{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,26]],"date-time":"2026-02-26T20:34:28Z","timestamp":1772138068887,"version":"3.50.1"},"reference-count":33,"publisher":"Oxford University Press (OUP)","issue":"6","license":[{"start":{"date-parts":[[2024,5,24]],"date-time":"2024-05-24T00:00:00Z","timestamp":1716508800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100000002","name":"National Institutes of Health","doi-asserted-by":"publisher","award":["R01 HL158796"],"award-info":[{"award-number":["R01 HL158796"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000002","name":"National Institutes of Health","doi-asserted-by":"publisher","award":["R01 CA244845"],"award-info":[{"award-number":["R01 CA244845"]}],"id":[{"id":"10.13039\/100000002","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>Although the human microbiome plays a key role in health and disease, the biological mechanisms underlying the interaction between the microbiome and its host are incompletely understood. Integration with other molecular profiling data offers an opportunity to characterize the role of the microbiome and elucidate therapeutic targets. However, this remains challenging to the high dimensionality, compositionality, and rare features found in microbiome profiling data. These challenges necessitate the use of methods that can achieve structured sparsity in learning cross-platform association patterns.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Results<\/jats:title>\n                    <jats:p>We propose Tree-Aggregated factor RegressiOn (TARO) for the integration of microbiome and metabolomic data. We leverage information on the taxonomic tree structure to flexibly aggregate rare features. We demonstrate through simulation studies that TARO accurately recovers a low-rank coefficient matrix and identifies relevant features. We applied TARO to microbiome and metabolomic profiles gathered from subjects being screened for colorectal cancer to understand how gut microrganisms shape intestinal metabolite abundances.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Availability and implementation<\/jats:title>\n                    <jats:p>The R package TARO implementing the proposed methods is available online at https:\/\/github.com\/amishra-stats\/taro-package.<\/jats:p>\n                  <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btae321","type":"journal-article","created":{"date-parts":[[2024,5,15]],"date-time":"2024-05-15T16:38:44Z","timestamp":1715791124000},"source":"Crossref","is-referenced-by-count":0,"title":["TARO: tree-aggregated factor regression for microbiome data integration"],"prefix":"10.1093","volume":"40","author":[{"given":"Aditya K","family":"Mishra","sequence":"first","affiliation":[{"name":"Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center , Houston, TX 77030, United States"},{"name":"Platform for Innovative Microbiome and Translational Research (PRIME-TR), The University of Texas MD Anderson Cancer Center , Houston, TX 77030, United States"}]},{"given":"Iqbal","family":"Mahmud","sequence":"additional","affiliation":[{"name":"Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center , Houston, TX 77030, United States"}]},{"given":"Philip L","family":"Lorenzi","sequence":"additional","affiliation":[{"name":"Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center , Houston, TX 77030, United States"}]},{"given":"Robert R","family":"Jenq","sequence":"additional","affiliation":[{"name":"Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center , Houston, TX 77030, United States"},{"name":"Platform for Innovative Microbiome and Translational Research (PRIME-TR), The University of Texas MD Anderson Cancer Center , Houston, TX 77030, United States"}]},{"given":"Jennifer A","family":"Wargo","sequence":"additional","affiliation":[{"name":"Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center , Houston, TX 77030, United States"},{"name":"Platform for Innovative Microbiome and Translational Research (PRIME-TR), The University of Texas MD Anderson Cancer Center , Houston, TX 77030, United States"},{"name":"Department of Surgical Oncology, The University of Texas MD Anderson Cancer Center , Houston, TX 77030, United States"}]},{"given":"Nadim J","family":"Ajami","sequence":"additional","affiliation":[{"name":"Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center , Houston, TX 77030, United States"},{"name":"Platform for Innovative Microbiome and Translational Research (PRIME-TR), The University of Texas MD Anderson Cancer Center , Houston, TX 77030, United States"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-3316-0468","authenticated-orcid":false,"given":"Christine B","family":"Peterson","sequence":"additional","affiliation":[{"name":"Platform for Innovative Microbiome and Translational Research (PRIME-TR), The University of Texas MD Anderson Cancer Center , Houston, TX 77030, United States"},{"name":"Department of Biostatistics, The University of Texas MD Anderson Cancer Center , Houston, TX 77030, United States"}]}],"member":"286","published-online":{"date-parts":[[2024,5,24]]},"reference":[{"key":"2024062208565325000_btae321-B1","doi-asserted-by":"crossref","first-page":"323","DOI":"10.1093\/biomet\/71.2.323","article-title":"Log contrast models for experiments with mixtures","volume":"71","author":"Aitchison","year":"1984","journal-title":"Biometrika"},{"key":"2024062208565325000_btae321-B2","doi-asserted-by":"crossref","first-page":"14505","DOI":"10.1038\/s41598-021-93645-3","article-title":"Tree-aggregated predictive modeling of 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