{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,1,9]],"date-time":"2026-01-09T14:39:17Z","timestamp":1767969557861,"version":"3.49.0"},"reference-count":10,"publisher":"Oxford University Press (OUP)","issue":"11","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2007,6,1]]},"abstract":"<jats:title>Abstract<\/jats:title><jats:p>Summary: The advent of high-density, high-volume genomic data has created the need for tools to summarize large datasets at multiple scales. HMMSeg is a command-line utility for the scale-specific segmentation of continuous genomic data using hidden Markov models (HMMs). Scale specificity is achieved by an optional wavelet-based smoothing operation. HMMSeg is capable of handling multiple datasets simultaneously, rendering it ideal for integrative analysis of expression, phylogenetic and functional genomic data.<\/jats:p><jats:p>Availability: http:\/\/noble.gs.washington.edu\/proj\/hmmseg<\/jats:p><jats:p>Contact: rthurman@u.washington.edu<\/jats:p>","DOI":"10.1093\/bioinformatics\/btm096","type":"journal-article","created":{"date-parts":[[2007,3,24]],"date-time":"2007-03-24T00:22:51Z","timestamp":1174695771000},"page":"1424-1426","source":"Crossref","is-referenced-by-count":98,"title":["Unsupervised segmentation of continuous genomic data"],"prefix":"10.1093","volume":"23","author":[{"given":"Nathan","family":"Day","sequence":"first","affiliation":[{"name":"1 Department of Computer Science and Engineering, 2Division of Medical Genetics, and 3Department of Genome Sciences, University of Washington, Seattle, WA, USA"}]},{"given":"Andrew","family":"Hemmaplardh","sequence":"additional","affiliation":[{"name":"1 Department of Computer Science and Engineering, 2Division of Medical Genetics, and 3Department of Genome Sciences, University of Washington, Seattle, WA, USA"}]},{"given":"Robert E.","family":"Thurman","sequence":"additional","affiliation":[{"name":"1 Department of Computer Science and Engineering, 2Division of Medical Genetics, and 3Department of Genome Sciences, University of Washington, Seattle, WA, USA"},{"name":"1 Department of Computer Science and Engineering, 2Division of Medical Genetics, and 3Department of Genome Sciences, University of Washington, Seattle, WA, USA"}]},{"given":"John A.","family":"Stamatoyannopoulos","sequence":"additional","affiliation":[{"name":"1 Department of Computer Science and Engineering, 2Division of Medical Genetics, and 3Department of Genome Sciences, University of Washington, Seattle, WA, USA"}]},{"given":"William S.","family":"Noble","sequence":"additional","affiliation":[]}],"member":"286","published-online":{"date-parts":[[2007,3,23]]},"reference":[{"key":"2023041104583305200_","first-page":"114","article-title":"Multiple alignment using hidden Markov models","author":"Eddy","year":"1995"},{"key":"2023041104583305200_","doi-asserted-by":"crossref","first-page":"636","DOI":"10.1126\/science.1105136","article-title":"The ENCODE (ENCyclopedia Of DNA Elements) project","volume":"306","author":"ENCODE Consortium","year":"2004","journal-title":"Science"},{"key":"2023041104583305200_","article-title":"Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project","author":"ENCODE Consortium","year":"2007","journal-title":"Nature"},{"key":"2023041104583305200_","doi-asserted-by":"crossref","first-page":"996","DOI":"10.1101\/gr.229102","article-title":"The human genome browser at UCSC","volume":"12","author":"Kent","year":"2002","journal-title":"Genome Res"},{"key":"2023041104583305200_","doi-asserted-by":"crossref","first-page":"2","DOI":"10.1093\/bioinformatics\/19.1.2","article-title":"Wavelets in bioinformatics and compuataional biology: state of art and perspectives","volume":"19","author":"Li\u00f2","year":"2003","journal-title":"Bioinformatics"},{"key":"2023041104583305200_","doi-asserted-by":"crossref","first-page":"2878","DOI":"10.1093\/bioinformatics\/bth315","article-title":"Tigrscan and GlimmerHMM: two open source ab initio eukaryotic gene-finders","volume":"20","author":"Majoros","year":"2004","journal-title":"Bioinformatics"},{"key":"2023041104583305200_","doi-asserted-by":"crossref","DOI":"10.1017\/CBO9780511841040","volume-title":"Wavelet Methods for Time Series Analysis","author":"Percival","year":"2000"},{"key":"2023041104583305200_","first-page":"257","article-title":"A tutorial on hidden Markov models and selected applications in speech recognition","author":"Rabiner","year":"1989"},{"key":"2023041104583305200_","doi-asserted-by":"crossref","DOI":"10.1101\/gr.6081407","article-title":"Stamatoyannopoulos. 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