{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,9]],"date-time":"2026-04-09T05:43:47Z","timestamp":1775713427691,"version":"3.50.1"},"reference-count":11,"publisher":"Oxford University Press (OUP)","issue":"13","license":[{"start":{"date-parts":[[2020,4,27]],"date-time":"2020-04-27T00:00:00Z","timestamp":1587945600000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/journals\/pages\/open_access\/funder_policies\/chorus\/standard_publication_model"}],"funder":[{"name":"MD Anderson Moon Shot Programs"},{"name":"Prostate Cancer SPORE","award":["P50CA140388"],"award-info":[{"award-number":["P50CA140388"]}]},{"DOI":"10.13039\/100000002","name":"NIH","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000054","name":"NCI","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100000054","id-type":"DOI","asserted-by":"publisher"}]},{"name":"CCSG","award":["P30CA016672"],"award-info":[{"award-number":["P30CA016672"]}]},{"name":"CCSG","award":["CCTS 5UL1TR000371"],"award-info":[{"award-number":["CCTS 5UL1TR000371"]}]},{"name":"CCSG","award":["CPRIT RP160693"],"award-info":[{"award-number":["CPRIT RP160693"]}]},{"DOI":"10.13039\/100000002","name":"NIH","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000054","name":"NCI","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100000054","id-type":"DOI","asserted-by":"publisher"}]},{"name":"CCSG","award":["P30CA016672"],"award-info":[{"award-number":["P30CA016672"]}]},{"name":"MD Anderson Moon Shot Programs"},{"DOI":"10.13039\/100000002","name":"NIH","doi-asserted-by":"publisher","award":["R01 HL124112"],"award-info":[{"award-number":["R01 HL124112"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100004917","name":"CPRIT","doi-asserted-by":"publisher","award":["RR160089"],"award-info":[{"award-number":["RR160089"]}],"id":[{"id":"10.13039\/100004917","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2020,7,1]]},"abstract":"<jats:title>Abstract<\/jats:title><jats:sec><jats:title>Summary<\/jats:title><jats:p>In fields, such as ecology, microbiology and genomics, non-Euclidean distances are widely applied to describe pairwise dissimilarity between samples. Given these pairwise distances, principal coordinates analysis is commonly used to construct a visualization of the data. However, confounding covariates can make patterns related to the scientific question of interest difficult to observe. We provide adjusted principal coordinates analysis as an easy-to-use tool, available as both an R package and a Shiny app, to improve data visualization in this context, enabling enhanced presentation of the effects of interest.<\/jats:p><\/jats:sec><jats:sec><jats:title>Availability and implementation<\/jats:title><jats:p>The R package \u2018aPCoA\u2019 and Shiny app can be accessed at https:\/\/cran.r-project.org\/web\/packages\/aPCoA\/index.html and https:\/\/biostatistics.mdanderson.org\/shinyapps\/aPCoA\/.<\/jats:p><\/jats:sec>","DOI":"10.1093\/bioinformatics\/btaa276","type":"journal-article","created":{"date-parts":[[2020,4,21]],"date-time":"2020-04-21T19:10:47Z","timestamp":1587496247000},"page":"4099-4101","source":"Crossref","is-referenced-by-count":61,"title":["aPCoA: covariate adjusted principal coordinates analysis"],"prefix":"10.1093","volume":"36","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-7575-9706","authenticated-orcid":false,"given":"Yushu","family":"Shi","sequence":"first","affiliation":[{"name":"Department of Biostatistics"}]},{"given":"Liangliang","family":"Zhang","sequence":"additional","affiliation":[{"name":"Department of Biostatistics"}]},{"given":"Kim-Anh","family":"Do","sequence":"additional","affiliation":[{"name":"Department of Biostatistics"}]},{"given":"Christine B","family":"Peterson","sequence":"additional","affiliation":[{"name":"Department of Biostatistics"}]},{"given":"Robert R","family":"Jenq","sequence":"additional","affiliation":[{"name":"Department of Genomic Medicine , University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA"}]}],"member":"286","published-online":{"date-parts":[[2020,4,27]]},"reference":[{"key":"2023062312040511900_btaa276-B1","doi-asserted-by":"crossref","first-page":"325","DOI":"10.2307\/1942268","article-title":"An ordination of the upland forest communities of southern Wisconsin","volume":"27","author":"Bray","year":"1957","journal-title":"Ecol. Monogr"},{"key":"2023062312040511900_btaa276-B2","doi-asserted-by":"crossref","first-page":"2387","DOI":"10.1109\/36.789637","article-title":"Interference and noise-adjusted principal components analysis","volume":"37","author":"Chang","year":"1999","journal-title":"IEEE Geosci. Remote Sens. Lett"},{"key":"2023062312040511900_btaa276-B3","doi-asserted-by":"crossref","first-page":"325","DOI":"10.1093\/biomet\/53.3-4.325","article-title":"Some distance properties of latent root and vector methods used in multivariate analysis","volume":"53","author":"Gower","year":"1966","journal-title":"Biometrika"},{"key":"2023062312040511900_btaa276-B4","doi-asserted-by":"crossref","first-page":"425","DOI":"10.1016\/B978-0-444-53868-0.50009-5","volume-title":"Numerical Ecology","author":"Legendre","year":"2012"},{"key":"2023062312040511900_btaa276-B5","doi-asserted-by":"crossref","first-page":"14662","DOI":"10.1073\/pnas.1617317113","article-title":"Simultaneous dimension reduction and adjustment for confounding variation","volume":"113","author":"Lin","year":"2016","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"2023062312040511900_btaa276-B6","doi-asserted-by":"crossref","first-page":"8228","DOI":"10.1128\/AEM.71.12.8228-8235.2005","article-title":"UniFrac: a new phylogenetic method for comparing microbial communities","volume":"71","author":"Lozupone","year":"2005","journal-title":"Appl. Environ. Microbiol"},{"key":"2023062312040511900_btaa276-B7","doi-asserted-by":"crossref","first-page":"1576","DOI":"10.1128\/AEM.01996-06","article-title":"Quantitative and qualitative \u03b2 diversity measures lead to different insights into factors that structure microbial communities","volume":"73","author":"Lozupone","year":"2007","journal-title":"Appl. Environ. Microbiol"},{"key":"2023062312040511900_btaa276-B8","doi-asserted-by":"crossref","first-page":"211","DOI":"10.1002\/gepi.20567","article-title":"Relationship between genomic distance-based regression and kernel machine regression for multi-marker association testing","volume":"35","author":"Pan","year":"2011","journal-title":"Genet. Epidemiol"},{"key":"2023062312040511900_btaa276-B9","doi-asserted-by":"crossref","first-page":"795","DOI":"10.1016\/j.cell.2019.07.008","article-title":"Tumor microbiome diversity and composition influence pancreatic cancer outcomes","volume":"178","author":"Riquelme","year":"2019","journal-title":"Cell"},{"key":"2023062312040511900_btaa276-B10","first-page":"471","author":"Wang"},{"key":"2023062312040511900_btaa276-B11","doi-asserted-by":"crossref","first-page":"19430","DOI":"10.1073\/pnas.0609333103","article-title":"Multivariate regression analysis of distance matrices for testing associations between gene expression patterns and related variables","volume":"103","author":"Zapala","year":"2006","journal-title":"Proc. Natl. Acad. Sci. USA"}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/academic.oup.com\/bioinformatics\/advance-article-pdf\/doi\/10.1093\/bioinformatics\/btaa276\/33383978\/btaa276.pdf","content-type":"application\/pdf","content-version":"am","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/36\/13\/4099\/50671412\/bioinformatics_36_13_4099.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/36\/13\/4099\/50671412\/bioinformatics_36_13_4099.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2024,8,4]],"date-time":"2024-08-04T11:11:10Z","timestamp":1722769870000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/36\/13\/4099\/5825727"}},"subtitle":[],"editor":[{"given":"Jonathan","family":"Wren","sequence":"additional","affiliation":[]}],"short-title":[],"issued":{"date-parts":[[2020,4,27]]},"references-count":11,"journal-issue":{"issue":"13","published-print":{"date-parts":[[2020,7,1]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btaa276","relation":{},"ISSN":["1367-4803","1367-4811"],"issn-type":[{"value":"1367-4803","type":"print"},{"value":"1367-4811","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2020,7]]},"published":{"date-parts":[[2020,4,27]]}}}