{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,5,16]],"date-time":"2026-05-16T22:14:15Z","timestamp":1778969655237,"version":"3.51.4"},"reference-count":7,"publisher":"Oxford University Press (OUP)","issue":"8","funder":[{"DOI":"10.13039\/100000002","name":"National Institutes of Health","doi-asserted-by":"publisher","award":["P01 GM085354"],"award-info":[{"award-number":["P01 GM085354"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000057","name":"National Institute of General Medical Sciences","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100000057","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2016,4,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Summary: Genome-wide association studies (GWASs) have successfully identified many sequence variants that are significantly associated with common diseases and traits. Tens of thousands of such trait-associated SNPs have already been cataloged, which we believe form a great resource for genomic research. Recent studies have demonstrated that the collection of trait-associated SNPs can be exploited to indicate whether a given genomic interval or intervals are likely to be functionally connected with certain phenotypes or diseases. Despite this importance, currently, there is no ready-to-use computational tool able to connect genomic intervals to phenotypes. Here, we present traseR, an easy-to-use R Bioconductor package that performs enrichment analyses of trait-associated SNPs in arbitrary genomic intervals with flexible options, including testing method, type of background and inclusion of SNPs in LD.<\/jats:p>\n               <jats:p>Availability and implementation: The traseR R package preloaded with up-to-date collection of trait-associated SNPs are freely available in Bioconductor<\/jats:p>\n               <jats:p>Contact: \u00a0zhaohui.qin@emory.edu<\/jats:p>\n               <jats:p>Supplementary information: \u00a0Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btv741","type":"journal-article","created":{"date-parts":[[2015,12,19]],"date-time":"2015-12-19T04:10:02Z","timestamp":1450498202000},"page":"1214-1216","source":"Crossref","is-referenced-by-count":26,"title":["traseR: an R package for performing trait-associated SNP enrichment analysis in genomic intervals"],"prefix":"10.1093","volume":"32","author":[{"given":"Li","family":"Chen","sequence":"first","affiliation":[{"name":"1 Department of Mathematics and Computer Science,"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Zhaohui S.","family":"Qin","sequence":"additional","affiliation":[{"name":"2 Department of Biostatistics and Bioinformatics, Rollins School of Public Health, Emory University, Atlanta, GA 30322 USA and"},{"name":"3 Department of Biomedical Informatics, Emory University School of Medicine, Atlanta, GA 30322, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2015,12,18]]},"reference":[{"key":"2023020112194669900_btv741-B1","doi-asserted-by":"crossref","first-page":"25","DOI":"10.1038\/75556","article-title":"Gene ontology: tool for the unification of biology. The Gene Ontology Consortium","volume":"25","author":"Ashburner","year":"2000","journal-title":"Nat. Genet"},{"key":"2023020112194669900_btv741-B2","doi-asserted-by":"crossref","first-page":"1190","DOI":"10.1126\/science.1222794","article-title":"Systematic localization of common disease-associated variation in regulatory DNA","volume":"337","author":"Maurano","year":"2012","journal-title":"Science"},{"key":"2023020112194669900_btv741-B3","doi-asserted-by":"crossref","first-page":"317","DOI":"10.1038\/nature14248","article-title":"Integrative analysis of 111 reference human epigenomes","volume":"518","author":"Roadmap Epigenomics","year":"2015","journal-title":"Nature"},{"key":"2023020112194669900_btv741-B4","doi-asserted-by":"crossref","first-page":"1748","DOI":"10.1101\/gr.136127.111","article-title":"Linking disease associations with regulatory information in the human genome","volume":"22","author":"Schaub","year":"2012","journal-title":"Genome Res"},{"key":"2023020112194669900_btv741-B5","doi-asserted-by":"crossref","first-page":"367","DOI":"10.1534\/genetics.110.120907","article-title":"Progress and promise of genome-wide association studies for human complex trait genetics","volume":"187","author":"Stranger","year":"2011","journal-title":"Genetics"},{"key":"2023020112194669900_btv741-B6","doi-asserted-by":"crossref","first-page":"15545","DOI":"10.1073\/pnas.0506580102","article-title":"Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles","volume":"102","author":"Subramanian","year":"2005","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"2023020112194669900_btv741-B7","doi-asserted-by":"crossref","first-page":"D1001","DOI":"10.1093\/nar\/gkt1229","article-title":"The NHGRI GWAS Catalog, a curated resource of SNP-trait associations","volume":"42","author":"Welter","year":"2014","journal-title":"Nucleic Acids Res"}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/32\/8\/1214\/49018546\/bioinformatics_32_8_1214.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/32\/8\/1214\/49018546\/bioinformatics_32_8_1214.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,2,1]],"date-time":"2023-02-01T22:17:02Z","timestamp":1675289822000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/32\/8\/1214\/1744655"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2015,12,18]]},"references-count":7,"journal-issue":{"issue":"8","published-print":{"date-parts":[[2016,4,15]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btv741","relation":{},"ISSN":["1367-4811","1367-4803"],"issn-type":[{"value":"1367-4811","type":"electronic"},{"value":"1367-4803","type":"print"}],"subject":[],"published-other":{"date-parts":[[2016,4,15]]},"published":{"date-parts":[[2015,12,18]]}}}