{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,29]],"date-time":"2026-10-29T02:10:16Z","timestamp":1793239816240,"version":"4.5.0"},"reference-count":35,"publisher":"Oxford University Press (OUP)","issue":"10","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2014,5,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:p>Motivation: The recently released Infinium HumanMethylation450 array (the \u2018450k\u2019 array) provides a high-throughput assay to quantify DNA methylation (DNAm) at \u223c450 000 loci across a range of genomic features. Although less comprehensive than high-throughput sequencing-based techniques, this product is more cost-effective and promises to be the most widely used DNAm high-throughput measurement technology over the next several years.<\/jats:p>\n                  <jats:p>Results: Here we describe a suite of computational tools that incorporate state-of-the-art statistical techniques for the analysis of DNAm data. The software is structured to easily adapt to future versions of the technology. We include methods for preprocessing, quality assessment and detection of differentially methylated regions from the kilobase to the megabase scale. We show how our software provides a powerful and flexible development platform for future methods. We also illustrate how our methods empower the technology to make discoveries previously thought to be possible only with sequencing-based methods.<\/jats:p>\n                  <jats:p>Availability and implementation: \u00a0http:\/\/bioconductor.org\/packages\/release\/bioc\/html\/minfi.html.<\/jats:p>\n                  <jats:p>Contact: \u00a0khansen@jhsph.edu; rafa@jimmy.harvard.edu<\/jats:p>\n                  <jats:p>Supplementary information: \u00a0Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btu049","type":"journal-article","created":{"date-parts":[[2014,1,29]],"date-time":"2014-01-29T20:49:23Z","timestamp":1391028563000},"page":"1363-1369","source":"Crossref","is-referenced-by-count":4229,"title":["Minfi: a flexible and comprehensive Bioconductor package for the analysis of Infinium DNA methylation microarrays"],"prefix":"10.1093","volume":"30","author":[{"given":"Martin J.","family":"Aryee","sequence":"first","affiliation":[{"name":"1 Department of Pathology, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA, 2Department of Biostatistics, Johns Hopkins School of Public Health, 615 N Wolfe Street, Baltimore, MD 21205, USA, 3Lieber Institute of Brain Development, Johns Hopkins Medical Campus, 855 N Wolfe Street, Baltimore, MD 21205, USA, 4Department of Computer Science, University of Maryland, College Park, MD 20742, USA, 5Department of Epidemiology, Johns Hopkins School of Public Health, 615 N Wolfe Street, Baltimore, MD 21205, USA, 6Center for Epigenetics and Department of Medicine, Johns Hopkins University School of Medicine, 570 Rangos, 725 N Wolfe Street, Baltimore, MD 21205, USA and 7Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Andrew E.","family":"Jaffe","sequence":"additional","affiliation":[{"name":"1 Department of Pathology, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA, 2Department of Biostatistics, Johns Hopkins School of Public Health, 615 N Wolfe Street, Baltimore, MD 21205, USA, 3Lieber Institute of Brain Development, Johns Hopkins Medical Campus, 855 N Wolfe Street, Baltimore, MD 21205, USA, 4Department of Computer Science, University of Maryland, College Park, MD 20742, USA, 5Department of Epidemiology, Johns Hopkins School of Public Health, 615 N Wolfe Street, Baltimore, MD 21205, USA, 6Center for Epigenetics and Department of Medicine, Johns Hopkins University School of Medicine, 570 Rangos, 725 N Wolfe Street, Baltimore, MD 21205, USA and 7Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA"},{"name":"1 Department of Pathology, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA, 2Department of Biostatistics, Johns Hopkins School of Public Health, 615 N Wolfe Street, Baltimore, MD 21205, USA, 3Lieber Institute of Brain Development, Johns Hopkins Medical Campus, 855 N Wolfe Street, Baltimore, MD 21205, USA, 4Department of Computer Science, University of Maryland, College Park, MD 20742, USA, 5Department of Epidemiology, Johns Hopkins School of Public Health, 615 N Wolfe Street, Baltimore, MD 21205, USA, 6Center for Epigenetics and Department of Medicine, Johns Hopkins University School of Medicine, 570 Rangos, 725 N Wolfe Street, Baltimore, MD 21205, USA and 7Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Hector","family":"Corrada-Bravo","sequence":"additional","affiliation":[{"name":"1 Department of Pathology, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA, 2Department of Biostatistics, Johns Hopkins School of Public Health, 615 N Wolfe Street, Baltimore, MD 21205, USA, 3Lieber Institute of Brain Development, Johns Hopkins Medical Campus, 855 N Wolfe Street, Baltimore, MD 21205, USA, 4Department of Computer Science, University of Maryland, College Park, MD 20742, USA, 5Department of Epidemiology, Johns Hopkins School of Public Health, 615 N Wolfe Street, Baltimore, MD 21205, USA, 6Center for Epigenetics and Department of Medicine, Johns Hopkins University School of Medicine, 570 Rangos, 725 N Wolfe Street, Baltimore, MD 21205, USA and 7Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Christine","family":"Ladd-Acosta","sequence":"additional","affiliation":[{"name":"1 Department of Pathology, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA, 2Department of Biostatistics, Johns Hopkins School of Public Health, 615 N Wolfe Street, Baltimore, MD 21205, USA, 3Lieber Institute of Brain Development, Johns Hopkins Medical Campus, 855 N Wolfe Street, Baltimore, MD 21205, USA, 4Department of Computer Science, University of Maryland, College Park, MD 20742, USA, 5Department of Epidemiology, Johns Hopkins School of Public Health, 615 N Wolfe Street, Baltimore, MD 21205, USA, 6Center for Epigenetics and Department of Medicine, Johns Hopkins University School of Medicine, 570 Rangos, 725 N Wolfe Street, Baltimore, MD 21205, USA and 7Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Andrew P.","family":"Feinberg","sequence":"additional","affiliation":[{"name":"1 Department of Pathology, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA, 2Department of Biostatistics, Johns Hopkins School of Public Health, 615 N Wolfe Street, Baltimore, MD 21205, USA, 3Lieber Institute of Brain Development, Johns Hopkins Medical Campus, 855 N Wolfe Street, Baltimore, MD 21205, USA, 4Department of Computer Science, University of Maryland, College Park, MD 20742, USA, 5Department of Epidemiology, Johns Hopkins School of Public Health, 615 N Wolfe Street, Baltimore, MD 21205, USA, 6Center for Epigenetics and Department of Medicine, Johns Hopkins University School of Medicine, 570 Rangos, 725 N Wolfe Street, Baltimore, MD 21205, USA and 7Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA"},{"name":"1 Department of Pathology, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA, 2Department of Biostatistics, Johns Hopkins School of Public Health, 615 N Wolfe Street, Baltimore, MD 21205, USA, 3Lieber Institute of Brain Development, Johns Hopkins Medical Campus, 855 N Wolfe Street, Baltimore, MD 21205, USA, 4Department of Computer Science, University of Maryland, College Park, MD 20742, USA, 5Department of Epidemiology, Johns Hopkins School of Public Health, 615 N Wolfe Street, Baltimore, MD 21205, USA, 6Center for Epigenetics and Department of Medicine, Johns Hopkins University School of Medicine, 570 Rangos, 725 N Wolfe Street, Baltimore, MD 21205, USA and 7Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Kasper D.","family":"Hansen","sequence":"additional","affiliation":[{"name":"1 Department of Pathology, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA, 2Department of Biostatistics, Johns Hopkins School of Public Health, 615 N Wolfe Street, Baltimore, MD 21205, USA, 3Lieber Institute of Brain Development, Johns Hopkins Medical Campus, 855 N Wolfe Street, Baltimore, MD 21205, USA, 4Department of Computer Science, University of Maryland, College Park, MD 20742, USA, 5Department of Epidemiology, Johns Hopkins School of Public Health, 615 N Wolfe Street, Baltimore, MD 21205, USA, 6Center for Epigenetics and Department of Medicine, Johns Hopkins University School of Medicine, 570 Rangos, 725 N Wolfe Street, Baltimore, MD 21205, USA and 7Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA"},{"name":"1 Department of Pathology, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA, 2Department of Biostatistics, Johns Hopkins School of Public Health, 615 N Wolfe Street, Baltimore, MD 21205, USA, 3Lieber Institute of Brain Development, Johns Hopkins Medical Campus, 855 N Wolfe Street, Baltimore, MD 21205, USA, 4Department of Computer Science, University of Maryland, College Park, MD 20742, USA, 5Department of Epidemiology, Johns Hopkins School of Public Health, 615 N Wolfe Street, Baltimore, MD 21205, USA, 6Center for Epigenetics and Department of Medicine, Johns Hopkins University School of Medicine, 570 Rangos, 725 N Wolfe Street, Baltimore, MD 21205, USA and 7Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Rafael A.","family":"Irizarry","sequence":"additional","affiliation":[{"name":"1 Department of Pathology, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA, 2Department of Biostatistics, Johns Hopkins School of Public Health, 615 N Wolfe Street, Baltimore, MD 21205, USA, 3Lieber Institute of Brain Development, Johns Hopkins Medical Campus, 855 N Wolfe Street, Baltimore, MD 21205, USA, 4Department of Computer Science, University of Maryland, College Park, MD 20742, USA, 5Department of Epidemiology, Johns Hopkins School of Public Health, 615 N Wolfe Street, Baltimore, MD 21205, USA, 6Center for Epigenetics and Department of Medicine, Johns Hopkins University School of Medicine, 570 Rangos, 725 N Wolfe Street, Baltimore, MD 21205, USA and 7Institute of Genetic Medicine, Johns Hopkins University 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