{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,24]],"date-time":"2026-04-24T21:00:58Z","timestamp":1777064458379,"version":"3.51.4"},"reference-count":7,"publisher":"Oxford University Press (OUP)","issue":"13","license":[{"start":{"date-parts":[[2018,2,13]],"date-time":"2018-02-13T00:00:00Z","timestamp":1518480000000},"content-version":"vor","delay-in-days":1,"URL":"https:\/\/academic.oup.com\/journals\/pages\/about_us\/legal\/notices"}],"funder":[{"DOI":"10.13039\/100000025","name":"National Institute of Mental Health","doi-asserted-by":"publisher","award":["R03MH102723"],"award-info":[{"award-number":["R03MH102723"]}],"id":[{"id":"10.13039\/100000025","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000025","name":"National Institute of Mental Health","doi-asserted-by":"publisher","award":["R01MH104576"],"award-info":[{"award-number":["R01MH104576"]}],"id":[{"id":"10.13039\/100000025","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000025","name":"National Institute of Mental Health","doi-asserted-by":"publisher","award":["R01MH099110"],"award-info":[{"award-number":["R01MH099110"]}],"id":[{"id":"10.13039\/100000025","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000025","name":"National Institute of Mental Health","doi-asserted-by":"publisher","award":["1R01MH104576"],"award-info":[{"award-number":["1R01MH104576"]}],"id":[{"id":"10.13039\/100000025","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000025","name":"National Institute of Mental Health","doi-asserted-by":"publisher","award":["RC2MH089996"],"award-info":[{"award-number":["RC2MH089996"]}],"id":[{"id":"10.13039\/100000025","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000026","name":"National Institute on Drug Abuse","doi-asserted-by":"publisher","award":["2R25DA026119"],"award-info":[{"award-number":["2R25DA026119"]}],"id":[{"id":"10.13039\/100000026","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2018,7,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Motivation<\/jats:title>\n                  <jats:p>Enrichment-based technologies can provide measurements of DNA methylation at tens of millions of CpGs for thousands of samples. Existing tools for methylome-wide association studies cannot analyze datasets of this size and lack important features like principal component analysis, combined analysis with SNP data and outcome predictions that are based on all informative methylation sites.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Results<\/jats:title>\n                  <jats:p>We present a Bioconductor R package called RaMWAS with a full set of tools for large-scale methylome-wide association studies. It is free, cross-platform, open source, memory efficient and fast.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>Release version and vignettes with small case study at bioconductor.org\/packages\/ramwas Development version at github.com\/andreyshabalin\/ramwas.<\/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\/bty069","type":"journal-article","created":{"date-parts":[[2018,2,12]],"date-time":"2018-02-12T20:11:35Z","timestamp":1518466295000},"page":"2283-2285","source":"Crossref","is-referenced-by-count":51,"title":["RaMWAS: fast methylome-wide association study pipeline for enrichment platforms"],"prefix":"10.1093","volume":"34","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-0309-6821","authenticated-orcid":false,"given":"Andrey A","family":"Shabalin","sequence":"first","affiliation":[{"name":"Center for Biomarker Research and Precision Medicine, Virginia Commonwealth University, Richmond, USA"},{"name":"Department of Psychiatry, University of Utah, Salt Lake City, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Mohammad W","family":"Hattab","sequence":"additional","affiliation":[{"name":"Center for Biomarker Research and Precision Medicine, Virginia Commonwealth University, Richmond, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Shaunna L","family":"Clark","sequence":"additional","affiliation":[{"name":"Center for Biomarker Research and Precision Medicine, Virginia Commonwealth University, Richmond, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Robin F","family":"Chan","sequence":"additional","affiliation":[{"name":"Center for Biomarker Research and Precision Medicine, Virginia Commonwealth University, Richmond, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Gaurav","family":"Kumar","sequence":"additional","affiliation":[{"name":"Center for Biomarker Research and Precision Medicine, Virginia Commonwealth University, Richmond, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Karolina A","family":"Aberg","sequence":"additional","affiliation":[{"name":"Center for Biomarker Research and Precision Medicine, Virginia Commonwealth University, Richmond, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Edwin J C G","family":"van den Oord","sequence":"additional","affiliation":[{"name":"Center for Biomarker Research and Precision Medicine, Virginia Commonwealth University, Richmond, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2018,2,12]]},"reference":[{"key":"2023051604100317300_bty069-B1","doi-asserted-by":"crossref","first-page":"743","DOI":"10.1080\/15592294.2017.1335849","article-title":"A MBD-seq protocol for large-scale methylome-wide studies with (very) low amounts of DNA","volume":"12","author":"Aberg","year":"2017","journal-title":"Epigenetics"},{"key":"2023051604100317300_bty069-B2","doi-asserted-by":"crossref","first-page":"991","DOI":"10.3390\/genes6040991","article-title":"Current and future prospects for epigenetic biomarkers of substance use disorders","volume":"6","author":"Andersen","year":"2015","journal-title":"Genes"},{"key":"2023051604100317300_bty069-B3","doi-asserted-by":"crossref","first-page":"e97","DOI":"10.1093\/nar\/gkx143","article-title":"Enrichment methods provide a feasible approach to comprehensive and adequately powered investigations of the brain methylome","volume":"45","author":"Chan","year":"2017","journal-title":"Nucleic Acids Res"},{"key":"2023051604100317300_bty069-B4","doi-asserted-by":"crossref","first-page":"R115.","DOI":"10.1186\/gb-2013-14-10-r115","article-title":"DNA methylation age of human tissues and cell types","volume":"14","author":"Horvath","year":"2013","journal-title":"Genome Biol"},{"key":"2023051604100317300_bty069-B5","doi-asserted-by":"crossref","first-page":"e44","DOI":"10.1093\/nar\/gkw1193","article-title":"QSEA\u2014modelling of genome-wide DNA methylation from sequencing enrichment experiments","volume":"45","author":"Lienhard","year":"2016","journal-title":"Nucleic Acids Res"},{"key":"2023051604100317300_bty069-B6","doi-asserted-by":"crossref","first-page":"50.","DOI":"10.1186\/1471-2105-14-50","article-title":"Estimation of CpG coverage in whole methylome next-generation sequencing studies","volume":"14","author":"van den Oord","year":"2013","journal-title":"BMC 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