{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2023,2,2]],"date-time":"2023-02-02T00:40:12Z","timestamp":1675298412438},"reference-count":6,"publisher":"Oxford University Press (OUP)","issue":"12","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2015,6,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Summary: Currently available bisulfite sequencing tools frequently suffer from low mapping rates and low methylation calls, especially for data generated from the Illumina sequencer, NextSeq. Here, we introduce a sequential trimming-and-retrieving alignment approach for investigating DNA methylation patterns, which significantly improves the number of mapped reads and covered CpG sites. The method is implemented in an automated analysis toolkit for processing bisulfite sequencing reads.<\/jats:p>\n               <jats:p>Availability and implementation: \u00a0http:\/\/mysbfiles.stonybrook.edu\/~xuefenwang\/software.html and https:\/\/github.com\/xfwang\/BStools.<\/jats:p>\n               <jats:p>Contact: \u00a0xuefeng.wang@stonybrook.edu<\/jats:p>\n               <jats:p>Supplementary information: \u00a0Supplementary materials are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btv089","type":"journal-article","created":{"date-parts":[[2015,2,14]],"date-time":"2015-02-14T05:33:46Z","timestamp":1423892026000},"page":"2040-2042","source":"Crossref","is-referenced-by-count":2,"title":["A trimming-and-retrieving alignment scheme for reduced representation bisulfite sequencing"],"prefix":"10.1093","volume":"31","author":[{"given":"Xuefeng","family":"Wang","sequence":"first","affiliation":[{"name":"1 Department of Preventive Medicine, 2Department of Biomedical Informatics, and 3Department of Applied Mathematics and Statistics, Stony Brook University, Stony Brook, NY 11794, 4Department of Biostatistics, Yale University, New Haven, CT 06520, 5Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, 6Department of Pathology, Stony Brook University, Stony Brook, NY 11794, 7Department of Medicine, Washington University St Louis, St Louis, MO 63110 and 8Department of Medicine, Stony Brook University, Stony Brook, NY 11794, USA"},{"name":"1 Department of Preventive Medicine, 2Department of Biomedical Informatics, and 3Department of Applied Mathematics and Statistics, Stony Brook University, Stony Brook, NY 11794, 4Department of Biostatistics, Yale University, New Haven, CT 06520, 5Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, 6Department of Pathology, Stony Brook University, Stony Brook, NY 11794, 7Department of Medicine, Washington University St Louis, St Louis, MO 63110 and 8Department of Medicine, Stony Brook University, Stony Brook, NY 11794, USA"},{"name":"1 Department of Preventive Medicine, 2Department of Biomedical Informatics, and 3Department of Applied Mathematics and Statistics, Stony Brook University, Stony Brook, NY 11794, 4Department of Biostatistics, Yale University, New Haven, CT 06520, 5Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, 6Department of Pathology, Stony Brook University, Stony Brook, NY 11794, 7Department of Medicine, Washington University St Louis, St Louis, MO 63110 and 8Department of Medicine, Stony Brook University, Stony Brook, NY 11794, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Xiaoqing","family":"Yu","sequence":"additional","affiliation":[{"name":"1 Department of Preventive Medicine, 2Department of Biomedical Informatics, and 3Department of Applied Mathematics and Statistics, Stony Brook University, Stony Brook, NY 11794, 4Department of Biostatistics, Yale University, New Haven, CT 06520, 5Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, 6Department of Pathology, Stony Brook University, Stony Brook, NY 11794, 7Department of Medicine, Washington University St Louis, St Louis, MO 63110 and 8Department of Medicine, Stony Brook University, Stony Brook, NY 11794, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Wei","family":"Zhu","sequence":"additional","affiliation":[{"name":"1 Department of Preventive Medicine, 2Department of Biomedical Informatics, and 3Department of Applied Mathematics and Statistics, Stony Brook University, Stony Brook, NY 11794, 4Department of Biostatistics, Yale University, New Haven, CT 06520, 5Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, 6Department of Pathology, Stony Brook University, Stony Brook, NY 11794, 7Department of Medicine, Washington University St Louis, St Louis, MO 63110 and 8Department of Medicine, Stony Brook University, Stony Brook, NY 11794, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"W. Richard","family":"McCombie","sequence":"additional","affiliation":[{"name":"1 Department of Preventive Medicine, 2Department of Biomedical Informatics, and 3Department of Applied Mathematics and Statistics, Stony Brook University, Stony Brook, NY 11794, 4Department of Biostatistics, Yale University, New Haven, CT 06520, 5Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, 6Department of Pathology, Stony Brook University, Stony Brook, NY 11794, 7Department of Medicine, Washington University St Louis, St Louis, MO 63110 and 8Department of Medicine, Stony Brook University, Stony Brook, NY 11794, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Eric","family":"Antoniou","sequence":"additional","affiliation":[{"name":"1 Department of Preventive Medicine, 2Department of Biomedical Informatics, and 3Department of Applied Mathematics and Statistics, Stony Brook University, Stony Brook, NY 11794, 4Department of Biostatistics, Yale University, New Haven, CT 06520, 5Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, 6Department of Pathology, Stony Brook University, Stony Brook, NY 11794, 7Department of Medicine, Washington University St Louis, St Louis, MO 63110 and 8Department of Medicine, Stony Brook University, Stony Brook, NY 11794, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"R. Scott","family":"Powers","sequence":"additional","affiliation":[{"name":"1 Department of Preventive Medicine, 2Department of Biomedical Informatics, and 3Department of Applied Mathematics and Statistics, Stony Brook University, Stony Brook, NY 11794, 4Department of Biostatistics, Yale University, New Haven, CT 06520, 5Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, 6Department of Pathology, Stony Brook University, Stony Brook, NY 11794, 7Department of Medicine, Washington University St Louis, St Louis, MO 63110 and 8Department of Medicine, Stony Brook University, Stony Brook, NY 11794, USA"},{"name":"1 Department of Preventive Medicine, 2Department of Biomedical Informatics, and 3Department of Applied Mathematics and Statistics, Stony Brook University, Stony Brook, NY 11794, 4Department of Biostatistics, Yale University, New Haven, CT 06520, 5Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, 6Department of Pathology, Stony Brook University, Stony Brook, NY 11794, 7Department of Medicine, Washington University St Louis, St Louis, MO 63110 and 8Department of Medicine, Stony Brook University, Stony Brook, NY 11794, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Nicholas O.","family":"Davidson","sequence":"additional","affiliation":[{"name":"1 Department of Preventive Medicine, 2Department of Biomedical Informatics, and 3Department of Applied Mathematics and Statistics, Stony Brook University, Stony Brook, NY 11794, 4Department of Biostatistics, Yale University, New Haven, CT 06520, 5Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, 6Department of Pathology, Stony Brook University, Stony Brook, NY 11794, 7Department of Medicine, Washington University St Louis, St Louis, MO 63110 and 8Department of Medicine, Stony Brook University, Stony Brook, NY 11794, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Ellen","family":"Li","sequence":"additional","affiliation":[{"name":"1 Department of Preventive Medicine, 2Department of Biomedical Informatics, and 3Department of Applied Mathematics and Statistics, Stony Brook University, Stony Brook, NY 11794, 4Department of Biostatistics, Yale University, New Haven, CT 06520, 5Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, 6Department of Pathology, Stony Brook University, Stony Brook, NY 11794, 7Department of Medicine, Washington University St Louis, St Louis, MO 63110 and 8Department of Medicine, Stony Brook University, Stony Brook, NY 11794, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Jennie","family":"Williams","sequence":"additional","affiliation":[{"name":"1 Department of Preventive Medicine, 2Department of Biomedical Informatics, and 3Department of Applied Mathematics and Statistics, Stony Brook University, Stony Brook, NY 11794, 4Department of Biostatistics, Yale University, New Haven, CT 06520, 5Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, 6Department of Pathology, Stony Brook University, Stony Brook, NY 11794, 7Department of Medicine, Washington University St Louis, St Louis, MO 63110 and 8Department of Medicine, Stony Brook University, Stony Brook, NY 11794, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2015,2,13]]},"reference":[{"key":"2023020115242286800_btv089-B1","doi-asserted-by":"crossref","first-page":"572","DOI":"10.1093\/bioinformatics\/btp706","article-title":"BRAT: bisulfite-treated reads analysis tool","volume":"26","author":"Harris","year":"2010","journal-title":"Bioinformatics"},{"key":"2023020115242286800_btv089-B2","doi-asserted-by":"crossref","first-page":"1795","DOI":"10.1093\/bioinformatics\/bts264","article-title":"BRAT-BW: efficient and accurate mapping of bisulfite-treated reads","volume":"28","author":"Harris","year":"2012","journal-title":"Bioinformatics"},{"key":"2023020115242286800_btv089-B3","doi-asserted-by":"crossref","first-page":"145","DOI":"10.1038\/nmeth.1828","article-title":"DNA methylome analysis using short bisulfite sequencing data","volume":"9","author":"Krueger","year":"2012","journal-title":"Nat. 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