{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,23]],"date-time":"2026-10-23T22:41:07Z","timestamp":1792795267854,"version":"4.5.0"},"reference-count":48,"publisher":"Oxford University Press (OUP)","issue":"10","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2026,10,2]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:sec>\n                    <jats:title>Motivation<\/jats:title>\n                    <jats:p>Sequencing-based epigenomic profiling methods are powerful but suffer from technical variability that complicates cross-sample comparisons and can obscure true biological signals. While existing normalization methods using spike-in controls or computational approaches have been proposed, they often rely on assumptions that may not hold across diverse experimental conditions or require additional data types.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Results<\/jats:title>\n                    <jats:p>We present Ryder, a flexible and robust Python package for the normalization of epigenomic signal tracks. Ryder leverages stable internal reference regions, such as invariant CTCF binding sites, to correct for technical artifacts genome-wide. Our results show that it effectively adjusts both background noise and signal intensity, ensuring accurate signal alignment across samples while preserving genuine biological differences. We demonstrate that Ryder performs robustly across diverse assays including DNase-seq, CUT&amp;RUN, ATAC-seq, MNase-seq, and ChIP-seq, with or without spike-in controls. By reducing technical noise, Ryder improves the detection of genuine biological changes, such as quantitative reduction of chromatin accessibility at key enhancer elements by depletion of BRG1, a key subunit of the chromatin remodeling BAF complexes.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Availability and implementation<\/jats:title>\n                    <jats:p>The Ryder source code, documentation and test data are freely available at: https:\/\/github.com\/YaqiangCao\/ryder. The software version used in this study is archived at Zenodo: https:\/\/zenodo.org\/records\/21267457.<\/jats:p>\n                  <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btag753","type":"journal-article","created":{"date-parts":[[2026,10,15]],"date-time":"2026-10-15T11:50:15Z","timestamp":1792065015000},"source":"Crossref","is-referenced-by-count":0,"title":["Ryder: epigenome normalization using a two-tier model and internal reference regions"],"prefix":"10.1093","volume":"42","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-4665-1517","authenticated-orcid":false,"given":"Yaqiang","family":"Cao","sequence":"first","affiliation":[{"name":"Division of Intramural Research, Laboratory of Epigenome Biology, Systems Biology Center, National Heart, Lung, and Blood Institute, National Institutes of Health , Bethesda, MD 20892,","place":["United States"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Guangzhe","family":"Ge","sequence":"additional","affiliation":[{"name":"Division of Intramural Research, Laboratory of Epigenome Biology, Systems Biology Center, National Heart, Lung, and Blood Institute, National Institutes of Health , Bethesda, MD 20892,","place":["United States"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-5559-6233","authenticated-orcid":false,"given":"Keji","family":"Zhao","sequence":"additional","affiliation":[{"name":"Division of Intramural Research, Laboratory of Epigenome Biology, Systems Biology Center, National Heart, Lung, and Blood Institute, National Institutes of Health , Bethesda, MD 20892,","place":["United States"]}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2026,10,15]]},"reference":[{"key":"2026102318315736400_btag753-B1","doi-asserted-by":"publisher","first-page":"9354","DOI":"10.1038\/s41598-019-45839-z","article-title":"The ENCODE blacklist: identification of problematic regions of the genome","volume":"9","author":"Amemiya","year":"2019","journal-title":"Sci Rep"},{"key":"2026102318315736400_btag753-B2","doi-asserted-by":"publisher","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":"2026102318315736400_btag753-B3","doi-asserted-by":"publisher","first-page":"e11002","DOI":"10.15252\/msb.202211002","article-title":"Aging is associated with increased chromatin accessibility and reduced polymerase pausing in liver","volume":"18","author":"Bozukova","year":"2022","journal-title":"Mol Syst Biol"},{"key":"2026102318315736400_btag753-B4","doi-asserted-by":"publisher","first-page":"496","DOI":"10.1038\/nature11142","article-title":"A map of nucleosome positions in yeast at base-pair resolution","volume":"486","author":"Brogaard","year":"2012","journal-title":"Nature"},{"key":"2026102318315736400_btag753-B5","doi-asserted-by":"publisher","first-page":"98","DOI":"10.1097\/COC.0000000000000239","article-title":"CTLA-4 and PD-1 pathways: similarities, differences, and implications of their inhibition","volume":"39","author":"Buchbinder","year":"2016","journal-title":"Am J Clin Oncol"},{"key":"2026102318315736400_btag753-B6","doi-asserted-by":"publisher","first-page":"1213","DOI":"10.1038\/nmeth.2688","article-title":"Transposition of native chromatin for fast and sensitive epigenomic profiling of open chromatin, DNA-binding proteins and nucleosome position","volume":"10","author":"Buenrostro","year":"2013","journal-title":"Nat Methods"},{"key":"2026102318315736400_btag753-B7","doi-asserted-by":"publisher","first-page":"6172","DOI":"10.1093\/nar\/gkad378","article-title":"Hi-TrAC detects active sub-TADs and reveals internal organizations of super-enhancers","volume":"51","author":"Cao","year":"2023","journal-title":"Nucleic Acids Res"},{"key":"2026102318315736400_btag753-B8","doi-asserted-by":"publisher","first-page":"57","DOI":"10.1093\/nar\/gkab1233","article-title":"cLoops2: a full-stack comprehensive analytical tool for chromatin interactions","volume":"50","author":"Cao","year":"2022","journal-title":"Nucleic Acids Res"},{"key":"2026102318315736400_btag753-B9","doi-asserted-by":"publisher","first-page":"7611","DOI":"10.1073\/pnas.1800656115","article-title":"Repression of human and mouse brain inflammaging transcriptome by broad gene-body histone hyperacetylation","volume":"115","author":"Cheng","year":"2018","journal-title":"Proc Natl Acad Sci USA"},{"key":"2026102318315736400_btag753-B10","doi-asserted-by":"publisher","first-page":"944","DOI":"10.1016\/j.immuni.2023.03.006","article-title":"Restraint of IFN-gamma expression through a distal silencer CNS-28 for tissue homeostasis","volume":"56","author":"Cui","year":"2023","journal-title":"Immunity"},{"key":"2026102318315736400_btag753-B11","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1016\/S0169-7439(99)00047-7","article-title":"The mahalanobis distance","volume":"50","author":"De Maesschalck","year":"2000","journal-title":"Chemom Intell Lab Syst"},{"key":"2026102318315736400_btag753-B12","doi-asserted-by":"publisher","first-page":"376","DOI":"10.1038\/nature11082","article-title":"Topological domains in mammalian genomes identified by analysis of chromatin interactions","volume":"485","author":"Dixon","year":"2012","journal-title":"Nature"},{"key":"2026102318315736400_btag753-B13","doi-asserted-by":"publisher","first-page":"e0166438","DOI":"10.1371\/journal.pone.0166438","article-title":"An alternative approach to ChIP-Seq normalization enables detection of genome-wide changes in histone H3 lysine 27 trimethylation upon EZH2 inhibition","volume":"11","author":"Egan","year":"2016","journal-title":"PLoS One"},{"key":"2026102318315736400_btag753-B14","doi-asserted-by":"publisher","DOI":"10.1038\/nature11247"},{"key":"2026102318315736400_btag753-B15","doi-asserted-by":"publisher","first-page":"247","DOI":"10.1186\/s13059-020-02152-7","article-title":"Cancer-specific CTCF binding facilitates oncogenic transcriptional dysregulation","volume":"21","author":"Fang","year":"2020","journal-title":"Genome Biol"},{"key":"2026102318315736400_btag753-B16","doi-asserted-by":"publisher","first-page":"D766","DOI":"10.1093\/nar\/gky955","article-title":"GENCODE reference annotation for the human and mouse genomes","volume":"47","author":"Frankish","year":"2019","journal-title":"Nucleic Acids Res"},{"key":"2026102318315736400_btag753-B17","doi-asserted-by":"publisher","first-page":"628","DOI":"10.1128\/CDLI.8.3.628-631.2001","article-title":"Gamma interferon expression in CD8(+) T cells is a marker for circulating cytotoxic T lymphocytes that recognize an HLA A2-restricted epitope of human cytomegalovirus phosphoprotein pp65","volume":"8","author":"Ghanekar","year":"2001","journal-title":"Clin Diagn Lab Immunol"},{"key":"2026102318315736400_btag753-B18","doi-asserted-by":"publisher","first-page":"1518","DOI":"10.1038\/s41596-022-00692-9","article-title":"Chromatin accessibility profiling by ATAC-seq","volume":"17","author":"Grandi","year":"2022","journal-title":"Nat Protoc"},{"key":"2026102318315736400_btag753-B19","doi-asserted-by":"publisher","first-page":"2250","DOI":"10.1038\/s41588-025-02305-z","article-title":"Precise modulation of BRG1 levels reveals features of mSWI\/SNF dosage sensitivity","volume":"57","author":"Hagihara","year":"2025","journal-title":"Nat Genet"},{"key":"2026102318315736400_btag753-B20","doi-asserted-by":"publisher","first-page":"73","DOI":"10.1038\/nmeth.2762","article-title":"Refined DNase-seq protocol and data analysis reveals intrinsic bias in transcription factor footprint identification","volume":"11","author":"He","year":"2014","journal-title":"Nat Methods"},{"key":"2026102318315736400_btag753-B21","doi-asserted-by":"publisher","first-page":"18318","DOI":"10.1073\/pnas.1110731108","article-title":"Epigenome characterization at single base-pair resolution","volume":"108","author":"Henikoff","year":"2011","journal-title":"Proc Natl Acad Sci USA"},{"key":"2026102318315736400_btag753-B22","doi-asserted-by":"publisher","first-page":"1650","DOI":"10.1101\/gr.121145.111","article-title":"Regulation of nucleosome landscape and transcription factor targeting at tissue-specific enhancers by BRG1","volume":"21","author":"Hu","year":"2011","journal-title":"Genome Res"},{"key":"2026102318315736400_btag753-B23","doi-asserted-by":"publisher","first-page":"501","DOI":"10.1016\/j.csbj.2025.01.018","article-title":"IGN: invariable gene set-based normalization for chromatin accessibility profile data analysis","volume":"27","author":"Hu","year":"2025","journal-title":"Comput Struct Biotechnol J"},{"key":"2026102318315736400_btag753-B24","doi-asserted-by":"publisher","first-page":"279","DOI":"10.1038\/s41588-020-00768-w","article-title":"Mammalian SWI\/SNF continuously restores local accessibility to chromatin","volume":"53","author":"Iurlaro","year":"2021","journal-title":"Nat Genet"},{"key":"2026102318315736400_btag753-B25","doi-asserted-by":"publisher","DOI":"10.7554\/eLife.22631","article-title":"The pioneer factor OCT4 requires the chromatin remodeller BRG1 to support gene regulatory element function in mouse embryonic stem cells","volume":"6","author":"King","year":"2017","journal-title":"eLife"},{"key":"2026102318315736400_btag753-B26","doi-asserted-by":"publisher","first-page":"317","DOI":"10.1038\/nature14248","article-title":"Integrative analysis of 111 reference human epigenomes","volume":"518","author":"Kundaje","year":"2015","journal-title":"Nature"},{"key":"2026102318315736400_btag753-B27","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btad018","article-title":"Cistrome Explorer: an interactive visual analysis tool for large-scale epigenomic data","volume":"39","author":"L\u2019yi","year":"2023","journal-title":"Bioinformatics"},{"key":"2026102318315736400_btag753-B28","doi-asserted-by":"publisher","first-page":"357","DOI":"10.1038\/nmeth.1923","article-title":"Fast gapped-read alignment with Bowtie 2","volume":"9","author":"Langmead","year":"2012","journal-title":"Nat Methods"},{"key":"2026102318315736400_btag753-B29","doi-asserted-by":"publisher","first-page":"550","DOI":"10.1186\/s13059-014-0550-8","article-title":"Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2","volume":"15","author":"Love","year":"2014","journal-title":"Genome Biol"},{"key":"2026102318315736400_btag753-B30","doi-asserted-by":"publisher","first-page":"1487","DOI":"10.3324\/haematol.2013.094243","article-title":"BLUEPRINT: mapping human blood cell epigenomes","volume":"98","author":"Martens","year":"2013","journal-title":"Haematologica"},{"key":"2026102318315736400_btag753-B31","doi-asserted-by":"publisher","first-page":"5290","DOI":"10.1016\/j.cell.2023.10.006","article-title":"Global identification of SWI\/SNF targets reveals compensation by EP400","volume":"186","author":"Martin","year":"2023","journal-title":"Cell"},{"key":"2026102318315736400_btag753-B32","doi-asserted-by":"publisher","first-page":"269","DOI":"10.1016\/j.ajhg.2021.01.001","article-title":"Topologically associating domain boundaries that are stable across diverse cell types are evolutionarily constrained and enriched for heritability","volume":"108","author":"McArthur","year":"2021","journal-title":"Am J Hum Genet"},{"key":"2026102318315736400_btag753-B33","doi-asserted-by":"publisher","first-page":"709","DOI":"10.1038\/nrg3788","article-title":"Identifying and mitigating bias in next-generation sequencing methods for chromatin biology","volume":"15","author":"Meyer","year":"2014","journal-title":"Nat Rev Genet"},{"key":"2026102318315736400_btag753-B34","doi-asserted-by":"publisher","first-page":"1789","DOI":"10.1007\/s11357-023-00986-0","article-title":"ATAC-clock: an aging clock based on chromatin accessibility","volume":"46","author":"Morandini","year":"2024","journal-title":"Geroscience"},{"key":"2026102318315736400_btag753-B35","doi-asserted-by":"publisher","first-page":"45","DOI":"10.1007\/978-1-4939-0512-6_3","article-title":"edgeR for differential RNA-seq and ChIP-seq analysis: an application to stem cell biology","volume":"1150","author":"Nikolayeva","year":"2014","journal-title":"Methods Mol Biol"},{"key":"2026102318315736400_btag753-B36","doi-asserted-by":"publisher","first-page":"1163","DOI":"10.1016\/j.celrep.2014.10.018","article-title":"Quantitative ChIP-Seq normalization reveals global modulation of the epigenome","volume":"9","author":"Orlando","year":"2014","journal-title":"Cell Rep"},{"key":"2026102318315736400_btag753-B37","doi-asserted-by":"publisher","first-page":"863","DOI":"10.1016\/s1074-7613(03)00328-5","article-title":"Critical roles for transcription factor GATA-3 in thymocyte development","volume":"19","author":"Pai","year":"2003","journal-title":"Immunity"},{"key":"2026102318315736400_btag753-B38","doi-asserted-by":"publisher","first-page":"669","DOI":"10.1038\/nrg2641","article-title":"ChIP-seq: advantages and challenges of a maturing technology","volume":"10","author":"Park","year":"2009","journal-title":"Nat Rev Genet"},{"key":"2026102318315736400_btag753-B39","doi-asserted-by":"publisher","first-page":"1343","DOI":"10.1038\/s41587-024-02377-y","article-title":"The Wild West of spike-in normalization","volume":"42","author":"Patel","year":"2024","journal-title":"Nat Biotechnol"},{"key":"2026102318315736400_btag753-B40","doi-asserted-by":"publisher","first-page":"D1243","DOI":"10.1093\/nar\/gkae974","article-title":"The UCSC Genome Browser database: 2025 update","volume":"53","author":"Perez","year":"2025","journal-title":"Nucleic Acids Res"},{"key":"2026102318315736400_btag753-B41","doi-asserted-by":"publisher","first-page":"841","DOI":"10.1093\/bioinformatics\/btq033","article-title":"BEDTools: a flexible suite of utilities for comparing genomic features","volume":"26","author":"Quinlan","year":"2010","journal-title":"Bioinformatics"},{"key":"2026102318315736400_btag753-B42","doi-asserted-by":"publisher","first-page":"W160","DOI":"10.1093\/nar\/gkw257","article-title":"deepTools2: a next generation web server for deep-sequencing data analysis","volume":"44","author":"Ram\u00edrez","year":"2016","journal-title":"Nucleic Acids Res"},{"key":"2026102318315736400_btag753-B43","doi-asserted-by":"publisher","first-page":"4561","DOI":"10.1038\/s41467-024-48911-z","article-title":"Acute depletion of BRG1 reveals its primary function as an activator of transcription","volume":"15","author":"Ren","year":"2024","journal-title":"Nat Commun"},{"key":"2026102318315736400_btag753-B44","doi-asserted-by":"publisher","first-page":"887","DOI":"10.1016\/j.cell.2008.02.022","article-title":"Dynamic regulation of nucleosome positioning in the human genome","volume":"132","author":"Schones","year":"2008","journal-title":"Cell"},{"key":"2026102318315736400_btag753-B45","doi-asserted-by":"publisher","first-page":"R16","DOI":"10.1186\/gb-2012-13-3-r16","article-title":"MAnorm: a robust model for quantitative comparison of ChIP-Seq data sets","volume":"13","author":"Shao","year":"2012","journal-title":"Genome Biol"},{"key":"2026102318315736400_btag753-B46","doi-asserted-by":"publisher","first-page":"pdb prot5384","DOI":"10.1101\/pdb.prot5384","article-title":"DNase-seq: a high-resolution technique for mapping active gene regulatory elements across the genome from mammalian cells","volume":"2010","author":"Song","year":"2010","journal-title":"Cold Spring Harb Protoc"},{"key":"2026102318315736400_btag753-B47","doi-asserted-by":"publisher","first-page":"1897","DOI":"10.1016\/j.cell.2016.12.002","article-title":"The International Human Epigenome Consortium: a blueprint for scientific collaboration and discovery","volume":"167","author":"Stunnenberg","year":"2016","journal-title":"Cell"},{"key":"2026102318315736400_btag753-B48","doi-asserted-by":"publisher","first-page":"e43","DOI":"10.1093\/nar\/gkaa105","article-title":"S3norm: simultaneous normalization of sequencing depth and signal-to-noise ratio in epigenomic data","volume":"48","author":"Xiang","year":"2020","journal-title":"Nucleic Acids Res"}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/advance-article-pdf\/doi\/10.1093\/bioinformatics\/btag753\/71964212\/btag753.pdf","content-type":"application\/pdf","content-version":"am","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/42\/10\/btag753\/71964212\/btag753.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/42\/10\/btag753\/71964212\/btag753.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,10,23]],"date-time":"2026-10-23T22:32:03Z","timestamp":1792794723000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/doi\/10.1093\/bioinformatics\/btag753\/8917313"}},"subtitle":[],"editor":[{"given":"Anthony","family":"Mathelier","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"editor"}]}],"short-title":[],"issued":{"date-parts":[[2026,10]]},"references-count":48,"journal-issue":{"issue":"10","published-print":{"date-parts":[[2026,10,2]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btag753","relation":{},"ISSN":["1367-4803","1367-4811"],"issn-type":[{"value":"1367-4803","type":"print"},{"value":"1367-4811","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2026,10]]},"published":{"date-parts":[[2026,10]]},"article-number":"btag753"}}