{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,1,24]],"date-time":"2026-01-24T08:03:13Z","timestamp":1769241793413,"version":"3.49.0"},"reference-count":3,"publisher":"Oxford University Press (OUP)","issue":"13","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2014,7,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Summary: Here we present the open-source R\/ Bioconductor software package BEAT (BS-Seq Epimutation Analysis Toolkit). It implements all bioinformatics steps required for the quantitative high-resolution analysis of DNA methylation patterns from bisulfite sequencing data, including the detection of regional epimutation events, i.e. loss or gain of DNA methylation at CG positions relative to a reference. Using a binomial mixture model, the BEAT package aggregates methylation counts per genomic position, thereby compensating for low coverage, incomplete conversion and sequencing errors.<\/jats:p>\n               <jats:p>Availability and implementation: \u00a0BEAT is freely available as part of Bioconductor at www.bioconductor.org\/packages\/devel\/bioc\/html\/BEAT.html . The package is distributed under the GNU Lesser General Public License 3.0.<\/jats:p>\n               <jats:p>Contact: \u00a0akman@mpipz.mpg.de<\/jats:p>\n               <jats:p>Supplementary information: \u00a0Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btu142","type":"journal-article","created":{"date-parts":[[2014,3,12]],"date-time":"2014-03-12T00:16:49Z","timestamp":1394583409000},"page":"1933-1934","source":"Crossref","is-referenced-by-count":17,"title":["Genome-wide quantitative analysis of DNA methylation from bisulfite sequencing data"],"prefix":"10.1093","volume":"30","author":[{"given":"Kemal","family":"Akman","sequence":"first","affiliation":[{"name":"1 Tresch Group, Max Planck Institute for Plant Breeding Research, 50829 Cologne, Germany, 2 AG Haaf, Institute of Human Genetics, Julius Maximilians University, 97070 Wuerzburg, Germany and 3 Department of Genetics, Albert Einstein College of Medicine, Bronx, NY 10461, USA"}]},{"given":"Thomas","family":"Haaf","sequence":"additional","affiliation":[{"name":"1 Tresch Group, Max Planck Institute for Plant Breeding Research, 50829 Cologne, Germany, 2 AG Haaf, Institute of Human Genetics, Julius Maximilians University, 97070 Wuerzburg, Germany and 3 Department of Genetics, Albert Einstein College of Medicine, Bronx, NY 10461, USA"}]},{"given":"Silvia","family":"Gravina","sequence":"additional","affiliation":[{"name":"1 Tresch Group, Max Planck Institute for Plant Breeding Research, 50829 Cologne, Germany, 2 AG Haaf, Institute of Human Genetics, Julius Maximilians University, 97070 Wuerzburg, Germany and 3 Department of Genetics, Albert Einstein College of Medicine, Bronx, NY 10461, USA"}]},{"given":"Jan","family":"Vijg","sequence":"additional","affiliation":[{"name":"1 Tresch Group, Max Planck Institute for Plant Breeding Research, 50829 Cologne, Germany, 2 AG Haaf, Institute of Human Genetics, Julius Maximilians University, 97070 Wuerzburg, Germany and 3 Department of Genetics, Albert Einstein College of Medicine, Bronx, NY 10461, USA"}]},{"given":"Achim","family":"Tresch","sequence":"additional","affiliation":[{"name":"1 Tresch Group, Max Planck Institute for Plant Breeding Research, 50829 Cologne, Germany, 2 AG Haaf, Institute of Human Genetics, Julius Maximilians University, 97070 Wuerzburg, Germany and 3 Department of Genetics, Albert Einstein College of Medicine, Bronx, NY 10461, USA"}]}],"member":"286","published-online":{"date-parts":[[2014,3,10]]},"reference":[{"key":"2023012711182696300_btu142-B2","doi-asserted-by":"crossref","first-page":"632, 634, 636","DOI":"10.2144\/02333rv01","article-title":"DNA methylation: a profile of methods and applications","volume":"33","author":"Fraga","year":"2002","journal-title":"Biotechniques"},{"key":"2023012711182696300_btu142-B3","doi-asserted-by":"crossref","first-page":"1827","DOI":"10.1073\/pnas.89.5.1827","article-title":"A genomic sequencing protocol that yields a positive display of 5-methylcytosine residues in individual DNA strands","volume":"89","author":"Frommer","year":"1992","journal-title":"Proc. Natl Acad. Sci. USA"},{"key":"2023012711182696300_btu142-B4","doi-asserted-by":"crossref","first-page":"133","DOI":"10.1038\/nmeth.1414","article-title":"Genome-scale DNA methylation mapping of clinical samples at single-nucleotide resolution","volume":"7","author":"Gu","year":"2010","journal-title":"Nat. Methods"}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/30\/13\/1933\/48925314\/bioinformatics_30_13_1933.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/30\/13\/1933\/48925314\/bioinformatics_30_13_1933.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,1,27]],"date-time":"2023-01-27T11:34:02Z","timestamp":1674819242000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/30\/13\/1933\/2422274"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2014,3,10]]},"references-count":3,"journal-issue":{"issue":"13","published-print":{"date-parts":[[2014,7,1]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btu142","relation":{},"ISSN":["1367-4811","1367-4803"],"issn-type":[{"value":"1367-4811","type":"electronic"},{"value":"1367-4803","type":"print"}],"subject":[],"published-other":{"date-parts":[[2014,7,1]]},"published":{"date-parts":[[2014,3,10]]}}}