{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,10,19]],"date-time":"2025-10-19T18:16:43Z","timestamp":1760897803445,"version":"3.30.2"},"reference-count":42,"publisher":"Oxford University Press (OUP)","issue":"16","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2007,8,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Motivation: Finding the regulatory modules for transcription factors binding is an important step in elucidating the complex molecular mechanisms underlying regulation of gene expression. There are numerous methods available for solving this problem, however, very few of them take advantage of the increasing availability of comparative genomic data.<\/jats:p>\n               <jats:p>Results: We develop a method for finding regulatory modules in Eukaryotic species using phylogenetic data. Using computer simulations and analysis of real data, we show that the use of phylogenetic hidden Markov model can lead to an increase in accuracy of prediction over methods that do not take advantage of the data from multiple species.<\/jats:p>\n               <jats:p>Availability: The new method is made accessible under GPL in a new publicly available JAVA program: EvoPromoter. It can be downloaded at http:\/\/sourceforge.net\/projects\/evopromoter\/<\/jats:p>\n               <jats:p>Contact: \u00a0sww8@cornell.edu<\/jats:p>","DOI":"10.1093\/bioinformatics\/btm299","type":"journal-article","created":{"date-parts":[[2007,6,6]],"date-time":"2007-06-06T01:48:58Z","timestamp":1181094538000},"page":"2031-2037","source":"Crossref","is-referenced-by-count":8,"title":["Finding <i>cis<\/i>-regulatory modules in <i>Drosophila<\/i> using phylogenetic hidden Markov models"],"prefix":"10.1093","volume":"23","author":[{"given":"Wendy S.W.","family":"Wong","sequence":"first","affiliation":[{"name":"1 Department of Biological Statistics and Computational Biology, Cornell University, Ithaca, NY 14853, USA, 2Department of Biology and Center for Comparative Genomics, University of Copenhagen, Universitetsparken 15, 2100 Kbh \u00d8, Denmark and 3Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK"},{"name":"1 Department of Biological Statistics and Computational Biology, Cornell University, Ithaca, NY 14853, USA, 2Department of Biology and Center for Comparative Genomics, University of Copenhagen, Universitetsparken 15, 2100 Kbh \u00d8, Denmark and 3Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK"}]},{"given":"Rasmus","family":"Nielsen","sequence":"additional","affiliation":[{"name":"1 Department of Biological Statistics and Computational Biology, Cornell University, Ithaca, NY 14853, USA, 2Department of Biology and Center for Comparative Genomics, University of Copenhagen, Universitetsparken 15, 2100 Kbh \u00d8, Denmark and 3Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK"}]}],"member":"286","published-online":{"date-parts":[[2007,6,5]]},"reference":[{"key":"2024121117585958300_B1","doi-asserted-by":"crossref","first-page":"W195","DOI":"10.1093\/nar\/gkh387","article-title":"MSCAN: identification of functional clusters of transcription factor binding sites","volume":"32","author":"Alkema","year":"2004","journal-title":"Nucleic Acids Res"},{"key":"2024121117585958300_B2","doi-asserted-by":"crossref","first-page":"14","DOI":"10.1186\/1748-7188-1-14","article-title":"A phylogenetic generalized hidden Markov model for predicting alternatively spliced exons","volume":"1","author":"Allen","year":"2006","journal-title":"Algorithms Mol. 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