{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2024,9,11]],"date-time":"2024-09-11T07:16:39Z","timestamp":1726038999485},"publisher-location":"Cham","reference-count":30,"publisher":"Springer International Publishing","isbn-type":[{"type":"print","value":"9783030280413"},{"type":"electronic","value":"9783030280420"}],"license":[{"start":{"date-parts":[[2019,1,1]],"date-time":"2019-01-01T00:00:00Z","timestamp":1546300800000},"content-version":"tdm","delay-in-days":0,"URL":"http:\/\/www.springer.com\/tdm"}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2019]]},"DOI":"10.1007\/978-3-030-28042-0_8","type":"book-chapter","created":{"date-parts":[[2019,8,1]],"date-time":"2019-08-01T01:03:46Z","timestamp":1564621426000},"page":"117-131","update-policy":"http:\/\/dx.doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":3,"title":["A Hybrid HMM Approach for the Dynamics of DNA Methylation"],"prefix":"10.1007","author":[{"given":"Charalampos","family":"Kyriakopoulos","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Pascal","family":"Giehr","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Alexander","family":"L\u00fcck","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"J\u00f6rn","family":"Walter","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Verena","family":"Wolf","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"297","published-online":{"date-parts":[[2019,8,1]]},"reference":[{"issue":"6","key":"8_CR1","doi-asserted-by":"publisher","first-page":"e1002750","DOI":"10.1371\/journal.pgen.1002750","volume":"8","author":"J Arand","year":"2012","unstructured":"Arand, J., et al.: In vivo control of CpG and non-CpG DNA methylation by DNA methyltransferases. PLoS Genet. 8(6), e1002750 (2012)","journal-title":"PLoS Genet."},{"issue":"18","key":"8_CR2","doi-asserted-by":"publisher","first-page":"5559","DOI":"10.1073\/pnas.80.18.5559","volume":"80","author":"TH Bestor","year":"1983","unstructured":"Bestor, T.H., Ingram, V.M.: Two DNA methyltransferases from murine erythroleukemia cells: purification, sequence specificity, and mode of interaction with DNA. Proc. Nat. Acad. Sci. 80(18), 5559\u20135563 (1983)","journal-title":"Proc. Nat. Acad. Sci."},{"issue":"6083","key":"8_CR3","doi-asserted-by":"publisher","first-page":"934","DOI":"10.1126\/science.1220671","volume":"336","author":"MJ Booth","year":"2012","unstructured":"Booth, M.J., et al.: Quantitative sequencing of 5-methylcytosine and 5-hydroxymethylcytosine at single-base resolution. Science 336(6083), 934\u2013937 (2012)","journal-title":"Science"},{"issue":"1","key":"8_CR4","doi-asserted-by":"publisher","first-page":"25","DOI":"10.1083\/jcb.147.1.25","volume":"147","author":"MC Cardoso","year":"1999","unstructured":"Cardoso, M.C., Leonhardt, H.: DNA methyltransferase is actively retained in the cytoplasm during early development. J. Cell Biol. 147(1), 25\u201332 (1999)","journal-title":"J. Cell Biol."},{"issue":"3","key":"8_CR5","doi-asserted-by":"publisher","first-page":"457","DOI":"10.1093\/biomet\/65.3.457","volume":"65","author":"B Efron","year":"1978","unstructured":"Efron, B., Hinkley, D.V.: Assessing the accuracy of the maximum likelihood estimator: observed versus expected fisher information. Biometrika 65(3), 457\u2013483 (1978)","journal-title":"Biometrika"},{"issue":"8","key":"8_CR6","doi-asserted-by":"publisher","first-page":"2709","DOI":"10.1093\/nar\/10.8.2709","volume":"10","author":"M Ehrlich","year":"1982","unstructured":"Ehrlich, M., et al.: Amount and distribution of 5-methylcytosine in human DNA from different types of tissues or cells. Nucleic Acids Res. 10(8), 2709\u20132721 (1982)","journal-title":"Nucleic Acids Res."},{"issue":"19","key":"8_CR7","doi-asserted-by":"publisher","first-page":"8689","DOI":"10.1073\/pnas.1002720107","volume":"107","author":"S Feng","year":"2010","unstructured":"Feng, S., et al.: Conservation and divergence of methylation patterning in plants and animals. Proc. Nat. Acad. Sci. 107(19), 8689\u20138694 (2010)","journal-title":"Proc. Nat. Acad. Sci."},{"issue":"3","key":"8_CR8","doi-asserted-by":"publisher","first-page":"351","DOI":"10.1016\/j.stem.2013.06.004","volume":"13","author":"G Ficz","year":"2013","unstructured":"Ficz, G., et al.: FGF signaling inhibition in ESCs drives rapid genome-wide demethylation to the epigenetic ground state of pluripotency. Cell Stem Cell 13(3), 351\u2013359 (2013)","journal-title":"Cell Stem Cell"},{"issue":"5","key":"8_CR9","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1371\/journal.pcbi.1004905","volume":"12","author":"P Giehr","year":"2016","unstructured":"Giehr, P., Kyriakopoulos, C., Ficz, G., Wolf, V., Walter, J.: The influence of hydroxylation on maintaining CpG methylation patterns: a hidden Markov model approach. PLoS Comput. Biol. 12(5), 1\u201316 (2016)","journal-title":"PLoS Comput. Biol."},{"issue":"15","key":"8_CR10","doi-asserted-by":"publisher","first-page":"e88","DOI":"10.1093\/nar\/gky422","volume":"46","author":"P Giehr","year":"2018","unstructured":"Giehr, P., Kyriakopoulos, C., Lepikhov, K., Wallner, S., Wolf, V., Walter, J.: Two are better than one: HPoxBS-hairpin oxidative bisulfite sequencing. Nucleic Acids Res. 46(15), e88 (2018)","journal-title":"Nucleic Acids Res."},{"key":"8_CR11","series-title":"Methods in Molecular Biology","doi-asserted-by":"publisher","first-page":"573","DOI":"10.1007\/978-1-4939-7481-8_29","volume-title":"DNA Methylation Protocols","author":"P Giehr","year":"2018","unstructured":"Giehr, P., Walter, J.: Hairpin bisulfite sequencing: synchronous methylation analysis on complementary DNA strands of individual chromosomes. In: Tost, J. (ed.) DNA Methylation Protocols. MMB, vol. 1708, pp. 573\u2013586. Springer, New York (2018). https:\/\/doi.org\/10.1007\/978-1-4939-7481-8_29"},{"issue":"12","key":"8_CR12","doi-asserted-by":"publisher","first-page":"e15367","DOI":"10.1371\/journal.pone.0015367","volume":"5","author":"D Globisch","year":"2010","unstructured":"Globisch, D., et al.: Tissue distribution of 5-hydroxymethylcytosine and search for active demethylation intermediates. PLoS ONE 5(12), e15367 (2010)","journal-title":"PLoS ONE"},{"issue":"11","key":"8_CR13","doi-asserted-by":"publisher","first-page":"4841","DOI":"10.1093\/nar\/gks155","volume":"40","author":"H Hashimoto","year":"2012","unstructured":"Hashimoto, H., et al.: Recognition and potential mechanisms for replication and erasure of cytosine hydroxymethylation. Nucleic Acids Res. 40(11), 4841\u20134849 (2012)","journal-title":"Nucleic Acids Res."},{"issue":"6047","key":"8_CR14","doi-asserted-by":"publisher","first-page":"1303","DOI":"10.1126\/science.1210944","volume":"333","author":"YF He","year":"2011","unstructured":"He, Y.F., et al.: Tet-mediated formation of 5-carboxylcytosine and its excision by TDG in mammalian DNA. Science 333(6047), 1303\u20131307 (2011)","journal-title":"Science"},{"issue":"46","key":"8_CR15","doi-asserted-by":"publisher","first-page":"48350","DOI":"10.1074\/jbc.M403427200","volume":"279","author":"A Hermann","year":"2004","unstructured":"Hermann, A., Goyal, R., Jeltsch, A.: The Dnmt1 DNA-(cytosine-C5)-methyltransferase methylates DNA processively with high preference for hemimethylated target sites. J. Biol. Chem. 279(46), 48350\u201348359 (2004)","journal-title":"J. Biol. Chem."},{"issue":"6047","key":"8_CR16","doi-asserted-by":"publisher","first-page":"1300","DOI":"10.1126\/science.1210597","volume":"333","author":"S Ito","year":"2011","unstructured":"Ito, S., et al.: Tet proteins can convert 5-methylcytosine to 5-formylcytosine and 5-carboxylcytosine. Science 333(6047), 1300\u20131303 (2011)","journal-title":"Science"},{"issue":"7","key":"8_CR17","doi-asserted-by":"publisher","first-page":"1749","DOI":"10.1039\/c4mb00150h","volume":"10","author":"D Ji","year":"2014","unstructured":"Ji, D., Lin, K., Song, J., Wang, Y.: Effects of Tet-induced oxidation products of 5-methylcytosine on Dnmt1-and DNMT3a-mediated cytosine methylation. Mol. BioSyst. 10(7), 1749\u20131752 (2014)","journal-title":"Mol. BioSyst."},{"issue":"7183","key":"8_CR18","doi-asserted-by":"publisher","first-page":"112","DOI":"10.1038\/nature06640","volume":"452","author":"S Kangaspeska","year":"2008","unstructured":"Kangaspeska, S., et al.: Transient cyclical methylation of promoter DNA. Nature 452(7183), 112 (2008)","journal-title":"Nature"},{"issue":"5929","key":"8_CR19","doi-asserted-by":"publisher","first-page":"929","DOI":"10.1126\/science.1169786","volume":"324","author":"S Kriaucionis","year":"2009","unstructured":"Kriaucionis, S., Heintz, N.: The nuclear DNA base 5-hydroxymethylcytosine is present in Purkinje neurons and the brain. Science 324(5929), 929\u2013930 (2009)","journal-title":"Science"},{"issue":"11","key":"8_CR20","doi-asserted-by":"crossref","first-page":"1733","DOI":"10.1093\/bioinformatics\/btx042","volume":"33","author":"C Kyriakopoulos","year":"2017","unstructured":"Kyriakopoulos, C., Giehr, P., Wolf, V.: H(O)TA: estimation of DNA methylation and hydroxylation levels and efficiencies from time course data. Bioinformatics 33(11), 1733\u20131734 (2017)","journal-title":"Bioinformatics"},{"issue":"1","key":"8_CR21","doi-asserted-by":"publisher","first-page":"204","DOI":"10.1073\/pnas.2536758100","volume":"101","author":"CD Laird","year":"2004","unstructured":"Laird, C.D., et al.: Hairpin-bisulfite PCR: assessing epigenetic methylation patterns on complementary strands of individual DNA molecules. Proc. Nat. Acad. Sci. 101(1), 204\u2013209 (2004)","journal-title":"Proc. Nat. Acad. Sci."},{"issue":"5","key":"8_CR22","doi-asserted-by":"publisher","first-page":"865","DOI":"10.1016\/0092-8674(92)90561-P","volume":"71","author":"H Leonhardt","year":"1992","unstructured":"Leonhardt, H., Page, A.W., Weier, H.U., Bestor, T.H.: A targeting sequence directs DNA methyltransferase to sites of DNA replication in mammalian nuclei. Cell 71(5), 865\u2013873 (1992)","journal-title":"Cell"},{"key":"8_CR23","series-title":"Lecture Notes in Computer Science","doi-asserted-by":"publisher","first-page":"160","DOI":"10.1007\/978-3-319-67471-1_10","volume-title":"Computational Methods in Systems Biology","author":"A L\u00fcck","year":"2017","unstructured":"L\u00fcck, A., Giehr, P., Walter, J., Wolf, V.: A stochastic model for the formation of spatial methylation patterns. In: Feret, J., Koeppl, H. (eds.) CMSB 2017. LNCS, vol. 10545, pp. 160\u2013178. Springer, Cham (2017). https:\/\/doi.org\/10.1007\/978-3-319-67471-1_10"},{"issue":"41","key":"8_CR24","doi-asserted-by":"publisher","first-page":"35334","DOI":"10.1074\/jbc.C111.284620","volume":"286","author":"A Maiti","year":"2011","unstructured":"Maiti, A., Drohat, A.C.: Thymine DNA glycosylase can rapidly excise 5-formylcytosine and 5-carboxylcytosine potential implications for active demethylation of CpG sites. J. Biol. Chem. 286(41), 35334\u201335338 (2011)","journal-title":"J. Biol. Chem."},{"issue":"7183","key":"8_CR25","doi-asserted-by":"publisher","first-page":"45","DOI":"10.1038\/nature06544","volume":"452","author":"R M\u00e9tivier","year":"2008","unstructured":"M\u00e9tivier, R., et al.: Cyclical DNA methylation of a transcriptionally active promoter. Nature 452(7183), 45 (2008)","journal-title":"Nature"},{"issue":"6","key":"8_CR26","doi-asserted-by":"publisher","first-page":"848","DOI":"10.1016\/j.molcel.2016.04.025","volume":"62","author":"F Meyenn von","year":"2016","unstructured":"von Meyenn, F., et al.: Impairment of DNA methylation maintenance is the main cause of global demethylation in naive embryonic stem cells. Mol. Cell 62(6), 848\u2013861 (2016)","journal-title":"Mol. Cell"},{"issue":"7","key":"8_CR27","doi-asserted-by":"publisher","first-page":"1191","DOI":"10.1038\/nprot.2016.063","volume":"11","author":"F Neri","year":"2016","unstructured":"Neri, F., Incarnato, D., Krepelova, A., Parlato, C., Oliviero, S.: Methylation-assisted bisulfite sequencing to simultaneously map 5fC and 5caC on a genome-wide scale for DNA demethylation analysis. Nat. Protoc. 11(7), 1191 (2016)","journal-title":"Nat. Protoc."},{"issue":"3","key":"8_CR28","doi-asserted-by":"publisher","first-page":"247","DOI":"10.1016\/S0092-8674(00)81656-6","volume":"99","author":"M Okano","year":"1999","unstructured":"Okano, M., Bell, D.W., Haber, D.A., Li, E.: DNA methyltransferases Dnmt3a and Dnmt3b are essential for de novo methylation and mammalian development. Cell 99(3), 247\u2013257 (1999)","journal-title":"Cell"},{"issue":"3","key":"8_CR29","doi-asserted-by":"publisher","first-page":"219","DOI":"10.1038\/890","volume":"19","author":"M Okano","year":"1998","unstructured":"Okano, M., Xie, S., Li, E.: Cloning and characterization of a family of novel mammalian DNA (cytosine-5) methyltransferases. Nat. Genet. 19(3), 219 (1998)","journal-title":"Nat. Genet."},{"issue":"5929","key":"8_CR30","doi-asserted-by":"publisher","first-page":"930","DOI":"10.1126\/science.1170116","volume":"324","author":"M Tahiliani","year":"2009","unstructured":"Tahiliani, M., et al.: Conversion of 5-methylcytosine to 5-hydroxymethylcytosine in mammalian DNA by MLL partner TET1. Science 324(5929), 930\u2013935 (2009)","journal-title":"Science"}],"container-title":["Lecture Notes in Computer Science","Hybrid Systems Biology"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1007\/978-3-030-28042-0_8","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,9,18]],"date-time":"2023-09-18T19:02:04Z","timestamp":1695063724000},"score":1,"resource":{"primary":{"URL":"http:\/\/link.springer.com\/10.1007\/978-3-030-28042-0_8"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2019]]},"ISBN":["9783030280413","9783030280420"],"references-count":30,"URL":"https:\/\/doi.org\/10.1007\/978-3-030-28042-0_8","relation":{},"ISSN":["0302-9743","1611-3349"],"issn-type":[{"type":"print","value":"0302-9743"},{"type":"electronic","value":"1611-3349"}],"subject":[],"published":{"date-parts":[[2019]]},"assertion":[{"value":"1 August 2019","order":1,"name":"first_online","label":"First Online","group":{"name":"ChapterHistory","label":"Chapter History"}},{"value":"HSB","order":1,"name":"conference_acronym","label":"Conference Acronym","group":{"name":"ConferenceInfo","label":"Conference Information"}},{"value":"International Workshop on Hybrid Systems Biology","order":2,"name":"conference_name","label":"Conference Name","group":{"name":"ConferenceInfo","label":"Conference Information"}},{"value":"Prague","order":3,"name":"conference_city","label":"Conference City","group":{"name":"ConferenceInfo","label":"Conference Information"}},{"value":"Czech Republic","order":4,"name":"conference_country","label":"Conference Country","group":{"name":"ConferenceInfo","label":"Conference Information"}},{"value":"2019","order":5,"name":"conference_year","label":"Conference Year","group":{"name":"ConferenceInfo","label":"Conference Information"}},{"value":"6 April 2019","order":7,"name":"conference_start_date","label":"Conference Start Date","group":{"name":"ConferenceInfo","label":"Conference Information"}},{"value":"7 April 2019","order":8,"name":"conference_end_date","label":"Conference End Date","group":{"name":"ConferenceInfo","label":"Conference Information"}},{"value":"6","order":9,"name":"conference_number","label":"Conference Number","group":{"name":"ConferenceInfo","label":"Conference Information"}},{"value":"hsb2019","order":10,"name":"conference_id","label":"Conference ID","group":{"name":"ConferenceInfo","label":"Conference Information"}},{"value":"http:\/\/hsb2019.fit.vutbr.cz","order":11,"name":"conference_url","label":"Conference URL","group":{"name":"ConferenceInfo","label":"Conference Information"}}]}}