{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,17]],"date-time":"2026-02-17T11:07:43Z","timestamp":1771326463465,"version":"3.50.1"},"reference-count":14,"publisher":"Oxford University Press (OUP)","issue":"8","license":[{"start":{"date-parts":[[2016,10,2]],"date-time":"2016-10-02T00:00:00Z","timestamp":1475366400000},"content-version":"vor","delay-in-days":2412,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc\/2.0\/uk\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2010,4,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Summary: Comparative genomics remains a pivotal strategy to study the evolution of gene organization, and this primacy is reinforced by the growing number of full genome sequences available in public repositories. Despite this growth, bioinformatic tools available to visualize and compare genomes and to infer evolutionary events remain restricted to two or three genomes at a time, thus limiting the breadth and the nature of the question that can be investigated. Here we present Genomicus, a new synteny browser that can represent and compare unlimited numbers of genomes in a broad phylogenetic view. In addition, Genomicus includes reconstructed ancestral gene organization, thus greatly facilitating the interpretation of the data.<\/jats:p>\n               <jats:p>Availability: Genomicus is freely available for online use at http:\/\/www.dyogen.ens.fr\/genomicus while data can be downloaded at ftp:\/\/ftp.biologie.ens.fr\/pub\/dyogen\/genomicus<\/jats:p>\n               <jats:p>Contact: \u00a0hrc@biologie.ens.fr<\/jats:p>","DOI":"10.1093\/bioinformatics\/btq079","type":"journal-article","created":{"date-parts":[[2010,2,26]],"date-time":"2010-02-26T01:13:25Z","timestamp":1267146805000},"page":"1119-1121","source":"Crossref","is-referenced-by-count":199,"title":["Genomicus: a database and a browser to study gene synteny in modern and ancestral genomes"],"prefix":"10.1093","volume":"26","author":[{"given":"Matthieu","family":"Muffato","sequence":"first","affiliation":[{"name":"Dyogen Group, Institut de Biologie de l'Ecole Normale Sup\u00e9rieure (IBENS), Centre National de la Recherche Scientifique UMR8197, Institut National de la Sant\u00e9 et de la Recherche M\u00e9dicale U1024, 75005 Paris, France"}]},{"given":"Alexandra","family":"Louis","sequence":"additional","affiliation":[{"name":"Dyogen Group, Institut de Biologie de l'Ecole Normale Sup\u00e9rieure (IBENS), Centre National de la Recherche Scientifique UMR8197, Institut National de la Sant\u00e9 et de la Recherche M\u00e9dicale U1024, 75005 Paris, France"}]},{"given":"Charles-Edouard","family":"Poisnel","sequence":"additional","affiliation":[{"name":"Dyogen Group, Institut de Biologie de l'Ecole Normale Sup\u00e9rieure (IBENS), Centre National de la Recherche Scientifique UMR8197, Institut National de la Sant\u00e9 et de la Recherche M\u00e9dicale U1024, 75005 Paris, France"}]},{"given":"Hugues Roest","family":"Crollius","sequence":"additional","affiliation":[{"name":"Dyogen Group, Institut de Biologie de l'Ecole Normale Sup\u00e9rieure (IBENS), Centre National de la Recherche Scientifique UMR8197, Institut National de la Sant\u00e9 et de la Recherche M\u00e9dicale U1024, 75005 Paris, France"}]}],"member":"286","published-online":{"date-parts":[[2010,2,24]]},"reference":[{"key":"2023012508075998000_B1","doi-asserted-by":"crossref","first-page":"943","DOI":"10.1101\/gr.082784.108","article-title":"Breakpoint graphs and ancestral genome reconstructions","volume":"19","author":"Alekseyev","year":"2009","journal-title":"Genome Res."},{"key":"2023012508075998000_B2","first-page":"26","article-title":"Genome-scale evolution: reconstructing gene orders in the ancestral species","volume":"12","author":"Bourque","year":"2002","journal-title":"Genome Res."},{"key":"2023012508075998000_B3","doi-asserted-by":"crossref","first-page":"1456","DOI":"10.1101\/gr.3672305","article-title":"The Yeast Gene Order Browser: combining curated homology and syntenic context reveals gene fate in polyploid species","volume":"15","author":"Byrne","year":"2005","journal-title":"Genome Res."},{"key":"2023012508075998000_B4","doi-asserted-by":"crossref","first-page":"D485","DOI":"10.1093\/nar\/gkm805","article-title":"Narcisse: a mirror view of conserved syntenies","volume":"36","author":"Courcelle","year":"2008","journal-title":"Nucleic Acids Res."},{"key":"2023012508075998000_B5","doi-asserted-by":"crossref","first-page":"498","DOI":"10.1093\/bioinformatics\/btl618","article-title":"AutoGRAPH: an interactive web server for automating and visualizing comparative genome maps","volume":"23","author":"Derrien","year":"2007","journal-title":"Bioinformatics"},{"key":"2023012508075998000_B6","doi-asserted-by":"crossref","first-page":"R86","DOI":"10.1186\/gb-2009-10-8-r86","article-title":"Synorth: exploring the evolution of synteny and long-range regulatory interactions in vertebrate genomes","volume":"10","author":"Dong","year":"2009","journal-title":"Genome Biol."},{"key":"2023012508075998000_B7","doi-asserted-by":"crossref","first-page":"D690","DOI":"10.1093\/nar\/gkn828","article-title":"Ensembl 2009","volume":"37","author":"Hubbard","year":"2009","journal-title":"Nucleic Acids Res."},{"key":"2023012508075998000_B8","doi-asserted-by":"crossref","first-page":"D412","DOI":"10.1093\/nar\/gkn760","article-title":"STRING 8\u2013a global view on proteins and their functional interactions in 630 organisms","volume":"37","author":"Jensen","year":"2009","journal-title":"Nucleic Acids Res."},{"key":"2023012508075998000_B9","doi-asserted-by":"crossref","first-page":"1772","DOI":"10.1104\/pp.108.124867","article-title":"Finding and comparing syntenic regions among Arabidopsis and the outgroups papaya, poplar, and grape: CoGe with rosids","volume":"148","author":"Lyons","year":"2008","journal-title":"Plant Physiol."},{"key":"2023012508075998000_B10","doi-asserted-by":"crossref","first-page":"1557","DOI":"10.1101\/gr.5383506","article-title":"Reconstructing contiguous regions of an ancestral genome","volume":"16","author":"Ma","year":"2006","journal-title":"Genome Res."},{"key":"2023012508075998000_B11","doi-asserted-by":"crossref","first-page":"3461","DOI":"10.1093\/bioinformatics\/bti555","article-title":"SynBrowse: a synteny browser for comparative sequence analysis","volume":"21","author":"Pan","year":"2005","journal-title":"Bioinformatics"},{"key":"2023012508075998000_B12","doi-asserted-by":"crossref","first-page":"1795","DOI":"10.1093\/molbev\/msn104","article-title":"Confirming the phylogeny of mammals by use of large comparative sequence data sets","volume":"25","author":"Prasad","year":"2008","journal-title":"Mol. Biol. Evol."},{"key":"2023012508075998000_B13","doi-asserted-by":"crossref","first-page":"82","DOI":"10.1186\/1471-2105-8-82","article-title":"Cinteny: flexible analysis and visualization of synteny and genome rearrangements in multiple organisms","volume":"8","author":"Sinha","year":"2007","journal-title":"BMC Bioinformatics"},{"key":"2023012508075998000_B14","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":"Vilella","year":"2009","journal-title":"Genome Res."}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/26\/8\/1119\/48856850\/bioinformatics_26_8_1119.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/26\/8\/1119\/48856850\/bioinformatics_26_8_1119.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,1,25]],"date-time":"2023-01-25T08:11:58Z","timestamp":1674634318000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/26\/8\/1119\/206096"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2010,2,24]]},"references-count":14,"journal-issue":{"issue":"8","published-print":{"date-parts":[[2010,4,15]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btq079","relation":{},"ISSN":["1367-4811","1367-4803"],"issn-type":[{"value":"1367-4811","type":"electronic"},{"value":"1367-4803","type":"print"}],"subject":[],"published-other":{"date-parts":[[2010,4,15]]},"published":{"date-parts":[[2010,2,24]]}}}