{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,6,18]],"date-time":"2025-06-18T13:27:39Z","timestamp":1750253259281,"version":"3.37.3"},"reference-count":9,"publisher":"Oxford University Press (OUP)","issue":"11","license":[{"start":{"date-parts":[[2018,1,12]],"date-time":"2018-01-12T00:00:00Z","timestamp":1515715200000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/journals\/pages\/about_us\/legal\/notices"}],"funder":[{"DOI":"10.13039\/100000009","name":"Foundation for the National Institutes of Health","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100000009","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000009","name":"FNIH","doi-asserted-by":"publisher","award":["R01GM095372"],"award-info":[{"award-number":["R01GM095372"]}],"id":[{"id":"10.13039\/100000009","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100006756","name":"Brigham Young University","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100006756","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100006756","name":"BYU","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100006756","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2018,6,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Summary<\/jats:title>\n                  <jats:p>Here we report on an R package for genome-wide association studies of orthologous genes in bacteria. Before using the software, orthologs from bacterial genomes or metagenomes are defined using local or online implementations of OrthoMCL. These presence\u2013absence patterns are statistically associated with variation in user-collected phenotypes using the Mono-Associated GNotobiotic Animals Metagenome-Wide Association R package (MAGNAMWAR). Genotype-phenotype associations can be performed with several different statistical tests based on the type and distribution of the data.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>MAGNAMWAR is available on CRAN.<\/jats:p>\n               <\/jats:sec>","DOI":"10.1093\/bioinformatics\/bty001","type":"journal-article","created":{"date-parts":[[2018,1,9]],"date-time":"2018-01-09T21:39:22Z","timestamp":1515533962000},"page":"1951-1952","source":"Crossref","is-referenced-by-count":15,"title":["MAGNAMWAR: an R package for genome-wide association studies of bacterial orthologs"],"prefix":"10.1093","volume":"34","author":[{"given":"Corinne E","family":"Sexton","sequence":"first","affiliation":[{"name":"Department of Biology, Brigham Young University, Provo, UT, USA"}]},{"given":"Hayden Z","family":"Smith","sequence":"additional","affiliation":[{"name":"Department of Biology, Brigham Young University, Provo, UT, USA"}]},{"given":"Peter D","family":"Newell","sequence":"additional","affiliation":[{"name":"Department of Biological Sciences, SUNY Oswego, Oswego, NY, USA"}]},{"given":"Angela E","family":"Douglas","sequence":"additional","affiliation":[{"name":"Department of Entomology and Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, USA"}]},{"given":"John M","family":"Chaston","sequence":"additional","affiliation":[{"name":"Department of Plant & Wildlife Sciences, Brigham Young University, Provo, UT, USA"}]}],"member":"286","published-online":{"date-parts":[[2018,1,12]]},"reference":[{"key":"2023012713565314500_bty001-B1","doi-asserted-by":"crossref","first-page":"68.","DOI":"10.1186\/1471-2180-13-68","article-title":"Genotype-phenotype matching analysis of 38 Lactococcus lactis strains using random forest methods","volume":"13","author":"Bayjanov","year":"2013","journal-title":"BMC Microbiol"},{"key":"2023012713565314500_bty001-B2","doi-asserted-by":"crossref","first-page":"238","DOI":"10.1186\/s13059-016-1108-8","article-title":"Rapid scoring of genes in microbial pan-genome-wide association studies with Scoary","volume":"17","author":"Brynildsrud","year":"2016","journal-title":"Genome Biol"},{"key":"2023012713565314500_bty001-B9","doi-asserted-by":"crossref","first-page":"e01631","DOI":"10.1128\/mBio.01631-14","article-title":"Metagenome-wide association of microbial determinants of host phenotype in Drosophila melanogaster","volume":"5","author":"Chaston","year":"2014","journal-title":"mBio"},{"key":"2023012713565314500_bty001-B3","doi-asserted-by":"crossref","first-page":"17","DOI":"10.1016\/j.mib.2015.03.002","article-title":"The advent of genome-wide association studies for bacteria","volume":"25","author":"Chen","year":"2015","journal-title":"Curr. Opin. Microbiol"},{"key":"2023012713565314500_bty001-B4","doi-asserted-by":"crossref","first-page":"12797","DOI":"10.1038\/ncomms12797","article-title":"Sequence element enrichment analysis to determine the genetic basis of bacterial phenotypes","volume":"7","author":"Lees","year":"2016","journal-title":"Nat. Commun"},{"key":"2023012713565314500_bty001-B5","doi-asserted-by":"crossref","first-page":"2178","DOI":"10.1101\/gr.1224503","article-title":"OrthoMCL: identification of ortholog groups for eukaryotic genomes","volume":"13","author":"Li","year":"2003","journal-title":"Genome Res"},{"key":"2023012713565314500_bty001-B6","doi-asserted-by":"crossref","first-page":"833","DOI":"10.1038\/nmeth.1681","article-title":"FaST linear mixed models for genome-wide association studies","volume":"8","author":"Lippert","year":"2011","journal-title":"Nat. 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Genet"},{"key":"2023012713565314500_bty001-B8","doi-asserted-by":"crossref","first-page":"55","DOI":"10.1038\/nature11450","article-title":"A metagenome-wide association study of gut microbiota in type 2 diabetes","volume":"490","author":"Qin","year":"2012","journal-title":"Nature"}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/34\/11\/1951\/48937872\/bioinformatics_34_11_1951.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/34\/11\/1951\/48937872\/bioinformatics_34_11_1951.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,1,27]],"date-time":"2023-01-27T14:29:10Z","timestamp":1674829750000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/34\/11\/1951\/4802219"}},"subtitle":[],"editor":[{"given":"Oliver","family":"Stegle","sequence":"additional","affiliation":[]}],"short-title":[],"issued":{"date-parts":[[2018,1,12]]},"references-count":9,"journal-issue":{"issue":"11","published-print":{"date-parts":[[2018,6,1]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/bty001","relation":{},"ISSN":["1367-4803","1367-4811"],"issn-type":[{"type":"print","value":"1367-4803"},{"type":"electronic","value":"1367-4811"}],"subject":[],"published-other":{"date-parts":[[2018,6,1]]},"published":{"date-parts":[[2018,1,12]]}}}