{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,10,30]],"date-time":"2025-10-30T07:11:43Z","timestamp":1761808303704,"version":"3.37.3"},"reference-count":22,"publisher":"Oxford University Press (OUP)","issue":"4","license":[{"start":{"date-parts":[[2019,9,3]],"date-time":"2019-09-03T00:00:00Z","timestamp":1567468800000},"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\/501100003725","name":"National Research Foundation of Korea","doi-asserted-by":"publisher","award":["2017M3A9F3046543"],"award-info":[{"award-number":["2017M3A9F3046543"]}],"id":[{"id":"10.13039\/501100003725","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Basic Science Research Program"},{"DOI":"10.13039\/501100003725","name":"National Research Foundation of Korea","doi-asserted-by":"crossref","id":[{"id":"10.13039\/501100003725","id-type":"DOI","asserted-by":"crossref"}]},{"DOI":"10.13039\/100009950","name":"Ministry of Education","doi-asserted-by":"publisher","award":["NRF-2016R1D1A1A09919610"],"award-info":[{"award-number":["NRF-2016R1D1A1A09919610"]}],"id":[{"id":"10.13039\/100009950","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Bio-Synergy Research Project","award":["NRF-2017M3A9C4065964"],"award-info":[{"award-number":["NRF-2017M3A9C4065964"]}]},{"DOI":"10.13039\/100011512","name":"National Research Foundation","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100011512","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>Motivation<\/jats:title>\n                  <jats:p>Ecological patterns of the human microbiota exhibit high inter-subject variation, with few operational taxonomic units (OTUs) shared across individuals. To overcome these issues, non-parametric approaches, such as the Mann\u2013Whitney U-test and Wilcoxon rank-sum test, have often been used to identify OTUs associated with host diseases. However, these approaches only use the ranks of observed relative abundances, leading to information loss, and are associated with high false-negative rates. In this study, we propose a phylogenetic tree-based microbiome association test (TMAT) to analyze the associations between microbiome OTU abundances and disease phenotypes. Phylogenetic trees illustrate patterns of similarity among different OTUs, and TMAT provides an efficient method for utilizing such information for association analyses. The proposed TMAT provides test statistics for each node, which are combined to identify mutations associated with host diseases.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Results<\/jats:title>\n                  <jats:p>Power estimates of TMAT were compared with existing methods using extensive simulations based on real absolute abundances. Simulation studies showed that TMAT preserves the nominal type-1 error rate, and estimates of its statistical power generally outperformed existing methods in the considered scenarios. Furthermore, TMAT can be used to detect phylogenetic mutations associated with host diseases, providing more in-depth insight into bacterial pathology.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>The 16S rRNA amplicon sequencing metagenomics datasets for colorectal carcinoma and myalgic encephalomyelitis\/chronic fatigue syndrome are available from the European Nucleotide Archive (ENA) database under project accession number PRJEB6070 and PRJEB13092, respectively. TMAT was implemented in the R package. Detailed information is available at http:\/\/healthstat.snu.ac.kr\/software\/tmat.<\/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\/btz686","type":"journal-article","created":{"date-parts":[[2019,9,1]],"date-time":"2019-09-01T03:40:44Z","timestamp":1567309244000},"page":"1000-1006","source":"Crossref","is-referenced-by-count":15,"title":["Phylogenetic tree-based microbiome association test"],"prefix":"10.1093","volume":"36","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-3966-3309","authenticated-orcid":false,"given":"Kang Jin","family":"Kim","sequence":"first","affiliation":[{"name":"Department of Public Health Sciences, Graduate School of Public Health , South Korea"}]},{"given":"Jaehyun","family":"Park","sequence":"additional","affiliation":[{"name":"Interdisciplinary Program for Bioinformatics, College of Natural Science , South Korea"}]},{"given":"Sang-Chul","family":"Park","sequence":"additional","affiliation":[{"name":"Institute of Health and Environment, Seoul National University , 1 Kwanak-ro Kwanak-gu, Seoul 151-742, South Korea"}]},{"given":"Sungho","family":"Won","sequence":"additional","affiliation":[{"name":"Department of Public Health Sciences, Graduate School of Public Health , South Korea"},{"name":"Interdisciplinary Program for Bioinformatics, College of Natural Science , South Korea"},{"name":"Institute of Health and Environment, Seoul National University , 1 Kwanak-ro Kwanak-gu, Seoul 151-742, South Korea"}]}],"member":"286","published-online":{"date-parts":[[2019,9,3]]},"reference":[{"key":"2023013110103910200_btz686-B1","doi-asserted-by":"crossref","first-page":"114.","DOI":"10.1186\/s12864-017-3501-4","article-title":"SILVA, RDP, Greengenes, NCBI and OTT\u2014how do these taxonomies compare?","volume":"18","author":"Balvo\u010di\u016bt\u0117","year":"2017","journal-title":"BMC Genomics"},{"key":"2023013110103910200_btz686-B2","doi-asserted-by":"crossref","first-page":"335","DOI":"10.1038\/nmeth.f.303","article-title":"QIIME allows analysis of high-throughput community sequencing data","volume":"7","author":"Caporaso","year":"2010","journal-title":"Nat. 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