{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,1,16]],"date-time":"2026-01-16T19:05:31Z","timestamp":1768590331168,"version":"3.49.0"},"reference-count":4,"publisher":"Oxford University Press (OUP)","issue":"7","license":[{"start":{"date-parts":[[2022,2,3]],"date-time":"2022-02-03T00:00:00Z","timestamp":1643846400000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/journals\/pages\/open_access\/funder_policies\/chorus\/standard_publication_model"}],"funder":[{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["11971017"],"award-info":[{"award-number":["11971017"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Shanghai Municipal Science and Technology Major Project","award":["2017SHZDZX01"],"award-info":[{"award-number":["2017SHZDZX01"]}]},{"name":"Multidisciplinary Cross Research Foundation of Shanghai Jiao Tong University","award":["19X190020184"],"award-info":[{"award-number":["19X190020184"]}]},{"name":"Multidisciplinary Cross Research Foundation of Shanghai Jiao Tong University","award":["19X190020194"],"award-info":[{"award-number":["19X190020194"]}]},{"name":"Multidisciplinary Cross Research Foundation of Shanghai Jiao Tong University","award":["21X010301669"],"award-info":[{"award-number":["21X010301669"]}]},{"name":"Neil Shen\u2019s SJTU Medical Research Fund of Shanghai Jiao Tong University"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2022,3,28]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Summary<\/jats:title>\n                  <jats:p>Analysis of compositions of microbiomes (ANCOM) compares the absolute abundances of microbes between two or more ecosystems using relative abundances in specimens derived from these ecosystems. Despite its impressive performance, there are two drawbacks to ANCOM. First, with K microbes it requires fitting K(K\u22121)\/2 models for log-ratios of counts, and so can be computationally intensive. Second, it does not output P-values for microbes detected as differentially abundant. We propose a fast implementation of ANCOM, fastANCOM, that fits only K models for log-transformed counts. fastANCOM provides P-values to declare statistical significance and outputs log fold changes of abundance between groups. We demonstrate that fastANCOM compares favorably with existing differential abundance testing methods in terms of running time, false discovery rate and power.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>fastANCOM is available at https:\/\/github.com\/ZRChao\/fastANCOM.<\/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\/btac060","type":"journal-article","created":{"date-parts":[[2022,1,27]],"date-time":"2022-01-27T12:15:18Z","timestamp":1643285718000},"page":"2039-2041","source":"Crossref","is-referenced-by-count":17,"title":["fastANCOM: a fast method for analysis of compositions of microbiomes"],"prefix":"10.1093","volume":"38","author":[{"given":"Chao","family":"Zhou","sequence":"first","affiliation":[{"name":"Department of Bioinformatics and Biostatistics, Shanghai Jiao Tong University , Shanghai, China"},{"name":"SJTU-Yale Joint Center for Biostatistics and Data Science, Shanghai Jiao Tong University , Shanghai, China"}]},{"given":"Huimin","family":"Wang","sequence":"additional","affiliation":[{"name":"Department of Biostatistics and Bioinformatics, Duke University School of Medicine , Durham, NC, USA"}]},{"given":"Hongyu","family":"Zhao","sequence":"additional","affiliation":[{"name":"SJTU-Yale Joint Center for Biostatistics and Data Science, Shanghai Jiao Tong University , Shanghai, China"},{"name":"Department of Biostatistics, Yale University , New Haven, CT, USA"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-1218-4017","authenticated-orcid":false,"given":"Tao","family":"Wang","sequence":"additional","affiliation":[{"name":"Department of Bioinformatics and Biostatistics, Shanghai Jiao Tong University , Shanghai, China"},{"name":"SJTU-Yale Joint Center for Biostatistics and Data Science, Shanghai Jiao Tong University , Shanghai, China"},{"name":"MoE Key Lab of Artificial Intelligence, AI Institute, Shanghai Jiao Tong University , Shanghai, China"}]}],"member":"286","published-online":{"date-parts":[[2022,2,3]]},"reference":[{"key":"2023020109014338700_btac060-B1","doi-asserted-by":"crossref","first-page":"3514","DOI":"10.1038\/s41467-020-17041-7","article-title":"Analysis of compositions of microbiomes with bias correction","volume":"11","author":"Lin","year":"2020","journal-title":"Nat. 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Biol"},{"key":"2023020109014338700_btac060-B4","doi-asserted-by":"crossref","first-page":"27","DOI":"10.1186\/s40168-017-0237-y","article-title":"Normalization and microbial differential abundance strategies depend upon data characteristics","volume":"5","author":"Weiss","year":"2017","journal-title":"Microbiome"}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/advance-article-pdf\/doi\/10.1093\/bioinformatics\/btac060\/42466315\/btac060.pdf","content-type":"application\/pdf","content-version":"am","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/38\/7\/2039\/49010434\/btac060.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/38\/7\/2039\/49010434\/btac060.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,2,1]],"date-time":"2023-02-01T20:47:02Z","timestamp":1675284422000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/38\/7\/2039\/6520804"}},"subtitle":[],"editor":[{"given":"Peter","family":"Robinson","sequence":"additional","affiliation":[]}],"short-title":[],"issued":{"date-parts":[[2022,2,3]]},"references-count":4,"journal-issue":{"issue":"7","published-print":{"date-parts":[[2022,3,28]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btac060","relation":{},"ISSN":["1367-4803","1367-4811"],"issn-type":[{"value":"1367-4803","type":"print"},{"value":"1367-4811","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2022,4,1]]},"published":{"date-parts":[[2022,2,3]]}}}