{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,2,21]],"date-time":"2025-02-21T10:52:44Z","timestamp":1740135164478,"version":"3.37.3"},"reference-count":10,"publisher":"Springer Science and Business Media LLC","issue":"1","license":[{"start":{"date-parts":[[2016,9,15]],"date-time":"2016-09-15T00:00:00Z","timestamp":1473897600000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0"},{"start":{"date-parts":[[2016,9,15]],"date-time":"2016-09-15T00:00:00Z","timestamp":1473897600000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0"}],"funder":[{"DOI":"10.13039\/501100001659","name":"Deutsche Forschungsgemeinschaft","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100001659","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100002347","name":"Bundesministerium f\u00fcr Bildung und Forschung","doi-asserted-by":"crossref","id":[{"id":"10.13039\/501100002347","id-type":"DOI","asserted-by":"crossref"}]},{"DOI":"10.13039\/501100002347","name":"Bundesministerium f\u00fcr Bildung und Forschung","doi-asserted-by":"crossref","id":[{"id":"10.13039\/501100002347","id-type":"DOI","asserted-by":"crossref"}]}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["BMC Bioinformatics"],"abstract":"<jats:title>Abstract<\/jats:title><jats:sec>\n                <jats:title>Background<\/jats:title>\n                <jats:p>Histone modifications play an important role in gene regulation. Their genomic locations are of great interest. Usually, the location is measured by ChIP-seq and analyzed with a peak-caller. Replicated ChIP-seq experiments become more and more available. However, their analysis is based on single-experiment peak-calling or on tools like PePr which allows peak-calling of replicates but whose underlying model might not be suitable for the conditions under which the experiments are performed.<\/jats:p>\n              <\/jats:sec><jats:sec>\n                <jats:title>Results<\/jats:title>\n                <jats:p>We propose a new peak-caller called \u2018Sierra Platinum\u2019 that allows peak-calling of replicated ChIP-seq experiments. Moreover, it provides a variety of quality measures together with integrated visualizations supporting the assessment of the replicates and the resulting peaks, as well as steering the peak-calling process.<\/jats:p>\n              <\/jats:sec><jats:sec>\n                <jats:title>Conclusion<\/jats:title>\n                <jats:p>We show that Sierra Platinum outperforms currently available methods using a newly generated benchmark data set and using real data from the NIH Roadmap Epigenomics Project. It is robust against noisy replicates.<\/jats:p>\n              <\/jats:sec>","DOI":"10.1186\/s12859-016-1248-6","type":"journal-article","created":{"date-parts":[[2016,9,15]],"date-time":"2016-09-15T11:09:21Z","timestamp":1473937761000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":10,"title":["Sierra platinum: a fast and robust peak-caller for replicated ChIP-seq experiments with visual quality-control and -steering"],"prefix":"10.1186","volume":"17","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-9544-121X","authenticated-orcid":false,"given":"Lydia","family":"M\u00fcller","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Daniel","family":"Gerighausen","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Mariam","family":"Farman","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Dirk","family":"Zeckzer","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"297","published-online":{"date-parts":[[2016,9,15]]},"reference":[{"issue":"5","key":"1248_CR1","doi-asserted-by":"publisher","first-page":"96303","DOI":"10.1371\/journal.pone.0096303","volume":"9","author":"H Koohy","year":"2014","unstructured":"Koohy H, Down TA, Spivakov M, Hubbard T. A Comparison of Peak Callers Used for DNase-Seq Data. PLoS ONE. 2014; 9(5):96303. doi:10.1371\/journal.pone.0096303.","journal-title":"PLoS ONE"},{"issue":"7","key":"1248_CR2","doi-asserted-by":"publisher","first-page":"11471","DOI":"10.1371\/journal.pone.0011471","volume":"5","author":"EG Wilbanks","year":"2010","unstructured":"Wilbanks EG, Facciotti MT. Evaluation of Algorithm Performance in ChIP-Seq Peak Detection. PLoS ONE. 2010; 5(7):11471. doi:10.1371\/journal.pone.0011471.","journal-title":"PLoS ONE"},{"issue":"7539","key":"1248_CR3","doi-asserted-by":"publisher","first-page":"317","DOI":"10.1038\/nature14248","volume":"518","author":"Roadmap Epigenomics Consortium","year":"2015","unstructured":"Roadmap Epigenomics Consortium. Integrative analysis of 111 reference human epigenomes. Nature. 2015; 518(7539):317\u201330. doi:10.1038\/nature14248.","journal-title":"Nature"},{"issue":"9","key":"1248_CR4","doi-asserted-by":"publisher","first-page":"137","DOI":"10.1186\/gb-2008-9-9-r137","volume":"9","author":"Y Zhang","year":"2008","unstructured":"Zhang Y, Liu T, Meyer CA, Eeckhoute J, Johnson DS, Bernstein BE, Nusbaum C, Myers RM, Brown M, Li W, et al.Model-based analysis of ChIP-Seq (MACS). Genome Biol. 2008; 9(9):137.","journal-title":"Genome Biol"},{"issue":"18","key":"1248_CR5","doi-asserted-by":"publisher","first-page":"2568","DOI":"10.1093\/bioinformatics\/btu372","volume":"30","author":"Y Zhang","year":"2014","unstructured":"Zhang Y, Lin YH, Johnson TD, Rozek LS, Sartor MA. PePr: a peak-calling prioritization pipeline to identify consistent or differential peaks from replicated ChIP-Seq data. Bioinformatics. 2014; 30(18):2568\u201375. doi:10.1093\/bioinformatics\/btu372.","journal-title":"Bioinformatics"},{"issue":"5","key":"1248_CR6","doi-asserted-by":"publisher","first-page":"45","DOI":"10.1093\/nar\/gkv1191","volume":"44","author":"ATL Lun","year":"2016","unstructured":"Lun ATL, Smyth GK. csaw: a Bioconductor package for differential binding analysis of ChIP-seq data using sliding windows. Nucleic Acids Res. 2016; 44(5):45. doi:10.1093\/nar\/gkv1191.","journal-title":"Nucleic Acids Res"},{"issue":"1","key":"1248_CR7","doi-asserted-by":"publisher","first-page":"139","DOI":"10.1093\/bioinformatics\/btp616","volume":"26","author":"MD Robinson","year":"2010","unstructured":"Robinson MD, McCarthy DJ, Smyth GK. edger: a bioconductor package for differential expression analysis of digital gene expression data. Bioinformatics. 2010; 26(1):139\u201340. doi:10.1093\/bioinformatics\/btp616.","journal-title":"Bioinformatics"},{"issue":"7381","key":"1248_CR8","doi-asserted-by":"crossref","first-page":"389","DOI":"10.1038\/nature10730","volume":"481","author":"CS Ross-Innes","year":"2012","unstructured":"Ross-Innes CS, Stark R, Teschendorff AE, Holmes KA, Ali HR, Dunning MJ, Brown GD, Gojis O, Ellis IO, Green AR, Ali S, Chin SF, Palmieri C, Caldas C, Carroll JS. Differential oestrogen receptor binding is associated with clinical outcome in breast cancer. Nature. 2012; 481(7381):389\u201393. doi:10.1038\/nature10730.","journal-title":"Nature"},{"key":"1248_CR9","volume-title":"Statistical Methods for Meta-analysis","author":"LV Hedges","year":"1985","unstructured":"Hedges LV, Olkin I. Statistical Methods for Meta-analysis. Orlando: Academic Press; 1985."},{"issue":"7","key":"1248_CR10","doi-asserted-by":"publisher","first-page":"540","DOI":"10.1038\/nrm1938","volume":"7","author":"E Meshorer","year":"2006","unstructured":"Meshorer E, Misteli T. Chromatin in pluripotent embryonic stem cells and differentiation. Nat Rev Mol Cell Biol. 2006; 7(7):540\u20136. doi:10.1038\/nrm1938.","journal-title":"Nat Rev Mol Cell Biol"}],"container-title":["BMC Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1186\/s12859-016-1248-6.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/link.springer.com\/article\/10.1186\/s12859-016-1248-6\/fulltext.html","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1186\/s12859-016-1248-6.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2024,2,1]],"date-time":"2024-02-01T18:11:26Z","timestamp":1706811086000},"score":1,"resource":{"primary":{"URL":"https:\/\/bmcbioinformatics.biomedcentral.com\/articles\/10.1186\/s12859-016-1248-6"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2016,9,15]]},"references-count":10,"journal-issue":{"issue":"1","published-online":{"date-parts":[[2016,12]]}},"alternative-id":["1248"],"URL":"https:\/\/doi.org\/10.1186\/s12859-016-1248-6","relation":{},"ISSN":["1471-2105"],"issn-type":[{"type":"electronic","value":"1471-2105"}],"subject":[],"published":{"date-parts":[[2016,9,15]]},"assertion":[{"value":"10 April 2016","order":1,"name":"received","label":"Received","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"8 September 2016","order":2,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"15 September 2016","order":3,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}}],"article-number":"377"}}