{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,7]],"date-time":"2026-03-07T15:14:47Z","timestamp":1772896487603,"version":"3.50.1"},"reference-count":0,"publisher":"Oxford University Press (OUP)","issue":"suppl_1","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2003,7,3]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Motivation: The discovery of cis-regulatory modules in metazoan genomes is crucial for understanding the connection between genes and organism diversity.<\/jats:p>\n               <jats:p>Results: We develop a computational method that uses Hidden Markov Models and an Expectation Maximization algorithm to detect such modules, given the weight matrices of a set of transcription factors known to work together. Two novel features of our probabilistic model are: (i) correlations between binding sites, known to be required for module activity, are exploited, and (ii) phylogenetic comparisons among sequences from multiple species are made to highlight a regulatory module. The novel features are shown to improve detection of modules, in experiments on synthetic as well as biological data.<\/jats:p>\n               <jats:p>Availability: The source code for the programs is available upon request from the authors.<\/jats:p>\n               <jats:p>Contact: {saurabh,erik,siggia}@lonnrot.rockefeller.edu<\/jats:p>\n               <jats:p>Keywords: hidden Markov model, cis-regulatory modules, motif correlations, phylogenetic comparison<\/jats:p>\n               <jats:p>*To whom correspondence should be addressed.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btg1040","type":"journal-article","created":{"date-parts":[[2003,7,10]],"date-time":"2003-07-10T23:49:03Z","timestamp":1057880943000},"page":"i292-i301","source":"Crossref","is-referenced-by-count":139,"title":["A probabilistic method to detect regulatory modules"],"prefix":"10.1093","volume":"19","author":[{"given":"Saurabh","family":"Sinha","sequence":"first","affiliation":[{"name":"Center for Studies in Physics and Biology, The Rockefeller University, New York, NY 0021, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Erik","family":"van Nimwegen","sequence":"additional","affiliation":[{"name":"Center for Studies in Physics and Biology, The Rockefeller University, New York, NY 0021, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Eric D.","family":"Siggia","sequence":"additional","affiliation":[{"name":"Center for Studies in Physics and Biology, The Rockefeller University, New York, NY 0021, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2003,7,3]]},"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/19\/suppl_1\/i292\/228197","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/19\/suppl_1\/i292\/228197","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,1,25]],"date-time":"2023-01-25T18:46:11Z","timestamp":1674672371000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/19\/suppl_1\/i292\/228197"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2003,7,3]]},"references-count":0,"journal-issue":{"issue":"suppl_1","published-print":{"date-parts":[[2003,7,3]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btg1040","relation":{},"ISSN":["1367-4811","1367-4803"],"issn-type":[{"value":"1367-4811","type":"electronic"},{"value":"1367-4803","type":"print"}],"subject":[],"published-other":{"date-parts":[[2003,7,3]]},"published":{"date-parts":[[2003,7,3]]}}}