{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,23]],"date-time":"2026-03-23T14:41:37Z","timestamp":1774276897996,"version":"3.50.1"},"reference-count":22,"publisher":"Oxford University Press (OUP)","issue":"4","license":[{"start":{"date-parts":[[2019,9,30]],"date-time":"2019-09-30T00:00:00Z","timestamp":1569801600000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/journals\/pages\/open_access\/funder_policies\/chorus\/standard_publication_model"}],"funder":[{"DOI":"10.13039\/100000054","name":"National Cancer Institute","doi-asserted-by":"publisher","award":["P30CA021765"],"award-info":[{"award-number":["P30CA021765"]}],"id":[{"id":"10.13039\/100000054","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000002","name":"National Institutes of Health","doi-asserted-by":"publisher","award":["P01CA096832"],"award-info":[{"award-number":["P01CA096832"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100012524","name":"American Lebanese Syrian Associated Charities","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100012524","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000002","name":"NIH","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2020,2,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Motivation<\/jats:title>\n                  <jats:p>The traditional reads per million normalization method is inappropriate for the evaluation of ChIP-seq data when treatments or mutations have global effects. Changes in global levels of histone modifications can be detected with exogenous reference spike-in controls. However, most ChIP-seq studies overlook the normalization that must be corrected with spike-in. A method that retrospectively renormalizes datasets without spike-in is lacking.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Results<\/jats:title>\n                  <jats:p>ChIPseqSpikeInFree is a novel ChIP-seq normalization method to effectively determine scaling factors for samples across various conditions and treatments, which does not rely on exogenous spike-in chromatin or peak detection to reveal global changes in histone modification occupancy. Application of ChIPseqSpikeInFree on five datasets demonstrates that this in silico approach reveals a similar magnitude of global changes as the spike-in method does.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>St. Jude Cloud (https:\/\/pecan.stjude.cloud\/permalink\/spikefree) and St. Jude Github ( https:\/\/github.com\/stjude\/ChIPseqSpikeInFree).<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Supplementary information<\/jats:title>\n                  <jats:p>Supplementary data are available at Bioinformatics online.<\/jats:p>\n               <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btz720","type":"journal-article","created":{"date-parts":[[2019,9,26]],"date-time":"2019-09-26T11:28:48Z","timestamp":1569497328000},"page":"1270-1272","source":"Crossref","is-referenced-by-count":46,"title":["ChIPseqSpikeInFree: a ChIP-seq normalization approach to reveal global changes in histone modifications without spike-in"],"prefix":"10.1093","volume":"36","author":[{"given":"Hongjian","family":"Jin","sequence":"first","affiliation":[{"name":"Department of Computational Biology, St. Jude Children\u2019s Research Hospital , Memphis, TN 38105, USA"}]},{"given":"Lawryn H","family":"Kasper","sequence":"additional","affiliation":[{"name":"Department of Developmental Neurobiology, St. Jude Children\u2019s Research Hospital , Memphis, TN 38105, USA"}]},{"given":"Jon D","family":"Larson","sequence":"additional","affiliation":[{"name":"Department of Developmental Neurobiology, St. Jude Children\u2019s Research Hospital , Memphis, TN 38105, USA"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-1678-5864","authenticated-orcid":false,"given":"Gang","family":"Wu","sequence":"additional","affiliation":[{"name":"Department of Computational Biology, St. Jude Children\u2019s Research Hospital , Memphis, TN 38105, USA"}]},{"given":"Suzanne J","family":"Baker","sequence":"additional","affiliation":[{"name":"Department of Developmental Neurobiology, St. Jude Children\u2019s Research Hospital , Memphis, TN 38105, USA"}]},{"given":"Jinghui","family":"Zhang","sequence":"additional","affiliation":[{"name":"Department of Computational Biology, St. Jude Children\u2019s Research Hospital , Memphis, TN 38105, USA"}]},{"given":"Yiping","family":"Fan","sequence":"additional","affiliation":[{"name":"Department of Computational Biology, St. Jude Children\u2019s Research Hospital , Memphis, TN 38105, USA"}]}],"member":"286","published-online":{"date-parts":[[2019,9,30]]},"reference":[{"key":"2023013110160674500_btz720-B1","doi-asserted-by":"crossref","first-page":"366ra161.","DOI":"10.1126\/scitranslmed.aah6904","article-title":"Lowered H3K27me3 and DNA hypomethylation define poorly prognostic pediatric posterior fossa ependymomas","volume":"8","author":"Bayliss","year":"2016","journal-title":"Sci. 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