-by":"crossref","first-page":"203","DOI":"10.1186\/1471-2105-14-203","article-title":"Prediction of gene-phenotype associations in humans, mice, and plants using phenologs","volume":"14","author":"Woods","year":"2013","journal-title":"BMC Bioinformatics"},{"key":"key\n\t\t\t\t20171011204855_B15","doi-asserted-by":"crossref","first-page":"bat037","DOI":"10.1093\/database\/bat037","article-title":"FSRD: fungal stress response database","volume":"2013","author":"Karanyi","year":"2013","journal-title":"Database"},{"key":"key\n\t\t\t\t20171011204855_B16","doi-asserted-by":"crossref","first-page":"384","DOI":"10.1093\/molbev\/mss235","article-title":"\u201cOrphan\u201d retrogenes in the human genome","volume":"30","author":"Ciomborowska","year":"2013","journal-title":"Mol. Biol. Evol."},{"key":"key\n\t\t\t\t20171011204855_B17","doi-asserted-by":"crossref","first-page":"183","DOI":"10.1186\/1471-2148-12-183","article-title":"Comparative genomics of eukaryotic small nucleolar RNAs reveals deep evolutionary ancestry amidst ongoing intragenomic mobility","volume":"12","author":"Hoeppner","year":"2012","journal-title":"BMC Evol. Biol."},{"key":"key\n\t\t\t\t20171011204855_B18","doi-asserted-by":"crossref","first-page":"D380","DOI":"10.1093\/nar\/gkt984","article-title":"FunCoup 3.0: database of genome-wide functional coupling networks","volume":"42","author":"Schmitt","year":"2014","journal-title":"Nucleic Acids Res."},{"key":"key\n\t\t\t\t20171011204855_B19","doi-asserted-by":"crossref","first-page":"2072","DOI":"10.1016\/j.jmb.2013.02.018","article-title":"Hieranoid: hierarchical orthology inference","volume":"425","author":"Schreiber","year":"2013","journal-title":"J. Mol. Biol."},{"key":"key\n\t\t\t\t20171011204855_B20","doi-asserted-by":"crossref","first-page":"D222","DOI":"10.1093\/nar\/gkt1223","article-title":"Pfam: the protein families database","volume":"42","author":"Finn","year":"2014","journal-title":"Nucleic Acids Res."}],"container-title":["Nucleic Acids Research"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/academic.oup.com\/nar\/article-pdf\/43\/D1\/D234\/7329284\/gku1203.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2024,6,5]],"date-time":"2024-06-05T11:18:16Z","timestamp":1717586296000},"score":1,"resource":{"primary":{"URL":"http:\/\/academic.oup.com\/nar\/article\/43\/D1\/D234\/2439077\/InParanoid-8-orthology-analysis-between-273"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2014,11,27]]},"references-count":20,"journal-issue":{"issue":"D1","published-online":{"date-parts":[[2014,11,27]]},"published-print":{"date-parts":[[2015,1,28]]}},"URL":"https:\/\/doi.org\/10.1093\/nar\/gku1203","relation":{},"ISSN":["1362-4962","0305-1048"],"issn-type":[{"value":"1362-4962","type":"electronic"},{"value":"0305-1048","type":"print"}],"subject":[],"published-other":{"date-parts":[[2015,1,28]]},"published":{"date-parts":[[2014,11,27]]}}}