{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,3,26]],"date-time":"2025-03-26T22:04:52Z","timestamp":1743026692586,"version":"3.40.3"},"publisher-location":"Cham","reference-count":46,"publisher":"Springer International Publishing","isbn-type":[{"type":"print","value":"9783030170820"},{"type":"electronic","value":"9783030170837"}],"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\/978-3-030-17083-7_3","type":"book-chapter","created":{"date-parts":[[2019,4,14]],"date-time":"2019-04-14T23:02:19Z","timestamp":1555282939000},"page":"35-50","update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":2,"title":["ModHMM: A Modular Supra-Bayesian Genome Segmentation Method"],"prefix":"10.1007","author":[{"given":"Philipp","family":"Benner","sequence":"first","affiliation":[]},{"given":"Martin","family":"Vingron","sequence":"additional","affiliation":[]}],"member":"297","published-online":{"date-parts":[[2019,4,2]]},"reference":[{"issue":"7493","key":"3_CR1","doi-asserted-by":"publisher","first-page":"455","DOI":"10.1038\/nature12787","volume":"507","author":"R Andersson","year":"2014","unstructured":"Andersson, R., et al.: An atlas of active enhancers across human cell types and tissues. Nature 507(7493), 455 (2014)","journal-title":"Nature"},{"issue":"4","key":"3_CR2","doi-asserted-by":"publisher","first-page":"823","DOI":"10.1016\/j.cell.2007.05.009","volume":"129","author":"A Barski","year":"2007","unstructured":"Barski, A., et al.: High-resolution profiling of histone methylations in the human genome. Cell 129(4), 823\u2013837 (2007)","journal-title":"Cell"},{"issue":"12","key":"3_CR3","doi-asserted-by":"publisher","first-page":"1213","DOI":"10.1038\/nmeth.2688","volume":"10","author":"JD Buenrostro","year":"2013","unstructured":"Buenrostro, J.D., Giresi, P.G., Zaba, L.C., Chang, H.Y., Greenleaf, W.J.: Transposition of native chromatin for fast and sensitive epigenomic profiling of open chromatin, DNA-binding proteins and nucleosome position. Nat. Methods 10(12), 1213 (2013)","journal-title":"Nat. Methods"},{"issue":"1","key":"3_CR4","doi-asserted-by":"crossref","first-page":"21","DOI":"10.1002\/0471142727.mb2129s109","volume":"109","author":"JD Buenrostro","year":"2015","unstructured":"Buenrostro, J.D., Wu, B., Chang, H.Y., Greenleaf, W.J.: ATAC-seq: a method for assaying chromatin accessibility genome-wide. Curr. Protoco. Mol. Biol. 109(1), 21\u201329 (2015)","journal-title":"Curr. Protoco. Mol. Biol."},{"issue":"1","key":"3_CR5","doi-asserted-by":"publisher","first-page":"78","DOI":"10.1006\/jmbi.1997.0951","volume":"268","author":"C Burge","year":"1997","unstructured":"Burge, C., Karlin, S.: Prediction of complete gene structures in human genomic DNA. J. Mol. Biol. 268(1), 78\u201394 (1997)","journal-title":"J. Mol. Biol."},{"issue":"5","key":"3_CR6","doi-asserted-by":"publisher","first-page":"825","DOI":"10.1016\/j.molcel.2013.01.038","volume":"49","author":"E Calo","year":"2013","unstructured":"Calo, E., Wysocka, J.: Modification of enhancer chromatin: what, how, and why? Mol. cell 49(5), 825\u2013837 (2013)","journal-title":"Mol. cell"},{"key":"3_CR7","doi-asserted-by":"publisher","DOI":"10.1007\/0-387-28982-8","volume-title":"Inference in Hidden Markov Models","author":"O Capp\u00e9","year":"2005","unstructured":"Capp\u00e9, O., Moulines, E., Ryd\u00e9n, T.: Inference in Hidden Markov Models, vol. 6. Springer, Heidelberg (2005). https:\/\/doi.org\/10.1007\/0-387-28982-8"},{"issue":"7414","key":"3_CR8","doi-asserted-by":"publisher","first-page":"57","DOI":"10.1038\/nature11247","volume":"489","author":"EP Consortium","year":"2012","unstructured":"Consortium, E.P., et al.: An integrated encyclopedia of DNA elements in the human genome. Nature 489(7414), 57 (2012)","journal-title":"Nature"},{"issue":"50","key":"3_CR9","doi-asserted-by":"publisher","first-page":"21931","DOI":"10.1073\/pnas.1016071107","volume":"107","author":"MP Creyghton","year":"2010","unstructured":"Creyghton, M.P., et al.: Histone H3K27ac separates active from poised enhancers and predicts developmental state. Proc. Nat. Acad. Sci. 107(50), 21931\u201321936 (2010)","journal-title":"Proc. Nat. Acad. Sci."},{"key":"3_CR10","unstructured":"Dempster, A.P., Laird, N.M., Rubin, D.B.: Maximum likelihood from incomplete data via the EM algorithm. J. Roy. Stat. Soc.: Ser. B (Methodol.) 39(1), 1\u201322 (1977)"},{"key":"3_CR11","volume-title":"Pattern Classification and Scene Analysis","author":"RO Duda","year":"1973","unstructured":"Duda, R.O., Hart, P.E.: Pattern Classification and Scene Analysis. A Wiley-Interscience Publication, New York (1973)"},{"issue":"3","key":"3_CR12","doi-asserted-by":"publisher","first-page":"215","DOI":"10.1038\/nmeth.1906","volume":"9","author":"J Ernst","year":"2012","unstructured":"Ernst, J., Kellis, M.: ChromHMM: automating chromatin-state discovery and characterization. Nat. Methods 9(3), 215 (2012)","journal-title":"Nat. Methods"},{"issue":"12","key":"3_CR13","doi-asserted-by":"publisher","first-page":"2478","DOI":"10.1038\/nprot.2017.124","volume":"12","author":"J Ernst","year":"2017","unstructured":"Ernst, J., Kellis, M.: Chromatin-state discovery and genome annotation with ChromHMM. Nat. Protoc. 12(12), 2478 (2017)","journal-title":"Nat. Protoc."},{"key":"3_CR14","series-title":"Lecture Notes in Computer Science (Lecture Notes in Artificial Intelligence)","doi-asserted-by":"publisher","first-page":"290","DOI":"10.1007\/978-3-540-74782-6_26","volume-title":"AI*IA 2007: Artificial Intelligence and Human-Oriented Computing","author":"U Galassi","year":"2007","unstructured":"Galassi, U., Giordana, A., Saitta, L.: Structured hidden markov model: a general framework for modeling complex sequences. In: Basili, R., Pazienza, M.T. (eds.) AI*IA 2007. LNCS (LNAI), vol. 4733, pp. 290\u2013301. Springer, Heidelberg (2007). https:\/\/doi.org\/10.1007\/978-3-540-74782-6_26"},{"issue":"430","key":"3_CR15","doi-asserted-by":"publisher","first-page":"598","DOI":"10.1080\/01621459.1995.10476552","volume":"90","author":"AE Gelfand","year":"1995","unstructured":"Gelfand, A.E., Mallick, B.K., Dey, D.K.: Modeling expert opinion arising as a partial probabilistic specification. J. Am. Stat. Assoc. 90(430), 598\u2013604 (1995)","journal-title":"J. Am. Stat. Assoc."},{"issue":"1","key":"3_CR16","doi-asserted-by":"publisher","first-page":"114","DOI":"10.1214\/ss\/1177013825","volume":"1","author":"C Genest","year":"1986","unstructured":"Genest, C., Zidek, J.V., et al.: Combining probability distributions: a critique and an annotated bibliography. Stat. Sci. 1(1), 114\u2013135 (1986)","journal-title":"Stat. Sci."},{"key":"3_CR17","doi-asserted-by":"crossref","unstructured":"Gorkin, D., et al.: Systematic mapping of chromatin state landscapes during mouse development. bioRxiv p. 166652 (2017)","DOI":"10.1101\/166652"},{"issue":"9","key":"3_CR18","doi-asserted-by":"publisher","first-page":"E1633","DOI":"10.1073\/pnas.1618353114","volume":"114","author":"Y He","year":"2017","unstructured":"He, Y., et al.: Improved regulatory element prediction based on tissue-specific local epigenomic signatures. Proc. Nat. Acad. Sci. 114(9), E1633\u2013E1640 (2017)","journal-title":"Proc. Nat. Acad. Sci."},{"issue":"3","key":"3_CR19","doi-asserted-by":"publisher","first-page":"311","DOI":"10.1038\/ng1966","volume":"39","author":"ND Heintzman","year":"2007","unstructured":"Heintzman, N.D., et al.: Distinct and predictive chromatin signatures of transcriptional promoters and enhancers in the human genome. Nat. Genet. 39(3), 311 (2007)","journal-title":"Nat. Genet."},{"issue":"3","key":"3_CR20","doi-asserted-by":"publisher","first-page":"144","DOI":"10.1038\/nrm3949","volume":"16","author":"S Heinz","year":"2015","unstructured":"Heinz, S., Romanoski, C.E., Benner, C., Glass, C.K.: The selection and function of cell type-specific enhancers. Nat. Rev. Mol. Cell Biol. 16(3), 144 (2015)","journal-title":"Nat. Rev. Mol. Cell Biol."},{"issue":"5","key":"3_CR21","doi-asserted-by":"publisher","first-page":"473","DOI":"10.1038\/nmeth.1937","volume":"9","author":"MM Hoffman","year":"2012","unstructured":"Hoffman, M.M., Buske, O.J., Wang, J., Weng, Z., Bilmes, J.A., Noble, W.S.: Unsupervised pattern discovery in human chromatin structure through genomic segmentation. Nat. Methods 9(5), 473 (2012)","journal-title":"Nat. Methods"},{"issue":"2","key":"3_CR22","doi-asserted-by":"publisher","first-page":"827","DOI":"10.1093\/nar\/gks1284","volume":"41","author":"MM Hoffman","year":"2012","unstructured":"Hoffman, M.M., et al.: Integrative annotation of chromatin elements from encode data. Nucleic Acids Res. 41(2), 827\u2013841 (2012)","journal-title":"Nucleic Acids Res."},{"issue":"5","key":"3_CR23","doi-asserted-by":"publisher","first-page":"867","DOI":"10.1162\/neco.1995.7.5.867","volume":"7","author":"RA Jacobs","year":"1995","unstructured":"Jacobs, R.A.: Methods for combining experts\u2019 probability assessments. Neural Comput. 7(5), 867\u2013888 (1995)","journal-title":"Neural Comput."},{"issue":"8","key":"3_CR24","doi-asserted-by":"publisher","first-page":"956","DOI":"10.1038\/nsmb.2085","volume":"18","author":"F Koch","year":"2011","unstructured":"Koch, F., et al.: Transcription initiation platforms and GTF recruitment at tissue-specific enhancers and promoters. Nat. Struct. Mol. Biol. 18(8), 956 (2011)","journal-title":"Nat. Struct. Mol. Biol."},{"issue":"7539","key":"3_CR25","doi-asserted-by":"publisher","first-page":"317","DOI":"10.1038\/nature14248","volume":"518","author":"A Kundaje","year":"2015","unstructured":"Kundaje, A., et al.: Integrative analysis of 111 reference human epigenomes. Nature 518(7539), 317 (2015)","journal-title":"Nature"},{"issue":"22","key":"3_CR26","doi-asserted-by":"publisher","first-page":"2893","DOI":"10.1101\/gad.1035902","volume":"16","author":"A Kuzmichev","year":"2002","unstructured":"Kuzmichev, A., Nishioka, K., Erdjument-Bromage, H., Tempst, P., Reinberg, D.: Histone methyltransferase activity associated with a human multiprotein complex containing the Enhancer of Zeste protein. Genes Dev. 16(22), 2893\u20132905 (2002)","journal-title":"Genes Dev."},{"issue":"5","key":"3_CR27","doi-asserted-by":"publisher","first-page":"1021","DOI":"10.1016\/j.cell.2013.01.052","volume":"152","author":"SM Lauberth","year":"2013","unstructured":"Lauberth, S.M., et al.: H3K4me3 interactions with TAF3 regulate preinitiation complex assembly and selective gene activation. Cell 152(5), 1021\u20131036 (2013)","journal-title":"Cell"},{"key":"3_CR28","doi-asserted-by":"publisher","first-page":"117","DOI":"10.2307\/2981425","volume":"145","author":"D Lindley","year":"1982","unstructured":"Lindley, D.: The improvement of probability judgements. J. Roy. Stat. Soc. Ser. A (Gen.) 145, 117\u2013126 (1982)","journal-title":"J. Roy. Stat. Soc. Ser. A (Gen.)"},{"key":"3_CR29","unstructured":"Lindley, D.: Reconciliation of discrete probability distributions. In: J. Bernardo, M. DeGroot, D. Lindley, A. Smith (eds.) Bayesian statistics 2: Proceedings of the Second Valencia International Meeting, pp. 375\u2013390. Valencia University Press (1985)"},{"key":"3_CR30","doi-asserted-by":"publisher","first-page":"146","DOI":"10.2307\/2345078","volume":"142","author":"DV Lindley","year":"1979","unstructured":"Lindley, D.V., Tversky, A., Brown, R.V.: On the reconciliation of probability assessments. J. Roy. Stat. Soc. Ser. A (Gen.) 142, 146\u2013180 (1979)","journal-title":"J. Roy. Stat. Soc. Ser. A (Gen.)"},{"issue":"1","key":"3_CR31","doi-asserted-by":"publisher","first-page":"151","DOI":"10.1186\/s13059-015-0708-z","volume":"16","author":"A Mammana","year":"2015","unstructured":"Mammana, A., Chung, H.R.: Chromatin segmentation based on a probabilistic model for read counts explains a large portion of the epigenome. Genome Biol. 16(1), 151 (2015)","journal-title":"Genome Biol."},{"issue":"7330","key":"3_CR32","doi-asserted-by":"publisher","first-page":"343","DOI":"10.1038\/nature09784","volume":"469","author":"R Margueron","year":"2011","unstructured":"Margueron, R., Reinberg, D.: The polycomb complex PRC2 and its mark in life. Nature 469(7330), 343 (2011)","journal-title":"Nature"},{"issue":"3","key":"3_CR33","doi-asserted-by":"publisher","first-page":"404","DOI":"10.1145\/321075.321084","volume":"8","author":"ME Maron","year":"1961","unstructured":"Maron, M.E.: Automatic indexing: an experimental inquiry. J. ACM (JACM) 8(3), 404\u2013417 (1961)","journal-title":"J. ACM (JACM)"},{"key":"3_CR34","volume-title":"Machine Learning","author":"TM Mitchell","year":"1997","unstructured":"Mitchell, T.M.: Machine Learning. McGraw-Hill Boston, MA (1997)"},{"issue":"7","key":"3_CR35","doi-asserted-by":"publisher","first-page":"621","DOI":"10.1038\/nmeth.1226","volume":"5","author":"A Mortazavi","year":"2008","unstructured":"Mortazavi, A., Williams, B.A., McCue, K., Schaeffer, L., Wold, B.: Mapping and quantifying mammalian transcriptomes by RNA-seq. Nature Methods 5(7), 621 (2008)","journal-title":"Nature Methods"},{"issue":"2","key":"3_CR36","doi-asserted-by":"publisher","first-page":"257","DOI":"10.1109\/5.18626","volume":"77","author":"LR Rabiner","year":"1989","unstructured":"Rabiner, L.R.: A tutorial on hidden markov models and selected applications in speech recognition. Proc. IEEE 77(2), 257\u2013286 (1989)","journal-title":"Proc. IEEE"},{"issue":"W1","key":"3_CR37","doi-asserted-by":"publisher","first-page":"W160","DOI":"10.1093\/nar\/gkw257","volume":"44","author":"F Ram\u00edrez","year":"2016","unstructured":"Ram\u00edrez, F., et al.: deepTools2: a next generation web server for deep-sequencing data analysis. Nucleic Acids Res. 44(W1), W160\u2013W165 (2016)","journal-title":"Nucleic Acids Res."},{"key":"3_CR38","volume-title":"Artificial Intelligence: A Modern Approach","author":"SJ Russell","year":"2016","unstructured":"Russell, S.J., Norvig, P.: Artificial Intelligence: A Modern Approach. Pearson Education Limited, Malaysia (2016)"},{"issue":"1","key":"3_CR39","doi-asserted-by":"publisher","first-page":"3","DOI":"10.1186\/1756-8935-8-3","volume":"8","author":"N Saksouk","year":"2015","unstructured":"Saksouk, N., Simboeck, E., D\u00e9jardin, J.: Constitutive heterochromatin formation and transcription in mammals. Epigenet. Chromatin 8(1), 3 (2015)","journal-title":"Epigenet. Chromatin"},{"issue":"26","key":"3_CR40","doi-asserted-by":"publisher","first-page":"15776","DOI":"10.1073\/pnas.2136655100","volume":"100","author":"T Shiraki","year":"2003","unstructured":"Shiraki, T., et al.: Cap analysis gene expression for high-throughput analysis of transcriptional starting point and identification of promoter usage. Proc. Nat. Acad. Sci. 100(26), 15776\u201315781 (2003)","journal-title":"Proc. Nat. Acad. Sci."},{"issue":"1","key":"3_CR41","doi-asserted-by":"publisher","first-page":"299","DOI":"10.1186\/1471-2105-10-299","volume":"10","author":"C Spyrou","year":"2009","unstructured":"Spyrou, C., Stark, R., Lynch, A.G., Tavar\u00e9, S.: BayesPeak: Bayesian analysis of ChIP-seq data. BMC Bioinf. 10(1), 299 (2009)","journal-title":"BMC Bioinf."},{"issue":"9","key":"3_CR42","doi-asserted-by":"publisher","first-page":"829","DOI":"10.1038\/nmeth.1246","volume":"5","author":"A Valouev","year":"2008","unstructured":"Valouev, A., et al.: Genome-wide analysis of transcription factor binding sites based on ChIP-seq data. Nat. Methods 5(9), 829 (2008)","journal-title":"Nat. Methods"},{"issue":"2","key":"3_CR43","doi-asserted-by":"publisher","first-page":"115","DOI":"10.1038\/nrm3274","volume":"13","author":"EJ Wagner","year":"2012","unstructured":"Wagner, E.J., Carpenter, P.B.: Understanding the language of Lys36 methylation at histone H3. Nature Rev. Mol. Cell Biol. 13(2), 115 (2012)","journal-title":"Nature Rev. Mol. Cell Biol."},{"issue":"7","key":"3_CR44","doi-asserted-by":"publisher","first-page":"e11471","DOI":"10.1371\/journal.pone.0011471","volume":"5","author":"EG Wilbanks","year":"2010","unstructured":"Wilbanks, E.G., Facciotti, M.T.: Evaluation of algorithm performance in ChIP-seq peak detection. PloS One 5(7), e11471 (2010)","journal-title":"PloS One"},{"issue":"8","key":"3_CR45","doi-asserted-by":"publisher","first-page":"4423","DOI":"10.1093\/nar\/gkt143","volume":"41","author":"KJ Won","year":"2013","unstructured":"Won, K.J., et al.: Comparative annotation of functional regions in the human genome using epigenomic data. Nucleic Acids Res. 41(8), 4423\u20134432 (2013)","journal-title":"Nucleic Acids Res."},{"issue":"9","key":"3_CR46","doi-asserted-by":"publisher","first-page":"R137","DOI":"10.1186\/gb-2008-9-9-r137","volume":"9","author":"Y Zhang","year":"2008","unstructured":"Zhang, Y., et al.: Model-based analysis of ChIP-seq (MACS). Genome Biol. 9(9), R137 (2008)","journal-title":"Genome Biol."}],"container-title":["Lecture Notes in Computer Science","Research in Computational Molecular Biology"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1007\/978-3-030-17083-7_3","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2020,12,6]],"date-time":"2020-12-06T09:53:03Z","timestamp":1607248383000},"score":1,"resource":{"primary":{"URL":"http:\/\/link.springer.com\/10.1007\/978-3-030-17083-7_3"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2019]]},"ISBN":["9783030170820","9783030170837"],"references-count":46,"URL":"https:\/\/doi.org\/10.1007\/978-3-030-17083-7_3","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":"2 April 2019","order":1,"name":"first_online","label":"First Online","group":{"name":"ChapterHistory","label":"Chapter History"}},{"value":"RECOMB","order":1,"name":"conference_acronym","label":"Conference Acronym","group":{"name":"ConferenceInfo","label":"Conference Information"}},{"value":"International Conference on Research in Computational Molecular Biology","order":2,"name":"conference_name","label":"Conference Name","group":{"name":"ConferenceInfo","label":"Conference Information"}},{"value":"Washington, DC","order":3,"name":"conference_city","label":"Conference City","group":{"name":"ConferenceInfo","label":"Conference Information"}},{"value":"USA","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":"5 May 2019","order":7,"name":"conference_start_date","label":"Conference Start Date","group":{"name":"ConferenceInfo","label":"Conference Information"}},{"value":"8 May 2019","order":8,"name":"conference_end_date","label":"Conference End Date","group":{"name":"ConferenceInfo","label":"Conference Information"}},{"value":"23","order":9,"name":"conference_number","label":"Conference Number","group":{"name":"ConferenceInfo","label":"Conference Information"}},{"value":"recomb2019","order":10,"name":"conference_id","label":"Conference ID","group":{"name":"ConferenceInfo","label":"Conference Information"}},{"value":"https:\/\/recomb2019.org\/","order":11,"name":"conference_url","label":"Conference URL","group":{"name":"ConferenceInfo","label":"Conference Information"}},{"value":"Single-blind","order":1,"name":"type","label":"Type","group":{"name":"ConfEventPeerReviewInformation","label":"Peer Review Information"}},{"value":"EasyChair","order":2,"name":"conference_management_system","label":"Conference Management System","group":{"name":"ConfEventPeerReviewInformation","label":"Peer Review Information"}},{"value":"175","order":3,"name":"number_of_submissions_sent_for_review","label":"Number of Submissions Sent for Review","group":{"name":"ConfEventPeerReviewInformation","label":"Peer Review Information"}},{"value":"17","order":4,"name":"number_of_full_papers_accepted","label":"Number of Full Papers Accepted","group":{"name":"ConfEventPeerReviewInformation","label":"Peer Review Information"}},{"value":"20","order":5,"name":"number_of_short_papers_accepted","label":"Number of Short Papers Accepted","group":{"name":"ConfEventPeerReviewInformation","label":"Peer Review Information"}},{"value":"10% - The value is computed by the equation \"Number of Full Papers Accepted \/ Number of Submissions Sent for Review * 100\" and then rounded to a whole number.","order":6,"name":"acceptance_rate_of_full_papers","label":"Acceptance Rate of Full Papers","group":{"name":"ConfEventPeerReviewInformation","label":"Peer Review Information"}},{"value":"3","order":7,"name":"average_number_of_reviews_per_paper","label":"Average Number of Reviews per Paper","group":{"name":"ConfEventPeerReviewInformation","label":"Peer Review Information"}},{"value":"7","order":8,"name":"average_number_of_papers_per_reviewer","label":"Average Number of Papers per Reviewer","group":{"name":"ConfEventPeerReviewInformation","label":"Peer Review Information"}},{"value":"Yes","order":9,"name":"external_reviewers_involved","label":"External Reviewers Involved","group":{"name":"ConfEventPeerReviewInformation","label":"Peer Review Information"}}]}}