{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,4,7]],"date-time":"2025-04-07T20:36:05Z","timestamp":1744058165398,"version":"3.37.3"},"reference-count":10,"publisher":"Oxford University Press (OUP)","issue":"17","license":[{"start":{"date-parts":[[2021,1,30]],"date-time":"2021-01-30T00:00:00Z","timestamp":1611964800000},"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\/100000002","name":"National Institutes of Health","doi-asserted-by":"publisher","award":["R01AG040211"],"award-info":[{"award-number":["R01AG040211"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100004606","name":"Chang Gung Medical Foundation","doi-asserted-by":"publisher","award":["CLRPG3J0012","BMRPE97"],"award-info":[{"award-number":["CLRPG3J0012","BMRPE97"]}],"id":[{"id":"10.13039\/501100004606","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2021,9,9]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Motivation<\/jats:title>\n                  <jats:p>We proposed a wiSDOM (web-based inclusionary analysis Suite for Disease-Oriented Metagenomics) R Shiny application which comprises six functional modules: (i) initial visualization of sampling effort and distribution of dominant bacterial taxa among groups or individual samples at different taxonomic levels; (ii) statistical and visual analysis of \u03b1 diversity; (iii) analysis of similarity (ANOSIM) of \u03b2 diversity on UniFrac, Bray-Curtis, Horn-Morisita or Jaccard distance and visualizations; (iv) microbial biomarker discovery between two or more groups with various statistical and machine learning approaches; (v) assessment of the clinical validity of selected biomarkers by creating the interactive receiver operating characteristic (ROC) curves and calculating the area under the curve (AUC) for binary classifiers; and lastly (vi) functional prediction of metagenomes with PICRUSt or Tax4Fun.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Results<\/jats:title>\n                  <jats:p>The performance of wiSDOM has been evaluated in several of our previous studies for exploring microbial biomarkers and their clinical validity as well as assessing the alterations in bacterial diversity and functionality. The wiSDOM can be customized and visualized as per users\u2019 needs and specifications, allowing researchers without programming background to conduct comprehensive data mining and illustration using an intuitive browser-based interface.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>The browser-based R Shiny interface can be accessible via (https:\/\/lun-ching.shinyapps.io\/wisdom\/) and freely available at (https:\/\/github.com\/lunching\/wiSDOM).<\/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\/btab057","type":"journal-article","created":{"date-parts":[[2021,1,25]],"date-time":"2021-01-25T21:02:11Z","timestamp":1611608531000},"page":"2795-2797","source":"Crossref","is-referenced-by-count":5,"title":["wiSDOM: a visual and statistical analytics for interrogating microbiome"],"prefix":"10.1093","volume":"37","author":[{"given":"Shih-Chi","family":"Su","sequence":"first","affiliation":[{"name":"Chang Gung Memorial Hospital Whole-Genome Research Core Laboratory of Human Diseases, , Keelung 204, Taiwan"},{"name":"Chang Gung Memorial Hospital Department of Dermatology, Drug Hypersensitivity Clinical and Research Center, , Linkou 333, Taiwan"},{"name":"XiaMen Chang Gung Hospital Central Research Laboratory, , Xiamen 361028, China"}]},{"given":"James E.","family":"Galvin","sequence":"additional","affiliation":[{"name":"University of Miami Comprehensive Center for Brain Health, Department of Neurology, Miller School of Medicine, , Miami, FL 33431, USA"}]},{"given":"Shun-Fa","family":"Yang","sequence":"additional","affiliation":[{"name":"Institute of Medicine, Chung Shan Medical University , Taichung 402, Taiwan"},{"name":"Chung Shan Medical University Hospital Department of Medical Research, , Taichung 402, Taiwan"}]},{"given":"Wen-Hung","family":"Chung","sequence":"additional","affiliation":[{"name":"Chang Gung Memorial Hospital Whole-Genome Research Core Laboratory of Human Diseases, , Keelung 204, Taiwan"},{"name":"Chang Gung Memorial Hospital Department of Dermatology, Drug Hypersensitivity Clinical and Research Center, , Linkou 333, Taiwan"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8039-5350","authenticated-orcid":false,"given":"Lun-Ching","family":"Chang","sequence":"additional","affiliation":[{"name":"Florida Atlantic University Department of Mathematical Sciences, , Boca Raton, FL 33431, USA"}]}],"member":"286","published-online":{"date-parts":[[2021,1,30]]},"reference":[{"key":"2023051609161824300_btab057-B1","doi-asserted-by":"crossref","first-page":"2639","DOI":"10.1038\/ismej.2017.119","article-title":"Exact sequence variants should replace operational taxonomic units in marker-gene data analysis","volume":"11","author":"Callahan","year":"2017","journal-title":"ISME J"},{"key":"2023051609161824300_btab057-B2","doi-asserted-by":"crossref","first-page":"581","DOI":"10.1038\/nmeth.3869","article-title":"DADA2: high-resolution sample inference from Illumina amplicon data","volume":"13","author":"Callahan","year":"2016","journal-title":"Nat. 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