{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,1,8]],"date-time":"2026-01-08T00:55:12Z","timestamp":1767833712244,"version":"3.49.0"},"reference-count":19,"publisher":"Oxford University Press (OUP)","issue":"24","license":[{"start":{"date-parts":[[2022,10,21]],"date-time":"2022-10-21T00:00:00Z","timestamp":1666310400000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100002428","name":"Austrian Science Fund","doi-asserted-by":"publisher","award":["P32190"],"award-info":[{"award-number":["P32190"]}],"id":[{"id":"10.13039\/501100002428","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2022,12,13]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Summary<\/jats:title>\n                  <jats:p>Current approaches detect conserved genomic order either at chromosomal (macrosynteny) or at subchromosomal scales (microsynteny). The latter generally requires collinearity and hard thresholds on syntenic region size, thus excluding a major proportion of syntenies with recent expansions or minor rearrangements. \u2018SYNPHONI\u2019 bridges the gap between micro- and macrosynteny detection, providing detailed information on both synteny conservation and transformation throughout the evolutionary history of animal genomes.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>Source code is freely available at https:\/\/github.com\/nsmro\/SYNPHONI, implemented in Python 3.9.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Supplementary information<\/jats:title>\n                  <jats:p>Supplementary data are available at Bioinformatics online.<\/jats:p>\n               <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btac695","type":"journal-article","created":{"date-parts":[[2022,10,21]],"date-time":"2022-10-21T15:45:05Z","timestamp":1666367105000},"page":"5434-5436","source":"Crossref","is-referenced-by-count":8,"title":["SYNPHONI: scale-free and phylogeny-aware reconstruction of synteny conservation and transformation across animal genomes"],"prefix":"10.1093","volume":"38","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-7367-2241","authenticated-orcid":false,"given":"Nicolas Serge Matthieu","family":"Robert","sequence":"first","affiliation":[{"name":"Department of Neurosciences and Developmental Biology, University of Vienna , Vienna A-1030, Austria"}]},{"given":"Fatih","family":"Sarigol","sequence":"additional","affiliation":[{"name":"Department of Neurosciences and Developmental Biology, University of Vienna , Vienna A-1030, Austria"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-3266-834X","authenticated-orcid":false,"given":"Elisabeth","family":"Zieger","sequence":"additional","affiliation":[{"name":"Department of Evolutionary Biology, University of Vienna , Vienna A-1030, Austria"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-3585-4511","authenticated-orcid":false,"given":"Oleg","family":"Simakov","sequence":"additional","affiliation":[{"name":"Department of Neurosciences and Developmental Biology, University of Vienna , Vienna A-1030, Austria"}]}],"member":"286","published-online":{"date-parts":[[2022,10,21]]},"reference":[{"key":"2022121418363035700_btac695-B2","doi-asserted-by":"crossref","first-page":"2356","DOI":"10.1101\/gr.139725.112","article-title":"Extensive conservation of ancient microsynteny across metazoans due to cis-regulatory constraints","volume":"22","author":"Irimia","year":"2012","journal-title":"Genome Res"},{"key":"2022121418363035700_btac695-B3","doi-asserted-by":"crossref","first-page":"e112341","DOI":"10.1371\/journal.pone.0112341","article-title":"Analysis of micro-rearrangements in 25 eukaryotic species pairs by SyntenyMapper","volume":"9","author":"Kaufmann","year":"2014","journal-title":"PLoS One"},{"key":"2022121418363035700_btac695-B4","doi-asserted-by":"crossref","first-page":"545","DOI":"10.1101\/gr.6086307","article-title":"Genomic regulatory blocks encompass multiple neighboring genes and maintain conserved synteny in vertebrates","volume":"17","author":"Kikuta","year":"2007","journal-title":"Genome Res"},{"key":"2022121418363035700_btac695-B5","doi-asserted-by":"crossref","first-page":"E5379","DOI":"10.1073\/pnas.1702012114","article-title":"Reconstruction and evolutionary history of eutherian chromosomes","volume":"114","author":"Kim","year":"2017","journal-title":"Proc. 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