{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,1,21]],"date-time":"2026-01-21T20:35:34Z","timestamp":1769027734347,"version":"3.49.0"},"reference-count":22,"publisher":"Oxford University Press (OUP)","issue":"24","license":[{"start":{"date-parts":[[2021,6,19]],"date-time":"2021-06-19T00:00:00Z","timestamp":1624060800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/journals\/pages\/open_access\/funder_policies\/chorus\/standard_publication_model"}],"funder":[{"name":"Hundred Talents Program"},{"DOI":"10.13039\/501100002367","name":"Chinese Academy of Sciences","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100002367","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Shanghai Pujiang Program","award":["20PJ1414700"],"award-info":[{"award-number":["20PJ1414700"]}]},{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["61972257"],"award-info":[{"award-number":["61972257"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2021,12,11]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Summary<\/jats:title>\n                  <jats:p>Bisulfite sequencing (BS-seq) is currently the gold standard for measuring genome-wide DNA methylation profiles at single-nucleotide resolution. Most analyses focus on mean CpG methylation and ignore methylation states on the same DNA fragments [DNA methylation haplotypes (mHaps)]. Here, we propose mHap, a simple DNA mHap format for storing DNA BS-seq data. This format reduces the size of a BAM file by 40- to 140-fold while retaining complete read-level CpG methylation information. It is also compatible with the Tabix tool for fast and random access. We implemented a command-line tool, mHapTools, for converting BAM\/SAM files from existing platforms to mHap files as well as post-processing DNA methylation data in mHap format. With this tool, we processed all publicly available human reduced representation bisulfite sequencing data and provided these data as a comprehensive mHap database.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>https:\/\/jiantaoshi.github.io\/mHap\/index.html.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Supplementary information<\/jats:title>\n                  <jats:p>Supplementary data are available at Bioinformatics online.<\/jats:p>\n               <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btab458","type":"journal-article","created":{"date-parts":[[2021,6,17]],"date-time":"2021-06-17T03:12:37Z","timestamp":1623899557000},"page":"4892-4894","source":"Crossref","is-referenced-by-count":12,"title":["The DNA methylation haplotype (mHap) format and mHapTools"],"prefix":"10.1093","volume":"37","author":[{"given":"Zhiqiang","family":"Zhang","sequence":"first","affiliation":[{"name":"State Key Laboratory of Molecular Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science Chinese Academy of Sciences , Shanghai 200031, China"}]},{"given":"Yuhao","family":"Dan","sequence":"additional","affiliation":[{"name":"Department of Mathematics, Shanghai Normal University , Shanghai 200234, China"}]},{"given":"Yaochen","family":"Xu","sequence":"additional","affiliation":[{"name":"State Key Laboratory of Molecular Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science Chinese Academy of Sciences , Shanghai 200031, China"}]},{"given":"Jiarui","family":"Zhang","sequence":"additional","affiliation":[{"name":"Shanghai Science and Technology Development Co., Ltd , Shanghai 200235, China"}]},{"given":"Xiaoqi","family":"Zheng","sequence":"additional","affiliation":[{"name":"Department of Mathematics, Shanghai Normal University , Shanghai 200234, China"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-0039-8800","authenticated-orcid":false,"given":"Jiantao","family":"Shi","sequence":"additional","affiliation":[{"name":"State Key Laboratory of Molecular Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science Chinese Academy of Sciences , Shanghai 200031, China"}]}],"member":"286","published-online":{"date-parts":[[2021,6,19]]},"reference":[{"key":"2023051607130164700_btab458-B1","doi-asserted-by":"crossref","first-page":"203","DOI":"10.1186\/1471-2105-11-203","article-title":"BS Seeker: precise mapping for bisulfite sequencing","volume":"11","author":"Chen","year":"2010","journal-title":"BMC Bioinformatics"},{"key":"2023051607130164700_btab458-B2","doi-asserted-by":"crossref","first-page":"503","DOI":"10.1038\/s41586-019-1186-3","article-title":"Next-generation characterization of the cancer cell line encyclopedia","volume":"569","author":"Ghandi","year":"2019","journal-title":"Nature"},{"key":"2023051607130164700_btab458-B3","doi-asserted-by":"crossref","first-page":"590","DOI":"10.1038\/s41580-019-0159-6","article-title":"The diverse roles of DNA methylation in mammalian development and disease","volume":"20","author":"Greenberg","year":"2019","journal-title":"Nat. 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