{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,6,3]],"date-time":"2026-06-03T00:49:59Z","timestamp":1780447799327,"version":"3.54.1"},"reference-count":8,"publisher":"Oxford University Press (OUP)","issue":"15","license":[{"start":{"date-parts":[[2018,3,1]],"date-time":"2018-03-01T00:00:00Z","timestamp":1519862400000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100008457","name":"University of Virginia","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100008457","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"}]},{"DOI":"10.13039\/100000092","name":"NLM","doi-asserted-by":"publisher","award":["5T32LM012416"],"award-info":[{"award-number":["5T32LM012416"]}],"id":[{"id":"10.13039\/100000092","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2018,8,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Summary<\/jats:title>\n                  <jats:p>DNA methylation contains information about the regulatory state of the cell. MIRA aggregates genome-scale DNA methylation data into a DNA methylation profile for a given region set with shared biological annotation. Using this profile, MIRA infers and scores the collective regulatory activity for the region set. MIRA facilitates regulatory analysis in situations where classical regulatory assays would be difficult and allows public sources of region sets to be leveraged for novel insight into the regulatory state of DNA methylation datasets.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>http:\/\/bioconductor.org\/packages\/MIRA.<\/jats:p>\n               <\/jats:sec>","DOI":"10.1093\/bioinformatics\/bty083","type":"journal-article","created":{"date-parts":[[2018,2,28]],"date-time":"2018-02-28T04:12:34Z","timestamp":1519791154000},"page":"2649-2650","source":"Crossref","is-referenced-by-count":21,"title":["MIRA: an R package for DNA methylation-based inference of regulatory activity"],"prefix":"10.1093","volume":"34","author":[{"given":"John T","family":"Lawson","sequence":"first","affiliation":[{"name":"Department of Biomedical Engineering, University of Virginia, Charlottesville, VA, USA"},{"name":"Center for Public Health Genomics, University of Virginia, Charlottesville, VA, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Eleni M","family":"Tomazou","sequence":"additional","affiliation":[{"name":"Children\u2019s Cancer Research Institute, St. Anna\u2019s Kinderkrebsforschung, Vienna, Austria"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-6091-3088","authenticated-orcid":false,"given":"Christoph","family":"Bock","sequence":"additional","affiliation":[{"name":"CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-5643-4068","authenticated-orcid":false,"given":"Nathan C","family":"Sheffield","sequence":"additional","affiliation":[{"name":"Center for Public Health Genomics, University of Virginia, Charlottesville, VA, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2018,3,1]]},"reference":[{"key":"2023012713050717600_bty083-B2","doi-asserted-by":"crossref","first-page":"1386","DOI":"10.1016\/j.celrep.2015.02.001","article-title":"Single-cell DNA methylome sequencing and bioinformatic inference of epigenomic cell-state dynamics","volume":"10","author":"Farlik","year":"2015","journal-title":"Cell Rep"},{"key":"2023012713050717600_bty083-B4","doi-asserted-by":"crossref","first-page":"i405","DOI":"10.1093\/bioinformatics\/btw432","article-title":"Higher order methylation features for clustering and prediction in epigenomic studies","volume":"32","author":"Kapourani","year":"2016","journal-title":"Bioinformatics"},{"key":"2023012713050717600_bty083-B5","doi-asserted-by":"crossref","first-page":"587","DOI":"10.1093\/bioinformatics\/btv612","article-title":"LOLA: enrichment analysis for genomic region sets and regulatory elements in R and Bioconductor","volume":"32","author":"Sheffield","year":"2016","journal-title":"Bioinformatics"},{"key":"2023012713050717600_bty083-B6","doi-asserted-by":"crossref","first-page":"386","DOI":"10.1038\/nm.4273","article-title":"DNA methylation heterogeneity defines a disease spectrum in ewing sarcoma","volume":"23","author":"Sheffield","year":"2017","journal-title":"Nature Medicine"},{"key":"2023012713050717600_bty083-B7","doi-asserted-by":"crossref","first-page":"490","DOI":"10.1038\/nature10716","article-title":"DNA-binding factors shape the mouse methylome at distal regulatory regions","volume":"480","author":"Stadler","year":"2011","journal-title":"Nature"},{"key":"2023012713050717600_bty083-B9","doi-asserted-by":"crossref","first-page":"2030","DOI":"10.1038\/onc.2016.340","article-title":"A pre-neoplastic epigenetic field defect in HCV-infected liver at transcription factor binding sites and polycomb targets","volume":"36","author":"Wijetunga","year":"2017","journal-title":"Oncogene"},{"key":"2023012713050717600_bty083-B10","doi-asserted-by":"crossref","DOI":"10.1186\/s13059-015-0668-3","article-title":"Inferring regulatory element landscapes and transcription factor networks from cancer methylomes","volume":"16","author":"Yao","year":"2015","journal-title":"Genome Biol"},{"key":"2023012713050717600_bty083-B11","doi-asserted-by":"crossref","first-page":"551","DOI":"10.1038\/nrg.2016.83","article-title":"Transcription factors as readers and effectors of DNA methylation","volume":"17","author":"Zhu","year":"2016","journal-title":"Nat. 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