{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,7,30]],"date-time":"2025-07-30T11:42:14Z","timestamp":1753875734673,"version":"3.41.2"},"reference-count":18,"publisher":"Oxford University Press (OUP)","issue":"6","license":[{"start":{"date-parts":[[2024,6,17]],"date-time":"2024-06-17T00:00:00Z","timestamp":1718582400000},"content-version":"vor","delay-in-days":16,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100000199","name":"United States Department of Agriculture","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100000199","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100005825","name":"National Institute of Food and Agriculture","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100005825","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Agriculture and Food Research Initiative"},{"DOI":"10.13039\/100000199","name":"United States Department of Agriculture","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100000199","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100009168","name":"Animal and Plant Health Inspection Service","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100009168","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Plant Protection Act"},{"DOI":"10.13039\/100000199","name":"United States Department of Agriculture","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100000199","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2024,6,3]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Motivation<\/jats:title>\n                  <jats:p>Single nucleotide polymorphism (SNP) markers are increasingly popular for population genomics and inferring ancestry for individuals of unknown origin. Because large SNP datasets are impractical for rapid and routine analysis, diagnostics rely on panels of highly informative markers. Strategies exist for selecting these markers, however, resources for efficiently evaluating their performance are limited for non-model systems.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Results<\/jats:title>\n                  <jats:p>snpAIMeR is a user-friendly R package that evaluates the efficacy of genomic markers for the cluster assignment of unknown individuals. It is intended to help minimize panel size and genotyping effort by determining the informativeness of candidate diagnostic markers. Provided genotype data from individuals of known origin, it uses leave-one-out cross-validation to determine population assignment rates for individual markers and marker combinations.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>snpAIMeR is available on CRAN (https:\/\/CRAN.R-project.org\/package=snpAIMeR).<\/jats:p>\n               <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btae377","type":"journal-article","created":{"date-parts":[[2024,6,17]],"date-time":"2024-06-17T20:58:19Z","timestamp":1718657899000},"source":"Crossref","is-referenced-by-count":0,"title":["snpAIMeR: R package for evaluating ancestry informative marker contributions in non-model population diagnostics"],"prefix":"10.1093","volume":"40","author":[{"ORCID":"https:\/\/orcid.org\/0009-0006-7097-5091","authenticated-orcid":false,"given":"Kim L","family":"Vertacnik","sequence":"first","affiliation":[{"name":"Department of Entomology, University of Kentucky , Lexington, KY 40546, United States"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-6444-3888","authenticated-orcid":false,"given":"Oksana V","family":"Vernygora","sequence":"additional","affiliation":[{"name":"Department of Entomology, University of Kentucky , Lexington, KY 40546, United States"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-6989-9179","authenticated-orcid":false,"given":"Julian R","family":"Dupuis","sequence":"additional","affiliation":[{"name":"Department of Entomology, University of Kentucky , Lexington, KY 40546, United States"}]}],"member":"286","published-online":{"date-parts":[[2024,6,17]]},"reference":[{"key":"2024062407562312400_btae377-B1","doi-asserted-by":"crossref","first-page":"1655","DOI":"10.1101\/gr.094052.109","article-title":"Fast model-based estimation of ancestry in unrelated individuals","volume":"19","author":"Alexander","year":"2009","journal-title":"Genome Res"},{"key":"2024062407562312400_btae377-B2","doi-asserted-by":"crossref","first-page":"81","DOI":"10.1038\/nrg.2015.28","article-title":"Harnessing the power of RADseq for ecological and evolutionary genomics","volume":"17","author":"Andrews","year":"2016","journal-title":"Nat Rev Genet"},{"year":"2021","author":"Chaichoompu","key":"2024062407562312400_btae377-B3"},{"key":"2024062407562312400_btae377-B4","doi-asserted-by":"crossref","first-page":"439","DOI":"10.1111\/2041-210X.12897","article-title":"assignPOP: an R package for population assignment using genetic, non-genetic, or integrated data in a machine-learning framework","volume":"9","author":"Chen","year":"2018","journal-title":"Methods Ecol Evol"},{"key":"2024062407562312400_btae377-B5","doi-asserted-by":"crossref","first-page":"246","DOI":"10.1093\/aesa\/saz069","article-title":"Identifying diagnostic genetic markers for a cryptic invasive agricultural pest: a test case using the Apple maggot fly (Diptera: Tephritidae)","volume":"113","author":"Doellman","year":"2020","journal-title":"Ann Entomol Soc Am"},{"key":"2024062407562312400_btae377-B6","doi-asserted-by":"crossref","first-page":"1641","DOI":"10.1111\/eva.12824","article-title":"Range-wide population genomics of the Mexican fruit fly: toward development of pathway analysis tools","volume":"12","author":"Dupuis","year":"2019","journal-title":"Evol Appl"},{"key":"2024062407562312400_btae377-B7","doi-asserted-by":"crossref","first-page":"51","DOI":"10.1016\/j.tree.2013.09.008","article-title":"Genome sequencing and population genomics in non-model organisms","volume":"29","author":"Ellegren","year":"2014","journal-title":"Trends Ecol Evol"},{"key":"2024062407562312400_btae377-B8","doi-asserted-by":"crossref","first-page":"2611","DOI":"10.1111\/j.1365-294X.2005.02553.x","article-title":"Detecting the number of clusters of individuals using the software STRUCTURE: a 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freshwater prawns of genus Macrobrachium in Cameroon","volume":"17","author":"Makombu","year":"2022","journal-title":"PLoS One"},{"key":"2024062407562312400_btae377-B15","doi-asserted-by":"crossref","first-page":"e0124365","DOI":"10.1371\/journal.pone.0124365","article-title":"Reduced SNP panels for genetic identification and introgression analysis in the dark honey bee (Apis mellifera mellifera)","volume":"10","author":"Mu\u00f1oz","year":"2015","journal-title":"PLoS One"},{"key":"2024062407562312400_btae377-B16","doi-asserted-by":"crossref","first-page":"102259","DOI":"10.1016\/j.fsigen.2020.102259","article-title":"How to choose sets of ancestry informative markers: a supervised feature selection approach","volume":"46","author":"Pfaffelhuber","year":"2020","journal-title":"Forensic Sci Int Genet"},{"key":"2024062407562312400_btae377-B17","doi-asserted-by":"crossref","first-page":"1402","DOI":"10.1086\/380416","article-title":"Informativeness of genetic markers for inference of 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