{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,10,6]],"date-time":"2025-10-06T17:52:36Z","timestamp":1759773156096},"reference-count":6,"publisher":"Oxford University Press (OUP)","issue":"16","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2011,8,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Summary: Methyl-Analyzer is a python package that analyzes genome-wide DNA methylation data produced by the Methyl-MAPS (methylation mapping analysis by paired-end sequencing) method. Methyl-MAPS is an enzymatic-based method that uses both methylation-sensitive and -dependent enzymes covering &amp;gt;80% of CpG dinucleotides within mammalian genomes. It combines enzymatic-based approaches with high-throughput next-generation sequencing technology to provide whole genome DNA methylation profiles. Methyl-Analyzer processes and integrates sequencing reads from methylated and unmethylated compartments and estimates CpG methylation probabilities at single base resolution.<\/jats:p>\n               <jats:p>Availability and implementation: Methyl-Analyzer is available at http:\/\/github.com\/epigenomics\/methylmaps. Sample dataset is available for download at http:\/\/epigenomicspub.columbia.edu\/methylanalyzer_data.html.<\/jats:p>\n               <jats:p>Contact: \u00a0fgh3@columbia.edu<\/jats:p>\n               <jats:p>Supplementary information: \u00a0Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btr356","type":"journal-article","created":{"date-parts":[[2011,6,18]],"date-time":"2011-06-18T04:15:07Z","timestamp":1308370507000},"page":"2296-2297","source":"Crossref","is-referenced-by-count":7,"title":["Methyl-Analyzer\u2014whole genome DNA methylation profiling"],"prefix":"10.1093","volume":"27","author":[{"given":"Yurong","family":"Xin","sequence":"first","affiliation":[{"name":"1 Department of Psychiatry, Columbia University and New York State Psychiatric Institute, New York, NY 10032 and 2Department of Neurology, Mount Sinai School of Medicine, New York, NY 10029, USA"}]},{"given":"Yongchao","family":"Ge","sequence":"additional","affiliation":[{"name":"1 Department of Psychiatry, Columbia University and New York State Psychiatric Institute, New York, NY 10032 and 2Department of Neurology, Mount Sinai School of Medicine, New York, NY 10029, USA"}]},{"given":"Fatemeh G.","family":"Haghighi","sequence":"additional","affiliation":[{"name":"1 Department of Psychiatry, Columbia University and New York State Psychiatric Institute, New York, NY 10032 and 2Department of Neurology, Mount Sinai School of Medicine, New York, NY 10029, USA"}]}],"member":"286","published-online":{"date-parts":[[2011,6,17]]},"reference":[{"key":"2023012511514517200_B1","doi-asserted-by":"crossref","first-page":"6","DOI":"10.1101\/gad.947102","article-title":"DNA methylation patterns and epigenetic memory","volume":"16","author":"Bird","year":"2002","journal-title":"Genes Dev."},{"key":"2023012511514517200_B2","doi-asserted-by":"crossref","first-page":"972","DOI":"10.1101\/gr.101535.109","article-title":"Chromatin and sequence features that define the fine and gross structure of genomic methylation patterns","volume":"20","author":"Edwards","year":"2010","journal-title":"Genome Res."},{"key":"2023012511514517200_B3","doi-asserted-by":"crossref","first-page":"1989","DOI":"10.1016\/j.yexcr.2006.03.006","article-title":"LUMA (LUminometric Methylation Assay)\u2013a high throughput method to the analysis of genomic DNA methylation","volume":"312","author":"Karimi","year":"2006","journal-title":"Exp Cell Res."},{"key":"2023012511514517200_B4","doi-asserted-by":"crossref","first-page":"89","DOI":"10.1016\/j.tibs.2005.12.008","article-title":"Genomic DNA methylation: the mark and its mediators","volume":"31","author":"Klose","year":"2006","journal-title":"Trends Biochem Sci."},{"key":"2023012511514517200_B5","doi-asserted-by":"crossref","first-page":"587","DOI":"10.2217\/epi.10.36","article-title":"Protocol matters: which methylome are you actually studying?","volume":"2","author":"Robinson","year":"2010","journal-title":"Epigenomics"},{"key":"2023012511514517200_B6","doi-asserted-by":"crossref","first-page":"157","DOI":"10.1101\/gr.4362006","article-title":"Large-scale structure of genomic methylation patterns","volume":"16","author":"Rollins","year":"2006","journal-title":"Genome Res."}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/27\/16\/2296\/48864979\/bioinformatics_27_16_2296.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/27\/16\/2296\/48864979\/bioinformatics_27_16_2296.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,1,25]],"date-time":"2023-01-25T11:52:01Z","timestamp":1674647521000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/27\/16\/2296\/253768"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2011,6,17]]},"references-count":6,"journal-issue":{"issue":"16","published-print":{"date-parts":[[2011,8,15]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btr356","relation":{},"ISSN":["1367-4811","1367-4803"],"issn-type":[{"value":"1367-4811","type":"electronic"},{"value":"1367-4803","type":"print"}],"subject":[],"published-other":{"date-parts":[[2011,8,15]]},"published":{"date-parts":[[2011,6,17]]}}}