{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,10,17]],"date-time":"2025-10-17T13:25:57Z","timestamp":1760707557765},"reference-count":13,"publisher":"Springer Science and Business Media LLC","issue":"1","content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["BMC Bioinformatics"],"abstract":"<jats:title>Abstract<\/jats:title><jats:sec>\n                <jats:title>Background<\/jats:title>\n                <jats:p>As genomes evolve after speciation, gene content, coding sequence, gene expression, and splicing all diverge with time from ancestors with close relatives. A minimum evolution general method for continuous character analysis in a phylogenetic perspective is presented that allows for reconstruction of ancestral character states and for measuring along branch evolution.<\/jats:p>\n              <\/jats:sec><jats:sec>\n                <jats:title>Results<\/jats:title>\n                <jats:p>A software package for reconstruction of continuous character traits, like relative gene expression levels or alternative splice site usage data is presented and is available for download at <jats:ext-link xmlns:xlink=\"http:\/\/www.w3.org\/1999\/xlink\" ext-link-type=\"uri\" xlink:href=\"http:\/\/www.rossnes.org\/phyrex\">http:\/\/www.rossnes.org\/phyrex<\/jats:ext-link>. This program was applied to a primate gene expression dataset to detect transcription factor binding sites that have undergone substitution, potentially having driven lineage-specific differences in gene expression.<\/jats:p>\n              <\/jats:sec><jats:sec>\n                <jats:title>Conclusion<\/jats:title>\n                <jats:p>Systematic analysis of lineage-specific evolution is becoming the cornerstone of comparative genomics. New methods, like phyrex, extend the capabilities of comparative genomics by tracing the evolution of additional biomolecular processes.<\/jats:p>\n              <\/jats:sec>","DOI":"10.1186\/1471-2105-6-127","type":"journal-article","created":{"date-parts":[[2005,5,27]],"date-time":"2005-05-27T18:48:43Z","timestamp":1117219723000},"update-policy":"http:\/\/dx.doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":6,"title":["Phylogenetic reconstruction of ancestral character states for gene expression and mRNA splicing data"],"prefix":"10.1186","volume":"6","author":[{"given":"Roald","family":"Rossnes","sequence":"first","affiliation":[]},{"given":"Ingvar","family":"Eidhammer","sequence":"additional","affiliation":[]},{"given":"David A","family":"Liberles","sequence":"additional","affiliation":[]}],"member":"297","published-online":{"date-parts":[[2005,5,27]]},"reference":[{"key":"452_CR1","doi-asserted-by":"publisher","first-page":"D495","DOI":"10.1093\/nar\/gki090","volume":"33","author":"C Roth","year":"2005","unstructured":"Roth C, Betts MJ, Steffansson P, Saelensminde G, Liberles DA: The Adaptive Evolution Database (TAED): A phylogeny based tool for comparative genomics. 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