{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,7,20]],"date-time":"2026-07-20T05:46:31Z","timestamp":1784526391533,"version":"3.55.0"},"reference-count":18,"publisher":"Oxford University Press (OUP)","issue":"4","license":[{"start":{"date-parts":[[2019,10,7]],"date-time":"2019-10-07T00:00:00Z","timestamp":1570406400000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100000001","name":"National Science Foundation","doi-asserted-by":"publisher","award":["DMS-1069303"],"award-info":[{"award-number":["DMS-1069303"]}],"id":[{"id":"10.13039\/100000001","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000001","name":"National Science Foundation","doi-asserted-by":"publisher","award":["DMS-1563159"],"award-info":[{"award-number":["DMS-1563159"]}],"id":[{"id":"10.13039\/100000001","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000936","name":"Gordon and Betty Moore Foundation","doi-asserted-by":"publisher","award":["#3300"],"award-info":[{"award-number":["#3300"]}],"id":[{"id":"10.13039\/100000936","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2020,2,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:sec>\n                    <jats:title>Summary<\/jats:title>\n                    <jats:p>Phylogenetic comparative methods are powerful but presently under-utilized ways to identify microbial genes underlying differences in community composition. These methods help to identify functionally important genes because they test for associations beyond those expected when related microbes occupy similar environments. We present phylogenize, a pipeline with web, QIIME 2 and R interfaces that allows researchers to perform phylogenetic regression on 16S amplicon and shotgun sequencing data and to visualize results. phylogenize applies broadly to both host-associated and environmental microbiomes. Using Human Microbiome Project and Earth Microbiome Project data, we show that phylogenize draws similar conclusions from 16S versus shotgun sequencing and reveals both known and candidate pathways associated with host colonization.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Availability and implementation<\/jats:title>\n                    <jats:p>phylogenize is available at https:\/\/phylogenize.org and https:\/\/bitbucket.org\/pbradz\/phylogenize.<\/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\/btz722","type":"journal-article","created":{"date-parts":[[2019,9,26]],"date-time":"2019-09-26T07:28:48Z","timestamp":1569482928000},"page":"1289-1290","source":"Crossref","is-referenced-by-count":5,"title":["<i>phylogenize<\/i>\n                    : correcting for phylogeny reveals genes associated with microbial distributions"],"prefix":"10.1093","volume":"36","author":[{"given":"Patrick H","family":"Bradley","sequence":"first","affiliation":[{"name":"Gladstone Institute of Data Science and Biotechnology , San Francisco, CA 94158, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Katherine S","family":"Pollard","sequence":"additional","affiliation":[{"name":"Gladstone Institute of Data Science and Biotechnology , San Francisco, CA 94158, USA"},{"name":"Department of Epidemiology and Biostatistics, University of California , San Francisco, CA 94158, USA"},{"name":"Chan\u2013Zuckerberg Biohub , San Francisco, CA 94158, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2019,10,7]]},"reference":[{"key":"2023013110150240500_btz722-B1","doi-asserted-by":"crossref","first-page":"2882","DOI":"10.1093\/bioinformatics\/btv287","article-title":"Tax4Fun: predicting functional profiles from metagenomic 16S rRNA data","volume":"31","author":"A\u00dfhauer","year":"2015","journal-title":"Bioinformatics"},{"key":"2023013110150240500_btz722-B2","article-title":"BURST enables optimal exhaustive DNA alignment for big data","author":"Al-Ghalith","year":"2017","journal-title":"Zenodo"},{"key":"2023013110150240500_btz722-B3","doi-asserted-by":"crossref","first-page":"e00191","DOI":"10.1128\/mSystems.00191-16","article-title":"Deblur rapidly resolves single-nucleotide community sequence patterns","volume":"2","author":"Amir","year":"2017","journal-title":"mSystems"},{"key":"2023013110150240500_btz722-B4","doi-asserted-by":"crossref","first-page":"852","DOI":"10.1038\/s41587-019-0209-9","article-title":"Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2","volume":"37","author":"Bolyen","year":"2019","journal-title":"Nat. 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