{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,1,13]],"date-time":"2026-01-13T23:59:52Z","timestamp":1768348792895,"version":"3.49.0"},"reference-count":8,"publisher":"Oxford University Press (OUP)","issue":"11","license":[{"start":{"date-parts":[[2017,1,27]],"date-time":"2017-01-27T00:00:00Z","timestamp":1485475200000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/journals\/pages\/about_us\/legal\/notices"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2017,6,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Motivation<\/jats:title>\n                  <jats:p>Methylation and hydroxylation of cytosines to form 5-methylcytosine (5mC) and 5-hydroxymethylcytosine (5hmC) belong to the most important epigenetic modifications and their vital role in the regulation of gene expression has been widely recognized. Recent experimental techniques allow to infer methylation and hydroxylation levels at CpG dinucleotides but require a sophisticated statistical analysis to achieve accurate estimates.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Results<\/jats:title>\n                  <jats:p>We present H(O)TA, a software tool based on a stochastic modeling approach, which simultaneously analyzes time course data from hairpin bisulfite sequencing and hairpin oxidative bisulfite sequencing.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and Implementation<\/jats:title>\n                  <jats:p>https:\/\/mosi.uni-saarland.de\/HOTA<\/jats:p>\n               <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btx042","type":"journal-article","created":{"date-parts":[[2017,1,28]],"date-time":"2017-01-28T01:25:31Z","timestamp":1485566731000},"page":"1733-1734","source":"Crossref","is-referenced-by-count":13,"title":["H(O)TA: estimation of DNA methylation and hydroxylation levels and efficiencies from time course data"],"prefix":"10.1093","volume":"33","author":[{"given":"Charalampos","family":"Kyriakopoulos","sequence":"first","affiliation":[{"name":"Computer Science Department, Saarland University, Saarbruecken, Germany"}]},{"given":"Pascal","family":"Giehr","sequence":"additional","affiliation":[{"name":"Department of Biological Sciences, Saarland University, Saarbruecken, Germany"}]},{"given":"Verena","family":"Wolf","sequence":"additional","affiliation":[{"name":"Computer Science Department, Saarland University, Saarbruecken, Germany"}]}],"member":"286","published-online":{"date-parts":[[2017,1,27]]},"reference":[{"key":"2023020205322204400_btx042-B1","doi-asserted-by":"crossref","first-page":"e1002750","DOI":"10.1371\/journal.pgen.1002750","article-title":"In vivo control of CpG and non-CpG DNA methylation by DNA methyltransferases","volume":"8","author":"Arand","year":"2012","journal-title":"PLoS Genet"},{"key":"2023020205322204400_btx042-B2","doi-asserted-by":"crossref","first-page":"934","DOI":"10.1126\/science.1220671","article-title":"Quantitative sequencing of 5-methylcytosine and 5-hydroxymethylcytosine at single-base resolution","volume":"336","author":"Booth","year":"2012","journal-title":"Science"},{"key":"2023020205322204400_btx042-B3","doi-asserted-by":"crossref","first-page":"96","DOI":"10.1038\/nature02886","article-title":"Meiotic catastrophe and retrotransposon reactivation in male germ cells lacking Dnmt3L","volume":"431","author":"Bourc\u2019his","year":"2004","journal-title":"Nature"},{"key":"2023020205322204400_btx042-B4","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":"PNAS"},{"key":"2023020205322204400_btx042-B5","doi-asserted-by":"crossref","first-page":"e1004905.","DOI":"10.1371\/journal.pcbi.1004905","article-title":"The influence of hydroxylation on maintaining cpg methylation patterns: a hidden markov model approach","volume":"12","author":"Giehr","year":"2016","journal-title":"PLoS Comput. Biol"},{"key":"2023020205322204400_btx042-B6","doi-asserted-by":"crossref","first-page":"359","DOI":"10.1006\/scbi.1999.0138","article-title":"Hypermethylation of tumor suppressor genes in cancer","volume":"9","author":"Herman","year":"1999","journal-title":"Sem. Cancer Biol"},{"key":"2023020205322204400_btx042-B7","doi-asserted-by":"crossref","first-page":"204","DOI":"10.1073\/pnas.2536758100","article-title":"Hairpin-bisulfite PCR: assessing epigenetic methylation patterns on complementary strands of individual DNA molecules","volume":"101","author":"Laird","year":"2004","journal-title":"PNAS"},{"key":"2023020205322204400_btx042-B8","doi-asserted-by":"crossref","first-page":"328","DOI":"10.1038\/nchembio.914","article-title":"Thymine DNA glycosylase specifically recognizes 5-carboxylcytosine-modified DNA","volume":"8","author":"Zhang","year":"2012","journal-title":"Nat. Chem. Biol"}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/33\/11\/1733\/49039968\/bioinformatics_33_11_1733.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/33\/11\/1733\/49039968\/bioinformatics_33_11_1733.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,2,2]],"date-time":"2023-02-02T05:35:54Z","timestamp":1675316154000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/33\/11\/1733\/2959907"}},"subtitle":[],"editor":[{"given":"Janet","family":"Kelso","sequence":"additional","affiliation":[]}],"short-title":[],"issued":{"date-parts":[[2017,1,27]]},"references-count":8,"journal-issue":{"issue":"11","published-print":{"date-parts":[[2017,6,1]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btx042","relation":{},"ISSN":["1367-4803","1367-4811"],"issn-type":[{"value":"1367-4803","type":"print"},{"value":"1367-4811","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2017,6,1]]},"published":{"date-parts":[[2017,1,27]]}}}