{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,5,9]],"date-time":"2026-05-09T07:12:33Z","timestamp":1778310753590,"version":"3.51.4"},"reference-count":44,"publisher":"Springer Science and Business Media LLC","issue":"1","license":[{"start":{"date-parts":[[2015,1,16]],"date-time":"2015-01-16T00:00:00Z","timestamp":1421366400000},"content-version":"unspecified","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0"}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["BMC Bioinformatics"],"published-print":{"date-parts":[[2015,12]]},"DOI":"10.1186\/s12859-014-0439-2","type":"journal-article","created":{"date-parts":[[2015,1,15]],"date-time":"2015-01-15T15:41:27Z","timestamp":1421336487000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":7,"title":["Nonparametric Bayesian clustering to detect bipolar methylated genomic loci"],"prefix":"10.1186","volume":"16","author":[{"given":"Xiaowei","family":"Wu","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Ming-an","family":"Sun","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Hongxiao","family":"Zhu","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Hehuang","family":"Xie","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"297","published-online":{"date-parts":[[2015,1,16]]},"reference":[{"key":"439_CR1","doi-asserted-by":"publisher","first-page":"6","DOI":"10.1101\/gad.947102","volume":"16","author":"A Bird","year":"2002","unstructured":"Bird A. DNA methylation patterns and epigenetic memory. Genes Dev. 2002; 16:6\u201321.","journal-title":"Genes Dev."},{"issue":"5","key":"439_CR2","doi-asserted-by":"publisher","first-page":"1827","DOI":"10.1073\/pnas.89.5.1827","volume":"89","author":"M Frommer","year":"1992","unstructured":"Frommer M, McDonald LE, Millar DS, Collis CM, Watt F, Grigg GW, et al. A genomic sequencing protocol that yields a positive display of 5-methylcytosine residues in individual DNA strands. Proc Natl Acad Sci. 1992; 89(5):1827\u201331.","journal-title":"Proc Natl Acad Sci."},{"issue":"12","key":"439_CR3","doi-asserted-by":"publisher","first-page":"e405","DOI":"10.1371\/journal.pbio.0020405","volume":"2","author":"VK Rakyan","year":"2004","unstructured":"Rakyan VK, Hildmann T, Novik KL, Lewin J, Tost J, Cox AV, et al. DNA methylation profiling of the human major histocompatibility complex: a pilot study for the human epigenome project. PLoS Biol. 2004; 2(12):e405.","journal-title":"PLoS Biol."},{"key":"439_CR4","doi-asserted-by":"publisher","first-page":"232","DOI":"10.1186\/1471-2105-10-232","volume":"10","author":"Y Xi","year":"2009","unstructured":"Xi Y, Li W. BSMAP: whole genome bisulfite sequence mapping program. BMC Bioinformatics. 2009; 10:232.","journal-title":"BMC Bioinformatics."},{"key":"439_CR5","doi-asserted-by":"crossref","unstructured":"Chen PY, Cokus SJ, Pellegrini M. BS Seeker: precise mapping for bisulfite sequencing. BMC Bioinformatics. 2010;11:203.","DOI":"10.1186\/1471-2105-11-203"},{"issue":"11","key":"439_CR6","doi-asserted-by":"publisher","first-page":"1571","DOI":"10.1093\/bioinformatics\/btr167","volume":"27","author":"F Krueger","year":"2011","unstructured":"Krueger F, Andrews SR. Bismark: a flexible aligner and methylation caller for Bisulfite-Seq applications. Bioinformatics. 2011; 27(11):1571\u20132.","journal-title":"Bioinformatics."},{"issue":"10","key":"439_CR7","doi-asserted-by":"publisher","first-page":"R82","DOI":"10.1186\/gb-2012-13-10-r82","volume":"13","author":"JQ Lim","year":"2012","unstructured":"Lim JQ, Tennakoon C, Li G, Wong E, Ruan Y, Wei CL, et al. BatMeth: improved mapper for bisulfite sequencing reads on DNA methylation. Genome Biol. 2012; 13(10):R82.","journal-title":"Genome Biol."},{"key":"439_CR8","doi-asserted-by":"publisher","first-page":"230","DOI":"10.1186\/1471-2105-11-230","volume":"11","author":"C Rohde","year":"2010","unstructured":"Rohde C, Zhang Y, Reinhardt R, Jeltsch A. BISMA: fast and accurate bisulfite sequencing data analysis of individual clones from unique and repetitive sequences. BMC Bioinformatics. 2010; 11:230.","journal-title":"BMC Bioinformatics."},{"key":"439_CR9","doi-asserted-by":"publisher","first-page":"e58","DOI":"10.1093\/nar\/gkr053","volume":"39","author":"Y Zhang","year":"2011","unstructured":"Zhang Y, Liu H, Lv J, Xiao X, Zhu J, Liu X, et al.QDMR: a quantitative method for identification of differentially methylated regions by entropy. Nucleic Acids Res. 2011; 39:e58.","journal-title":"Nucleic Acids Res."},{"key":"439_CR10","doi-asserted-by":"publisher","first-page":"W551","DOI":"10.1093\/nar\/gkr312","volume":"39","author":"P Lutsik","year":"2011","unstructured":"Lutsik P, Feuerbach L, Arand J, Lengauer T, Walter J, Bock C. BiQ Analyzer HT: locus-specific analysis of DNA methylation by high-throughput bisulfite sequencing. Nucleic Acids Res. 2011; 39:W551\u20136.","journal-title":"Nucleic Acids Res."},{"issue":"1","key":"439_CR11","doi-asserted-by":"publisher","first-page":"e4","DOI":"10.1093\/nar\/gks829","volume":"41","author":"J Su","year":"2013","unstructured":"Su J, Yan H, Wei Y, Liu H, Wang F, Lv J, et al. CpG_MPs: identification of CpG methylation patterns of genomic regions from high-throughput bisulfite sequencing data. Nucleic Acids Res. 2013; 41(1):e4.","journal-title":"Nucleic Acids Res."},{"issue":"10","key":"439_CR12","doi-asserted-by":"publisher","first-page":"4099","DOI":"10.1093\/nar\/gkr017","volume":"39","author":"H Xie","year":"2011","unstructured":"Xie H, Wang M, de Andrade A, Bonaldo MF, Galat V, Arndt K, et al. Genome-wide quantitative assessment of variation in DNA methylation patterns. Nucleic Acids Res. 2011; 39(10):4099\u2013108.","journal-title":"Nucleic Acids Res."},{"issue":"13","key":"439_CR13","doi-asserted-by":"publisher","first-page":"4331","DOI":"10.1093\/nar\/gkp393","volume":"37","author":"H Xie","year":"2009","unstructured":"Xie H, Wang M, Bonaldo MF, Smith C, Rajaram V, Goldman S, et al. High-throughput sequence-based epigenomic analysis of Alu repeats in human cerebellum. Nucleic Acids Res. 2009; 37(13):4331\u201340.","journal-title":"Nucleic Acids Res."},{"issue":"15","key":"439_CR14","doi-asserted-by":"publisher","first-page":"6952","DOI":"10.1073\/pnas.0913836107","volume":"107","author":"H Xie","year":"2010","unstructured":"Xie H, Wang M, Bonaldo MF, Rajaram V, Stellpflug W, Smith C, et al. Epigenomic analysis of Alu repeats in human ependymomas. Proc Natl Acad Sci. 2010; 107(15):6952\u20137.","journal-title":"Proc Natl Acad Sci."},{"issue":"1","key":"439_CR15","doi-asserted-by":"publisher","first-page":"21","DOI":"10.1038\/35047554","volume":"2","author":"W Reik","year":"2001","unstructured":"Reik W, Walter J. Genomic imprinting: parental influence on the genome. Nat Rev Genet. 2001; 2(1):21\u201332.","journal-title":"Nat Rev Genet."},{"issue":"5","key":"439_CR16","doi-asserted-by":"publisher","first-page":"270","DOI":"10.1016\/j.diff.2011.01.007","volume":"81","author":"RM John","year":"2011","unstructured":"John RM, Lefebvre L. Developmental regulation of somatic imprints. Differentiation. 2011; 81(5):270\u201380.","journal-title":"Differentiation."},{"issue":"4","key":"439_CR17","doi-asserted-by":"publisher","first-page":"816","DOI":"10.1016\/j.cell.2011.12.035","volume":"148","author":"W Xie","year":"2012","unstructured":"Xie W, Barr CL, Kim A, Yue F, Lee AY, Eubanks J, et al. Base-resolution analyses of sequence and parent-of-origin dependent DNA methylation in the mouse genome. Cell. 2012; 148(4):816\u201331.","journal-title":"Cell."},{"key":"439_CR18","doi-asserted-by":"publisher","first-page":"D29","DOI":"10.1093\/nar\/gkj101","volume":"34","author":"RL Glaser","year":"2006","unstructured":"Glaser RL, Ramsay JP, Morison IM. The imprinted gene and parent-of-origin effect database now includes parental origin of de novo mutations. Nucleic Acids Res. 2006; 34:D29\u201331.","journal-title":"Nucleic Acids Res."},{"issue":"1","key":"439_CR19","doi-asserted-by":"publisher","first-page":"17","DOI":"10.1016\/j.molcel.2011.08.026","volume":"44","author":"E Hodges","year":"2011","unstructured":"Hodges E, Molaro A, Dos Santos CO, Thekkat P, Song Q, Uren PJ, et al. Directional DNA methylation changes and complex intermediate states accompany lineage specificity in the adult hematopoietic compartment. Mol Cell. 2011; 44(1):17\u201328.","journal-title":"Mol Cell."},{"issue":"1","key":"439_CR20","doi-asserted-by":"publisher","first-page":"116","DOI":"10.1093\/nar\/gkr685","volume":"40","author":"V Calvanese","year":"2012","unstructured":"Calvanese V, Fernandez AF, Urdinguio RG, Suarez-Alvarez B, Mangas C, Perez-Garcia V, et al. A promoter DNA demethylation landscape of human hematopoietic differentiation. Nucleic Acids Res. 2012; 40(1):116\u201331.","journal-title":"Nucleic Acids Res."},{"issue":"7","key":"439_CR21","doi-asserted-by":"publisher","first-page":"1074","DOI":"10.1101\/gr.118703.110","volume":"21","author":"AM Deaton","year":"2011","unstructured":"Deaton AM, Webb S, Kerr AR, Illingworth RS, Guy J, Andrews R, et al. Cell type-specific DNA methylation at intragenic CpG islands in the immune system. Genome Res. 2011; 21(7):1074\u201386.","journal-title":"Genome Res."},{"key":"439_CR22","doi-asserted-by":"publisher","first-page":"338","DOI":"10.1038\/nature09367","volume":"467","author":"H Ji","year":"2010","unstructured":"Ji H, Ehrlich LI, Seita J, Murakami P, Doi A, Lindau P, et al. Comprehensive methylome map of lineage commitment from haematopoietic progenitors. Nature. 2010; 467:338\u201342.","journal-title":"Nature."},{"issue":"8","key":"439_CR23","doi-asserted-by":"publisher","first-page":"1407","DOI":"10.1101\/gr.132878.111","volume":"22","author":"A Hogart","year":"2012","unstructured":"Hogart A, Lichtenberg J, Ajay SS, Anderson S, Margulies EH, Bodine DM. Genome-wide DNA methylation profiles in hematopoietic stem and progenitor cells reveal overrepresentation of ETS transcription factor binding sites. Genome Res. 2012; 22(8):1407\u201318.","journal-title":"Genome Res."},{"key":"439_CR24","unstructured":"Daum\u00e9 III H. Fast search for Dirichlet process mixture models. In: Proceedings of the Eleventh International Conference on Artificial Intelligence and Statistics (AIStats) 2007; 2: 83\u201390, San Juan, Puerto Rico."},{"issue":"12","key":"439_CR25","doi-asserted-by":"publisher","first-page":"i163","DOI":"10.1093\/bioinformatics\/bts231","volume":"28","author":"Q Peng","year":"2012","unstructured":"Peng Q, Ecker JR. Detection of allele-specific methylation through a generalized heterogeneous epigenome model. Bioinformatics. 2012; 28(12):i163\u201371.","journal-title":"Bioinformatics."},{"key":"439_CR26","doi-asserted-by":"publisher","first-page":"7332","DOI":"10.1073\/pnas.1201310109","volume":"109","author":"F Fang","year":"2012","unstructured":"Fang F, Hodges E, Molaro A, Dean M, Hannon GJ, Smith AD. Genomic landscape of human allele-specific DNA methylation. Proc Natl Acad Sci. 2012; 109:7332\u20137.","journal-title":"Proc Natl Acad Sci."},{"issue":"3","key":"439_CR27","doi-asserted-by":"publisher","first-page":"455","DOI":"10.1016\/j.ajhg.2012.07.024","volume":"91","author":"J Zeng","year":"2012","unstructured":"Zeng J, Konopka G, Hunt BG, Preuss TM, Geschwind D, Yi SV. Divergent whole-genome methylation maps of human and chimpanzee brains reveal epigenetic basis of human regulatory evolution. Am J Hum Genet. 2012; 91(3):455\u201365.","journal-title":"Am J Hum Genet."},{"issue":"10","key":"439_CR28","doi-asserted-by":"publisher","first-page":"1198","DOI":"10.1038\/ng.2746","volume":"45","author":"GC Hon","year":"2013","unstructured":"Hon GC, Rajagopal N, Shen Y, McCleary DF, Yue F, Dang MD, et al. Epigenetic memory at embryonic enhancers identified in DNA methylation maps from adult mouse tissues. Nat Genet. 2013; 45(10):1198\u2013206.","journal-title":"Nat Genet."},{"key":"439_CR29","doi-asserted-by":"publisher","first-page":"1237905","DOI":"10.1126\/science.1237905","volume":"341","author":"R Lister","year":"2013","unstructured":"Lister R, Mukamel EA, Nery JR, Urich M, Puddifoot CA, Johnson ND, et al. Global epigenomic reconfiguration during mammalian brain development. Science. 2013; 341:1237905.","journal-title":"Science."},{"issue":"1","key":"439_CR30","doi-asserted-by":"publisher","first-page":"44","DOI":"10.1038\/nprot.2008.211","volume":"4","author":"W Huang da","year":"2009","unstructured":"Huang da W, Sherman BT, Lempicki RA. Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources. Nat Protoc. 2009; 4(1):44\u201357.","journal-title":"Nat Protoc."},{"issue":"2","key":"439_CR31","doi-asserted-by":"publisher","first-page":"144","DOI":"10.1093\/bib\/bbs038","volume":"14","author":"RM Kuhn","year":"2013","unstructured":"Kuhn RM, Haussler D, Kent WJ. The UCSC genome browser and associated tools. Brief Bioinform. 2013; 14(2):144\u201361.","journal-title":"Brief Bioinform."},{"issue":"2","key":"439_CR32","doi-asserted-by":"publisher","first-page":"178","DOI":"10.1002\/neu.10245","volume":"56","author":"EL Tsalik","year":"2003","unstructured":"Tsalik EL, Hobert O. Functional mapping of neurons that control locomotory behavior in Caenorhabditis elegans. J Neurobiol. 2003; 56(2):178\u201397.","journal-title":"J Neurobiol."},{"key":"439_CR33","doi-asserted-by":"publisher","first-page":"16","DOI":"10.1186\/1749-8104-4-16","volume":"4","author":"TA Starich","year":"2009","unstructured":"Starich TA, Xu J, Skerrett IM, Nicholson BJ, Shaw JE. Interactions between innexins UNC-7 and UNC-9 mediate electrical synapse specificity in the Caenorhabditis elegans locomotory nervous system. Neural Dev. 2009; 4:16.","journal-title":"Neural Dev."},{"issue":"10","key":"439_CR34","doi-asserted-by":"publisher","first-page":"778","DOI":"10.1038\/nri2172","volume":"7","author":"AM Scharenberg","year":"2007","unstructured":"Scharenberg AM, Humphries LA, Rawlings DJ. Calcium signalling and cell-fate choice in B cells. Nat Rev Immunol. 2007; 7(10):778\u201389.","journal-title":"Nat Rev Immunol."},{"issue":"2","key":"439_CR35","doi-asserted-by":"publisher","first-page":"491","DOI":"10.1172\/JCI114464","volume":"85","author":"KH Krause","year":"1990","unstructured":"Krause KH, Welsh MJ. Voltage-dependent and Ca2(+)-activated ion channels in human neutrophils. J Clin Invest. 1990; 85(2):491\u20138.","journal-title":"J Clin Invest."},{"issue":"22","key":"439_CR36","doi-asserted-by":"crossref","first-page":"13777","DOI":"10.1016\/S0021-9258(18)89813-1","volume":"259","author":"M Prentki","year":"1984","unstructured":"Prentki M, Wollheim CB, Lew PD. Ca2+ homeostasis in permeabilized human neutrophils. Characterization of Ca2+-sequestering pools and the action of inositol 1,4,5-triphosphate. J Biol Chem. 1984; 259(22):13777\u201382.","journal-title":"J Biol Chem."},{"issue":"3","key":"439_CR37","doi-asserted-by":"publisher","first-page":"671","DOI":"10.1073\/pnas.0812399106","volume":"106","author":"TA Rauch","year":"2009","unstructured":"Rauch TA, Wu X, Zhong X, Riggs AD, Pfeifer GP. A human B cells methylome at 100-base pair resolution. Proc Natl Acad Sci. 2009; 106(3):671\u20138.","journal-title":"Proc Natl Acad Sci."},{"issue":"1-2","key":"439_CR38","doi-asserted-by":"publisher","first-page":"15","DOI":"10.1016\/j.jneuroim.2005.01.023","volume":"163","author":"B Schuhmann","year":"2005","unstructured":"Schuhmann B, Dietrich A, Sel S, Hahn C, Klingenspor M, Lommatzsch M, et al. A role for brain-derived neurotrophic factor in B cells development. J Neuroimmunol. 2005; 163(1-2):15\u201323.","journal-title":"J Neuroimmunol."},{"issue":"10","key":"439_CR39","doi-asserted-by":"publisher","first-page":"1573","DOI":"10.1111\/ejn.12190","volume":"37","author":"M Torigoe","year":"2013","unstructured":"Torigoe M, Yamauchi K, Tamada A, Matsuda I, Aiba A, Castellani V, et al. Role of neuropilin-2 in the ipsilateral growth of midbrain dopaminergic axons. Eur J Neurosci. 2013; 37(10):1573\u201383.","journal-title":"Eur J Neurosci."},{"issue":"4","key":"439_CR40","doi-asserted-by":"publisher","first-page":"554","DOI":"10.1101\/gr.164913.113","volume":"24","author":"F Court","year":"2014","unstructured":"Court F, Tayama C, Romanelli V, Martin-Trujillo A, Iglesias-Platas I, Okamura K, et al. Genome-wide parent-of-origin DNA methylation analysis reveals the intricacies of human imprinting and suggests a germline methylation-independent mechanism of establishment. Genome Res. 2014; 24(4):554\u201369.","journal-title":"Genome Res."},{"issue":"8","key":"439_CR41","doi-asserted-by":"publisher","first-page":"1296","DOI":"10.1101\/gr.163147.113","volume":"24","author":"L Zhao","year":"2014","unstructured":"Zhao L, Sun M, Li Z, Bai X, Yu M, Wang M, et al. The dynamics of DNA methylation fidelity during mouse embryonic stem cell self-renewal and differentiation. Genome Res. 2014; 24(8):1296\u2013307.","journal-title":"Genome Res."},{"issue":"3","key":"439_CR42","doi-asserted-by":"publisher","first-page":"290","DOI":"10.4161\/epi.23924","volume":"8","author":"J Guintivano","year":"2013","unstructured":"Guintivano J, Aryee MJ, Kaminsky ZA. A cell epigenotype specific model for the correction of brain cellular heterogeneity bias and its application to age, brain region and major depression. Epigenetics. 2013; 8(3):290\u2013302.","journal-title":"Epigenetics."},{"key":"439_CR43","doi-asserted-by":"publisher","first-page":"86","DOI":"10.1186\/1471-2105-13-86","volume":"13","author":"EA Houseman","year":"2012","unstructured":"Houseman EA, Accomando WP, Koestler DC, Christensen BC, Marsit CJ, Nelson HH, et al. DNA methylation arrays as surrogate measures of cell mixture distribution. BMC Bioinformatics. 2012; 13:86.","journal-title":"BMC Bioinformatics."},{"issue":"8","key":"439_CR44","doi-asserted-by":"publisher","first-page":"R94","DOI":"10.1186\/gb-2013-14-8-r94","volume":"14","author":"CM Monta\u00f1o","year":"2013","unstructured":"Monta\u00f1o CM, Irizarry RA, Kaufmann WE, Talbot K, Gur RE, Feinberg AP, et al. Measuring cell-type specific differential methylation in human brain tissue. Genome Biol. 2013; 14(8):R94.","journal-title":"Genome Biol."}],"container-title":["BMC Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/link.springer.com\/article\/10.1186\/s12859-014-0439-2\/fulltext.html","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1186\/s12859-014-0439-2.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1186\/s12859-014-0439-2","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"},{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1186\/s12859-014-0439-2.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2021,9,2]],"date-time":"2021-09-02T07:25:08Z","timestamp":1630567508000},"score":1,"resource":{"primary":{"URL":"https:\/\/bmcbioinformatics.biomedcentral.com\/articles\/10.1186\/s12859-014-0439-2"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2015,1,16]]},"references-count":44,"journal-issue":{"issue":"1","published-print":{"date-parts":[[2015,12]]}},"alternative-id":["439"],"URL":"https:\/\/doi.org\/10.1186\/s12859-014-0439-2","relation":{},"ISSN":["1471-2105"],"issn-type":[{"value":"1471-2105","type":"electronic"}],"subject":[],"published":{"date-parts":[[2015,1,16]]},"assertion":[{"value":"10 July 2014","order":1,"name":"received","label":"Received","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"18 December 2014","order":2,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"16 January 2015","order":3,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}}],"article-number":"11"}}