{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,11]],"date-time":"2026-04-11T16:14:27Z","timestamp":1775924067938,"version":"3.50.1"},"reference-count":29,"publisher":"Oxford University Press (OUP)","issue":"4","license":[{"start":{"date-parts":[[2024,4,3]],"date-time":"2024-04-03T00:00:00Z","timestamp":1712102400000},"content-version":"vor","delay-in-days":5,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"ELIXIR-DE"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2024,3,29]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:sec>\n                    <jats:title>Motivation<\/jats:title>\n                    <jats:p>Automated chromatin segmentation based on ChIP-seq (chromatin immunoprecipitation followed by sequencing) data reveals insights into the epigenetic regulation of chromatin accessibility. Existing segmentation methods are constrained by simplifying modeling assumptions, which may have a negative impact on the segmentation quality.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Results<\/jats:title>\n                    <jats:p>We introduce EpiSegMix, a novel segmentation method based on a hidden Markov model with flexible read count distribution types and state duration modeling, allowing for a more flexible modeling of both histone signals and segment lengths. In a comparison with existing tools, ChromHMM, Segway, and EpiCSeg, we show that EpiSegMix is more predictive of cell biology, such as gene expression. Its flexible framework enables it to fit an accurate probabilistic model, which has the potential to increase the biological interpretability of chromatin states.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Availability and implementation<\/jats:title>\n                    <jats:p>Source code: https:\/\/gitlab.com\/rahmannlab\/episegmix.<\/jats:p>\n                  <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btae178","type":"journal-article","created":{"date-parts":[[2024,4,2]],"date-time":"2024-04-02T20:46:40Z","timestamp":1712090800000},"source":"Crossref","is-referenced-by-count":3,"title":["EpiSegMix: a flexible distribution hidden Markov model with duration modeling for chromatin state discovery"],"prefix":"10.1093","volume":"40","author":[{"ORCID":"https:\/\/orcid.org\/0009-0002-6377-2561","authenticated-orcid":false,"given":"Johanna Elena","family":"Schmitz","sequence":"first","affiliation":[{"name":"Algorithmic Bioinformatics, Center for Bioinformatics Saar, Saarland Informatics Campus , 66123 Saarbr\u00fccken, Germany"},{"name":"Fakult\u00e4t MI, Saarland University, Saarland Informatics Campus , 66123 Saarbr\u00fccken, Germany"},{"name":"Saarbr\u00fccken Graduate School of Computer Science, Saarland Informatics Campus , 66123 Saarbr\u00fccken, Germany"}]},{"given":"Nihit","family":"Aggarwal","sequence":"additional","affiliation":[{"name":"Department of Genetics, Saarland University , 66123 Saarbr\u00fccken, Germany"}]},{"given":"Lukas","family":"Laufer","sequence":"additional","affiliation":[{"name":"Department of Genetics, Saarland University , 66123 Saarbr\u00fccken, Germany"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-0563-7417","authenticated-orcid":false,"given":"J\u00f6rn","family":"Walter","sequence":"additional","affiliation":[{"name":"Department of Genetics, Saarland University , 66123 Saarbr\u00fccken, Germany"}]},{"given":"Abdulrahman","family":"Salhab","sequence":"additional","affiliation":[{"name":"Department of Genetics, Saarland University , 66123 Saarbr\u00fccken, Germany"},{"name":"Genomics Data Science Core, Integrated Genomics Services, Sidra Medicine , Doha, Qatar"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8536-6065","authenticated-orcid":false,"given":"Sven","family":"Rahmann","sequence":"additional","affiliation":[{"name":"Algorithmic Bioinformatics, Center for Bioinformatics Saar, Saarland Informatics Campus , 66123 Saarbr\u00fccken, Germany"},{"name":"Fakult\u00e4t MI, Saarland University, Saarland Informatics Campus , 66123 Saarbr\u00fccken, Germany"}]}],"member":"286","published-online":{"date-parts":[[2024,4,2]]},"reference":[{"key":"2024041900043672900_btae178-B1","doi-asserted-by":"crossref","first-page":"487","DOI":"10.1038\/nrg.2016.59","article-title":"The molecular hallmarks of epigenetic control","volume":"17","author":"Allis","year":"2016","journal-title":"Nat Rev Genet"},{"key":"2024041900043672900_btae178-B2","doi-asserted-by":"crossref","first-page":"717","DOI":"10.1038\/nmeth.1673","article-title":"Making sense of chromatin states","volume":"8","author":"Baker","year":"2011","journal-title":"Nat Methods"},{"key":"2024041900043672900_btae178-B3","doi-asserted-by":"crossref","first-page":"381","DOI":"10.1038\/cr.2011.22","article-title":"Regulation of chromatin by histone modifications","volume":"21","author":"Bannister","year":"2011","journal-title":"Cell Res"},{"key":"2024041900043672900_btae178-B4","doi-asserted-by":"crossref","first-page":"823","DOI":"10.1016\/j.cell.2007.05.009","article-title":"High-resolution profiling of histone methylations in the human genome","volume":"129","author":"Barski","year":"2007","journal-title":"Cell"},{"key":"2024041900043672900_btae178-B5","doi-asserted-by":"crossref","first-page":"138","DOI":"10.1186\/s13148-021-01126-1","article-title":"The dynamic broad epigenetic (H3K4me3, H3K27ac) domain as a mark of essential genes","volume":"13","author":"Beacon","year":"2021","journal-title":"Clin Epigenet"},{"key":"2024041900043672900_btae178-B6","article-title":"A gentle tutorial of the EM algorithm and its application to parameter estimation for Gaussian mixture and hidden Markov models","author":"Bilmes","year":"1998","journal-title":"ICSI Tech Rep Ser vol. 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