{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,3]],"date-time":"2026-04-03T16:27:09Z","timestamp":1775233629838,"version":"3.50.1"},"reference-count":39,"publisher":"Public Library of Science (PLoS)","issue":"3","license":[{"start":{"date-parts":[[2010,3,26]],"date-time":"2010-03-26T00:00:00Z","timestamp":1269561600000},"content-version":"unspecified","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":["www.ploscompbiol.org"],"crossmark-restriction":false},"short-container-title":["PLoS Comput Biol"],"DOI":"10.1371\/journal.pcbi.1000703","type":"journal-article","created":{"date-parts":[[2010,3,25]],"date-time":"2010-03-25T22:17:31Z","timestamp":1269555451000},"page":"e1000703","update-policy":"https:\/\/doi.org\/10.1371\/journal.pcbi.corrections_policy","source":"Crossref","is-referenced-by-count":110,"title":["Getting Started in Gene Orthology and Functional Analysis"],"prefix":"10.1371","volume":"6","author":[{"given":"Gang","family":"Fang","sequence":"first","affiliation":[]},{"given":"Nitin","family":"Bhardwaj","sequence":"additional","affiliation":[]},{"given":"Rebecca","family":"Robilotto","sequence":"additional","affiliation":[]},{"given":"Mark B.","family":"Gerstein","sequence":"additional","affiliation":[]}],"member":"340","published-online":{"date-parts":[[2010,3,26]]},"reference":[{"key":"ref1","doi-asserted-by":"crossref","first-page":"73","DOI":"10.1038\/416073a","article-title":"Laser\u2013Raman imagery of Earth&apos;s earliest fossils.","volume":"416","author":"JW Schopf","year":"2002","journal-title":"Nature"},{"key":"ref2","first-page":"227","article-title":"Homology a personal view on some of the problems.","volume":"16","author":"WM Fitch","year":"2000","journal-title":"Trends Genet"},{"key":"ref3","doi-asserted-by":"crossref","first-page":"334","DOI":"10.1016\/0168-9525(96)20010-1","article-title":"Non-orthologous gene displacement.","volume":"12","author":"EV Koonin","year":"1996","journal-title":"Trends Genet"},{"key":"ref4","doi-asserted-by":"crossref","first-page":"631","DOI":"10.1126\/science.278.5338.631","article-title":"A genomic perspective on protein families.","volume":"278","author":"RL Tatusov","year":"1997","journal-title":"Science"},{"key":"ref5","first-page":"160 p","article-title":"Evolution by gene duplication.","author":"S Ohno","year":"1970"},{"key":"ref6","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":"M Remm","year":"2001","journal-title":"J Mol Biol"},{"key":"ref7","doi-asserted-by":"crossref","first-page":"233","DOI":"10.1006\/jmbi.2000.3550","article-title":"Assessing annotation transfer for genomics: quantifying the relations between protein sequence, structure and function through traditional and probabilistic scores.","volume":"297","author":"CA Wilson","year":"2000","journal-title":"J Mol Biol"},{"key":"ref8","doi-asserted-by":"crossref","first-page":"459","DOI":"10.1093\/genetics\/154.1.459","article-title":"The probability of duplicate gene preservation by subfunctionalization.","volume":"154","author":"M Lynch","year":"2000","journal-title":"Genetics"},{"key":"ref9","first-page":"0706.0117v1","article-title":"Reciprocal best hits are not a logically sufficient condition for orthology.","author":"T Johnson","year":"2007","journal-title":"arXiv"},{"key":"ref10","doi-asserted-by":"crossref","first-page":"2896","DOI":"10.1073\/pnas.96.6.2896","article-title":"The use of gene clusters to infer functional coupling.","volume":"96","author":"R Overbeek","year":"1999","journal-title":"Proc Natl Acad Sci U S A"},{"key":"ref11","doi-asserted-by":"crossref","first-page":"4","DOI":"10.1186\/1471-2164-9-4","article-title":"Persistence drives gene clustering in bacterial genomes.","volume":"9","author":"G Fang","year":"2008","journal-title":"BMC Genomics"},{"key":"ref12","doi-asserted-by":"crossref","first-page":"D250","DOI":"10.1093\/nar\/gkm796","article-title":"eggNOG: automated construction and annotation of orthologous groups of genes.","volume":"36","author":"LJ Jensen","year":"2008","journal-title":"Nucleic Acids Res"},{"key":"ref13","doi-asserted-by":"crossref","first-page":"D281","DOI":"10.1093\/nar\/gkm960","article-title":"The Pfam protein families database.","volume":"36","author":"RD Finn","year":"2008","journal-title":"Nucleic Acids Res"},{"key":"ref14","doi-asserted-by":"crossref","first-page":"D229","DOI":"10.1093\/nar\/gkn808","article-title":"SMART 6: recent updates and new developments.","volume":"37","author":"I Letunic","year":"2009","journal-title":"Nucleic Acids Res"},{"key":"ref15","doi-asserted-by":"crossref","first-page":"41","DOI":"10.1186\/1471-2105-4-41","article-title":"The COG database: an updated version includes eukaryotes.","volume":"4","author":"RL Tatusov","year":"2003","journal-title":"BMC Bioinformatics"},{"key":"ref16","doi-asserted-by":"crossref","first-page":"1401","DOI":"10.1126\/science.1089370","article-title":"The origins of genome complexity.","volume":"302","author":"M Lynch","year":"2003","journal-title":"Science"},{"key":"ref17","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":"L Li","year":"2003","journal-title":"Genome Res"},{"key":"ref18","doi-asserted-by":"crossref","first-page":"2180","DOI":"10.1093\/bioinformatics\/btm295","article-title":"OMA Browser\u2013exploring orthologous relations across 352 complete genomes.","volume":"23","author":"A Schneider","year":"2007","journal-title":"Bioinformatics"},{"key":"ref19","doi-asserted-by":"crossref","first-page":"2044","DOI":"10.1093\/bioinformatics\/btl286","article-title":"Roundup: a multi-genome repository of orthologs and evolutionary distances.","volume":"22","author":"TF Deluca","year":"2006","journal-title":"Bioinformatics"},{"key":"ref20","doi-asserted-by":"crossref","first-page":"1710","DOI":"10.1093\/bioinformatics\/btg213","article-title":"Detecting putative orthologs.","volume":"19","author":"DP Wall","year":"2003","journal-title":"Bioinformatics"},{"key":"ref21","doi-asserted-by":"crossref","first-page":"D491","DOI":"10.1093\/nar\/gkm899","article-title":"PhylomeDB: a database for genome-wide collections of gene phylogenies.","volume":"36","author":"J Huerta-Cepas","year":"2008","journal-title":"Nucleic Acids Res"},{"key":"ref22","doi-asserted-by":"crossref","first-page":"2129","DOI":"10.1101\/gr.772403","article-title":"PANTHER: a library of protein families and subfamilies indexed by function.","volume":"13","author":"PD Thomas","year":"2003","journal-title":"Genome Res"},{"key":"ref23","doi-asserted-by":"crossref","first-page":"D572","DOI":"10.1093\/nar\/gkj118","article-title":"TreeFam: a curated database of phylogenetic trees of animal gene families.","volume":"34","author":"H Li","year":"2006","journal-title":"Nucleic Acids Res"},{"key":"ref24","doi-asserted-by":"crossref","first-page":"327","DOI":"10.1101\/gr.073585.107","article-title":"EnsemblCompara GeneTrees: complete, duplication-aware phylogenetic trees in vertebrates.","volume":"19","author":"AJ Vilella","year":"2009","journal-title":"Genome Res"},{"key":"ref25","doi-asserted-by":"crossref","first-page":"2596","DOI":"10.1093\/bioinformatics\/bti325","article-title":"Tree pattern matching in phylogenetic trees: automatic search for orthologs or paralogs in homologous gene sequence databases.","volume":"21","author":"JF Dufayard","year":"2005","journal-title":"Bioinformatics"},{"key":"ref26","doi-asserted-by":"crossref","first-page":"54","DOI":"10.1038\/nature06107","article-title":"Natural history and evolutionary principles of gene duplication in fungi.","volume":"449","author":"I Wapinski","year":"2007","journal-title":"Nature"},{"key":"ref27","doi-asserted-by":"crossref","first-page":"235","DOI":"10.1186\/gb-2008-9-10-235","article-title":"Large-scale assignment of orthology: back to phylogenetics?","volume":"9","author":"T Gabaldon","year":"2008","journal-title":"Genome Biol"},{"key":"ref28","doi-asserted-by":"crossref","first-page":"25","DOI":"10.1038\/75556","article-title":"Gene ontology: tool for the unification of biology. The Gene Ontology Consortium.","volume":"25","author":"M Ashburner","year":"2000","journal-title":"Nat Genet"},{"key":"ref29","doi-asserted-by":"crossref","first-page":"3784","DOI":"10.1093\/nar\/gkg563","article-title":"ExPASy: the proteomics server for in-depth protein knowledge and analysis.","volume":"31","author":"E Gasteiger","year":"2003","journal-title":"Nucleic Acids Res"},{"key":"ref30","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":"AM Altenhoff","year":"2009","journal-title":"PLoS Comput Biol"},{"key":"ref31","doi-asserted-by":"crossref","first-page":"2163","DOI":"10.1093\/bioinformatics\/btm291","article-title":"Total ancestry measure: quantifying the similarity in tree-like classification, with genomic applications.","volume":"23","author":"H Yu","year":"2007","journal-title":"Bioinformatics"},{"key":"ref32","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":"T Hulsen","year":"2006","journal-title":"Genome Biol"},{"key":"ref33","doi-asserted-by":"crossref","first-page":"428","DOI":"10.1101\/gr.4526006","article-title":"Systematic identification of functional orthologs based on protein network comparison.","volume":"16","author":"S Bandyopadhyay","year":"2006","journal-title":"Genome Res"},{"key":"ref34","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":"F Chen","year":"2007","journal-title":"PLoS ONE"},{"key":"ref35","volume":"1848-1858","author":"N Lan","year":"2002"},{"key":"ref36","doi-asserted-by":"crossref","first-page":"393","DOI":"10.1016\/S0966-842X(02)02420-4","article-title":"Is there a role for replication fork asymmetry in the distribution of genes in bacterial genomes?","volume":"10","author":"E Rocha","year":"2002","journal-title":"Trends Microbiol"},{"key":"ref37","doi-asserted-by":"crossref","first-page":"1107","DOI":"10.1101\/gr.1774904","article-title":"Annotation transfer between genomes: protein-protein interologs and protein-DNA regulogs.","volume":"14","author":"H Yu","year":"2004","journal-title":"Genome Res"},{"key":"ref38","doi-asserted-by":"crossref","first-page":"2147","DOI":"10.1093\/molbev\/msi211","article-title":"How essential are nonessential genes?","volume":"22","author":"G Fang","year":"2005","journal-title":"Mol Biol Evol"},{"key":"ref39","doi-asserted-by":"crossref","first-page":"4285","DOI":"10.1073\/pnas.96.8.4285","article-title":"Assigning protein functions by comparative genome analysis: protein phylogenetic profiles.","volume":"96","author":"M Pellegrini","year":"1999","journal-title":"Proc Natl Acad Sci U S A"}],"container-title":["PLoS Computational Biology"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/dx.plos.org\/10.1371\/journal.pcbi.1000703","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2021,10,25]],"date-time":"2021-10-25T06:07:06Z","timestamp":1635142026000},"score":1,"resource":{"primary":{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.pcbi.1000703"}},"subtitle":[],"editor":[{"given":"Olga","family":"Troyanskaya","sequence":"first","affiliation":[]}],"short-title":[],"issued":{"date-parts":[[2010,3,26]]},"references-count":39,"journal-issue":{"issue":"3","published-online":{"date-parts":[[2010,3,26]]}},"URL":"https:\/\/doi.org\/10.1371\/journal.pcbi.1000703","relation":{},"ISSN":["1553-7358"],"issn-type":[{"value":"1553-7358","type":"electronic"}],"subject":[],"published":{"date-parts":[[2010,3,26]]}}}