{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,6,20]],"date-time":"2026-06-20T06:34:23Z","timestamp":1781937263250,"version":"3.54.5"},"reference-count":14,"publisher":"Hindawi Limited","license":[{"start":{"date-parts":[[2010,5,6]],"date-time":"2010-05-06T00:00:00Z","timestamp":1273104000000},"content-version":"unspecified","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/3.0\/"}],"funder":[{"name":"European Union Marie Curie International Reintegration Grant","award":["PIRG05-GA-2009-248639"],"award-info":[{"award-number":["PIRG05-GA-2009-248639"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Advances in Bioinformatics"],"published-print":{"date-parts":[[2010,5,6]]},"abstract":"<jats:p>Evolutionary binary characters are features of species or genes, indicating the absence (value zero) or presence (value one) of some property. Examples include eukaryotic gene architecture (the presence or absence of an intron in a particular locus), gene content, and morphological characters. In many studies, the acquisition of such binary characters is assumed to represent a rare evolutionary event, and consequently, their evolution is analyzed using various flavors of parsimony. However, when gain and loss of the character are not rare enough, a probabilistic analysis becomes essential. Here, we present a comprehensive probabilistic model to describe the evolution of binary characters on a bifurcating phylogenetic tree. A fast software tool, EREM, is provided, using maximum likelihood to estimate the parameters of the model and to reconstruct ancestral states (presence and absence in internal nodes) and events (gain and loss events along branches).<\/jats:p>","DOI":"10.1155\/2010\/167408","type":"journal-article","created":{"date-parts":[[2010,5,6]],"date-time":"2010-05-06T14:58:54Z","timestamp":1273157934000},"page":"1-4","source":"Crossref","is-referenced-by-count":6,"title":["EREM: Parameter Estimation and Ancestral Reconstruction by Expectation-Maximization Algorithm for a Probabilistic Model of Genomic Binary Characters Evolution"],"prefix":"10.1155","volume":"2010","author":[{"given":"Liran","family":"Carmel","sequence":"first","affiliation":[{"name":"Department of Genetics, The Alexander Silberman Institute of Life Sciences, Faculty of Science, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat Ram, Jerusalem 91904, Israel"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yuri I.","family":"Wolf","sequence":"additional","affiliation":[{"name":"National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Igor B.","family":"Rogozin","sequence":"additional","affiliation":[{"name":"National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Eugene V.","family":"Koonin","sequence":"additional","affiliation":[{"name":"National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"98","reference":[{"key":"1","year":"2004"},{"key":"2","doi-asserted-by":"publisher","DOI":"10.1093\/molbev\/msm088"},{"key":"3","year":"2005"},{"key":"4","year":"2003"},{"issue":"10","key":"5","doi-asserted-by":"crossref","first-page":"1368","DOI":"10.1093\/oxfordjournals.molbev.a025583","volume":"13","year":"1996","journal-title":"Molecular Biology and Evolution"},{"key":"6","doi-asserted-by":"publisher","DOI":"10.1006\/jmbi.2002.5405"},{"key":"7","doi-asserted-by":"publisher","DOI":"10.1093\/molbev\/msh039"},{"issue":"11","key":"8","doi-asserted-by":"crossref","first-page":"4164","DOI":"10.1073\/pnas.73.11.4164","volume":"73","year":"1976","journal-title":"Proceedings of the National Academy of Sciences of the United States of America"},{"issue":"3988","key":"9","doi-asserted-by":"crossref","first-page":"1089","DOI":"10.1126\/science.172.3988.1089","volume":"172","year":"1971","journal-title":"Science"},{"key":"10","doi-asserted-by":"publisher","DOI":"10.1007\/11554714_4"},{"key":"11","doi-asserted-by":"publisher","DOI":"10.1186\/1471-2148-7-192"},{"key":"12","doi-asserted-by":"publisher","DOI":"10.1101\/gr.6438607"},{"key":"13","doi-asserted-by":"publisher","DOI":"10.1101\/gr.5978207"},{"key":"14","doi-asserted-by":"publisher","DOI":"10.1186\/gb-2007-8-10-r223"}],"container-title":["Advances in Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/downloads.hindawi.com\/archive\/2010\/167408.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"http:\/\/downloads.hindawi.com\/archive\/2010\/167408.xml","content-type":"application\/xml","content-version":"vor","intended-application":"text-mining"},{"URL":"http:\/\/downloads.hindawi.com\/archive\/2010\/167408.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2020,12,8]],"date-time":"2020-12-08T21:10:29Z","timestamp":1607461829000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.hindawi.com\/journals\/abi\/2010\/167408\/"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2010,5,6]]},"references-count":14,"alternative-id":["167408","167408"],"URL":"https:\/\/doi.org\/10.1155\/2010\/167408","relation":{},"ISSN":["1687-8027","1687-8035"],"issn-type":[{"value":"1687-8027","type":"print"},{"value":"1687-8035","type":"electronic"}],"subject":[],"published":{"date-parts":[[2010,5,6]]}}}