{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,6,24]],"date-time":"2026-06-24T13:48:34Z","timestamp":1782308914114,"version":"3.54.5"},"reference-count":18,"publisher":"Oxford University Press (OUP)","issue":"6","license":[{"start":{"date-parts":[[2026,5,25]],"date-time":"2026-05-25T00:00:00Z","timestamp":1779667200000},"content-version":"vor","delay-in-days":1,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100014013","name":"United Kingdom Research and Innovation","doi-asserted-by":"crossref","award":["MR\/T020504\/1"],"award-info":[{"award-number":["MR\/T020504\/1"]}],"id":[{"id":"10.13039\/100014013","id-type":"DOI","asserted-by":"crossref"}]},{"DOI":"10.13039\/100014013","name":"United Kingdom Research and Innovation","doi-asserted-by":"crossref","award":["UKRI1069"],"award-info":[{"award-number":["UKRI1069"]}],"id":[{"id":"10.13039\/100014013","id-type":"DOI","asserted-by":"crossref"}]},{"DOI":"10.13039\/501100002203","name":"The Brain Tumour Charity","doi-asserted-by":"publisher","award":["ET_2023_2 10759"],"award-info":[{"award-number":["ET_2023_2 10759"]}],"id":[{"id":"10.13039\/501100002203","id-type":"DOI","asserted-by":"publisher"}]},{"name":"The Oman Medical Specialty Board"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2026,6,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:sec>\n                    <jats:title>Motivation<\/jats:title>\n                    <jats:p>Chromatin regulation is crucial for modulating gene expression and cellular function by altering DNA accessibility. Defining and understanding chromatin regulation across diverse biological conditions, including health and disease, requires quantification of both the presence and enrichment level of diverse DNA-binding factors and chromatin modifications across defined genomic regions. Existing approaches mainly rely on peak-based or genome-wide models, which identify high-signal regions but do not annotate chromatin status at predefined functional genomic regions, such as promoters or enhancers. This lack of region-based annotation limits downstream comparative and integrative analyses across multiple factors and datasets, prompting us to create ChromCall.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Results<\/jats:title>\n                    <jats:p>ChromCall is an R package for region-based chromatin enrichment analysis that provides a robust and extensible foundation for transparent and reproducible epigenomic profiling at predefined genomic regions. We applied ChromCall to ChIP-seq data from glioblastoma (GBM) brain tumours and found that the promoters of genes implicated in treatment resistance are significantly more likely to exhibit a combination of histone marks associated with phenotypic plasticity. This highlights a potential novel mechanism of therapeutic escape in these deadly tumours.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Availability and Implementation<\/jats:title>\n                    <jats:p>The R package is available on https:\/\/github.com\/GliomaGenomics\/ChromCall and the version used in this paper is archived at https:\/\/doi.org\/10.5281\/zenodo.19580967<\/jats:p>\n                  <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btag336","type":"journal-article","created":{"date-parts":[[2026,5,21]],"date-time":"2026-05-21T11:46:10Z","timestamp":1779363970000},"source":"Crossref","is-referenced-by-count":0,"title":["ChromCall: assigning chromatin status to defined genomic regions using epigenomic profiling data"],"prefix":"10.1093","volume":"42","author":[{"given":"Bo","family":"Wang","sequence":"first","affiliation":[{"name":"University of Leeds , Leeds, LS9 7TF,","place":["United Kingdom"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Muna","family":"Al-Jabri","sequence":"additional","affiliation":[{"name":"University of Leeds , Leeds, LS9 7TF,","place":["United Kingdom"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Udayaraja","family":"GK","sequence":"additional","affiliation":[{"name":"University of Leeds , Leeds, LS9 7TF,","place":["United Kingdom"]},{"name":"Aarhus University , Aarhus, 8000,","place":["Denmark"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Alastair","family":"Droop","sequence":"additional","affiliation":[{"name":"University of York , York, YO10 5DD,","place":["United Kingdom"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-9550-4150","authenticated-orcid":false,"given":"Lucy F","family":"Stead","sequence":"additional","affiliation":[{"name":"University of Leeds , Leeds, LS9 7TF,","place":["United Kingdom"]}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2026,5,24]]},"reference":[{"key":"2026062409112050700_btag336-B1","doi-asserted-by":"crossref","first-page":"71","DOI":"10.1038\/s41576-019-0173-8","article-title":"Determinants of enhancer and promoter activities of regulatory elements","volume":"21","author":"Andersson","year":"2020","journal-title":"Nat Rev Genet"},{"key":"2026062409112050700_btag336-B2","doi-asserted-by":"crossref","first-page":"315","DOI":"10.1016\/j.cell.2006.02.041","article-title":"A bivalent chromatin structure marks key developmental genes in embryonic stem cells","volume":"125","author":"Bernstein","year":"2006","journal-title":"Cell"},{"key":"2026062409112050700_btag336-B3","doi-asserted-by":"crossref","first-page":"399","DOI":"10.3389\/fgene.2014.00399","article-title":"Quantifying the impact of inter-site heterogeneity on the distribution of ChIP-seq data","volume":"5","author":"Cairns","year":"2014","journal-title":"Front Genet"},{"key":"2026062409112050700_btag336-B4","doi-asserted-by":"crossref","first-page":"45","DOI":"10.1146\/annurev-genom-091416-035537","article-title":"Gene regulatory elements, major drivers of human disease","volume":"18","author":"Chatterjee","year":"2017","journal-title":"Annu Rev Genomics Hum Genet"},{"key":"2026062409112050700_btag336-B5","doi-asserted-by":"crossref","first-page":"215","DOI":"10.1038\/nmeth.1906","article-title":"ChromHMM: automating chromatin-state discovery and characterization","volume":"9","author":"Ernst","year":"2012","journal-title":"Nat Methods"},{"key":"2026062409112050700_btag336-B6","doi-asserted-by":"crossref","first-page":"2478","DOI":"10.1038\/nprot.2017.124","article-title":"Chromatin-state discovery and genome annotation with ChromHMM","volume":"12","author":"Ernst","year":"2017","journal-title":"Nat Protoc"},{"key":"2026062409112050700_btag336-B7","doi-asserted-by":"crossref","first-page":"1728","DOI":"10.1038\/nprot.2012.101","article-title":"Identifying ChIP-seq enrichment using MACS","volume":"7","author":"Feng","year":"2012","journal-title":"Nat Protoc"},{"key":"2026062409112050700_btag336-B8","doi-asserted-by":"crossref","first-page":"2463","DOI":"10.1158\/0008-5472.CAN-17-1724","article-title":"Bivalent chromatin domains in glioblastoma reveal a subtype-specific signature of glioma stem cells","volume":"78","author":"Hall","year":"2018","journal-title":"Cancer Res"},{"key":"2026062409112050700_btag336-B9","doi-asserted-by":"crossref","first-page":"618","DOI":"10.1038\/ncb2065","article-title":"Jarid2 is a PRC2 component in embryonic stem cells required for multi-lineage differentiation and recruitment of PRC1 and RNA polymerase II to developmental regulators","volume":"12","author":"Landeira","year":"2010","journal-title":"Nat Cell Biol"},{"key":"2026062409112050700_btag336-B10","doi-asserted-by":"crossref","first-page":"e45","DOI":"10.1093\/nar\/gkv1191","article-title":"csaw: a bioconductor package for differential binding analysis of ChIP-seq data using sliding windows","volume":"44","author":"Lun","year":"2016","journal-title":"Nucleic Acids Res"},{"key":"2026062409112050700_btag336-B11","doi-asserted-by":"crossref","first-page":"42","DOI":"10.1186\/s13072-019-0287-4","article-title":"Peak calling by sparse enrichment analysis for CUT&RUN chromatin profiling","volume":"12","author":"Meers","year":"2019","journal-title":"Epigenetics Chromatin"},{"key":"2026062409112050700_btag336-B12","doi-asserted-by":"crossref","first-page":"553","DOI":"10.1038\/nature06008","article-title":"Genome-wide maps of chromatin state in pluripotent and lineage-committed cells","volume":"448","author":"Mikkelsen","year":"2007","journal-title":"Nature"},{"key":"2026062409112050700_btag336-B13","doi-asserted-by":"crossref","first-page":"156","DOI":"10.1016\/j.cell.2010.09.006","article-title":"Comparative epigenomic analysis of murine and human adipogenesis","volume":"143","author":"Mikkelsen","year":"2010","journal-title":"Cell"},{"key":"2026062409112050700_btag336-B14","doi-asserted-by":"crossref","first-page":"W187","DOI":"10.1093\/nar\/gku365","article-title":"deepTools: a flexible platform for exploring deep-sequencing data","volume":"42","author":"Ram\u00edrez","year":"2014","journal-title":"Nucleic Acids Res"},{"key":"2026062409112050700_btag336-B15","doi-asserted-by":"crossref","first-page":"1567","DOI":"10.1016\/j.celrep.2013.04.021","article-title":"An aberrant transcription factor network essential for wnt signaling and stem cell maintenance in glioblastoma","volume":"3","author":"Rheinbay","year":"2013","journal-title":"Cell Rep"},{"key":"2026062409112050700_btag336-B16","author":"Stark","year":"2024"},{"key":"2026062409112050700_btag336-B17","doi-asserted-by":"crossref","first-page":"200255","DOI":"10.1098\/rsob.200255","article-title":"Establishment and function of chromatin modification at enhancers","volume":"10","author":"Tafessu","year":"2020","journal-title":"Open Biol"},{"key":"2026062409112050700_btag336-B18","doi-asserted-by":"crossref","first-page":"45","DOI":"10.1186\/s13059-024-03172-3","article-title":"IDHwt glioblastomas can be stratified by their transcriptional response to standard treatment, with implications for targeted therapy","volume":"25","author":"Tanner","year":"2024","journal-title":"Genome Biol"}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/advance-article-pdf\/doi\/10.1093\/bioinformatics\/btag336\/68377445\/btag336.pdf","content-type":"application\/pdf","content-version":"am","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/42\/6\/btag336\/68377445\/btag336.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/42\/6\/btag336\/68377445\/btag336.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,6,24]],"date-time":"2026-06-24T13:11:32Z","timestamp":1782306692000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/doi\/10.1093\/bioinformatics\/btag336\/8691839"}},"subtitle":[],"editor":[{"given":"Lucy F","family":"Stead","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"editor"}]}],"short-title":[],"issued":{"date-parts":[[2026,5,24]]},"references-count":18,"journal-issue":{"issue":"6","published-print":{"date-parts":[[2026,6,1]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btag336","relation":{},"ISSN":["1367-4803","1367-4811"],"issn-type":[{"value":"1367-4803","type":"print"},{"value":"1367-4811","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2026,6]]},"published":{"date-parts":[[2026,5,24]]},"article-number":"btag336"}}