{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2023,1,27]],"date-time":"2023-01-27T16:35:33Z","timestamp":1674837333142},"reference-count":33,"publisher":"Oxford University Press (OUP)","issue":"24","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2011,12,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Motivation: Metagenomics involves sampling and studying the genetic materials in microbial communities. Several statistical methods have been proposed for comparative analysis of microbial community compositions. Most of the methods are based on the estimated abundances of taxonomic units or functional groups from metagenomic samples. However, such estimated abundances might deviate from the true abundances in habitats due to sampling biases and other systematic artifacts in metagenomic data processing.<\/jats:p>\n               <jats:p>Results: We developed the MetaRank scheme to convert abundances into ranks. MetaRank employs a series of statistical hypothesis tests to compare abundances within a microbial community and determine their ranks. We applied MetaRank to synthetic samples and real metagenomes. The results confirm that MetaRank can reduce the effects of sampling biases and clarify the characteristics of metagenomes in comparative studies of microbial communities. Therefore, MetaRank provides a useful rank-based approach to analyzing microbiomes.<\/jats:p>\n               <jats:p>Contact: \u00a0hktsai@iis.sinica.edu.tw<\/jats:p>\n               <jats:p>Supplementary Information: \u00a0Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btr583","type":"journal-article","created":{"date-parts":[[2011,10,21]],"date-time":"2011-10-21T02:07:11Z","timestamp":1319162831000},"page":"3341-3347","source":"Crossref","is-referenced-by-count":4,"title":["MetaRank: a rank conversion scheme for comparative analysis of microbial community compositions"],"prefix":"10.1093","volume":"27","author":[{"given":"Tse-Yi","family":"Wang","sequence":"first","affiliation":[{"name":"1 Institute of Information Science, 2Research Center for Information Technology Innovation, Academia Sinica, Taipei, 115 and 3Department of Computer Science and Information Engineering, National Taiwan University, Taipei, 106, Taiwan"}]},{"given":"Chien-Hao","family":"Su","sequence":"additional","affiliation":[{"name":"1 Institute of Information Science, 2Research Center for Information Technology Innovation, Academia Sinica, Taipei, 115 and 3Department of Computer Science and Information Engineering, National Taiwan University, Taipei, 106, Taiwan"},{"name":"1 Institute of Information Science, 2Research Center for Information Technology Innovation, Academia Sinica, Taipei, 115 and 3Department of Computer Science and Information Engineering, National Taiwan University, Taipei, 106, Taiwan"},{"name":"1 Institute of Information Science, 2Research Center for Information Technology Innovation, Academia Sinica, Taipei, 115 and 3Department of Computer Science and Information Engineering, National Taiwan University, Taipei, 106, Taiwan"}]},{"given":"Huai-Kuang","family":"Tsai","sequence":"additional","affiliation":[{"name":"1 Institute of Information Science, 2Research Center for Information Technology Innovation, Academia Sinica, Taipei, 115 and 3Department of Computer Science and Information Engineering, National Taiwan University, Taipei, 106, Taiwan"},{"name":"1 Institute of Information Science, 2Research Center for Information Technology Innovation, Academia Sinica, Taipei, 115 and 3Department of Computer Science and Information Engineering, National Taiwan University, Taipei, 106, Taiwan"}]}],"member":"286","published-online":{"date-parts":[[2011,10,20]]},"reference":[{"key":"2023012511314394700_B1","doi-asserted-by":"crossref","first-page":"7724","DOI":"10.1128\/AEM.71.12.7724-7736.2005","article-title":"At least 1 in 20 16S rRNA sequence records currently held in public repositories is estimated to contain substantial anomalies","volume":"71","author":"Ashelford","year":"2005","journal-title":"Appl. Environ. Microbiol."},{"key":"2023012511314394700_B2","doi-asserted-by":"crossref","first-page":"2221","DOI":"10.1128\/AEM.02118-08","article-title":"Prokaryotic genomes and diversity in surface ocean waters: interrogating the global ocean sampling metagenome","volume":"75","author":"Biers","year":"2009","journal-title":"Appl. Environ. Microbiol."},{"key":"2023012511314394700_B3","doi-asserted-by":"crossref","first-page":"673","DOI":"10.1038\/nmeth.1358","article-title":"Phymm and PhymmBL: metagenomic phylogenetic classification with interpolated Markov models","volume":"6","author":"Brady","year":"2009","journal-title":"Nat. Methods"},{"key":"2023012511314394700_B4","doi-asserted-by":"crossref","first-page":"1374","DOI":"10.1093\/jn\/121.9.1374","article-title":"Inhibitory effect of dietary soybean protein vs. casein on magnesium absorption in rats","volume":"121","author":"Brink","year":"1991","journal-title":"J. Nutr."},{"key":"2023012511314394700_B5","doi-asserted-by":"crossref","first-page":"D141","DOI":"10.1093\/nar\/gkn879","article-title":"The Ribosomal Database Project: improved alignments and new tools for rRNA analysis","volume":"37","author":"Cole","year":"2009","journal-title":"Nucleic Acids Res."},{"key":"2023012511314394700_B6","doi-asserted-by":"crossref","first-page":"629","DOI":"10.1038\/nature06810","article-title":"Functional metagenomic profiling of nine biomes","volume":"452","author":"Dinsdale","year":"2008","journal-title":"Nature"},{"key":"2023012511314394700_B7","doi-asserted-by":"crossref","first-page":"22427","DOI":"10.1073\/pnas.0908284106","article-title":"Ecology of the rare microbial biosphere of the Arctic Ocean","volume":"106","author":"Galand","year":"2009","journal-title":"Proc. Natl Acad. Sci. USA"},{"key":"2023012511314394700_B8","doi-asserted-by":"crossref","first-page":"461","DOI":"10.1038\/ismej.2010.141","article-title":"Quantitative analysis of a deeply sequenced marine microbial metatranscriptome","volume":"5","author":"Gifford","year":"2011","journal-title":"ISME J."},{"key":"2023012511314394700_B9","doi-asserted-by":"crossref","first-page":"1314","DOI":"10.1038\/ismej.2009.72","article-title":"Systematic artifacts in metagenomes from complex microbial communities","volume":"3","author":"Gomez-Alvarez","year":"2009","journal-title":"ISME J."},{"key":"2023012511314394700_B10","doi-asserted-by":"crossref","first-page":"1691","DOI":"10.1093\/jn\/119.11.1691","article-title":"Interactions of lactose with calcium, magnesium and zinc in rats","volume":"119","author":"Greger","year":"1989","journal-title":"J. Nutr."},{"key":"2023012511314394700_B11","doi-asserted-by":"crossref","first-page":"1141","DOI":"10.1101\/gr.085464.108","article-title":"Microbial community profiling for human microbiome projects: Tools, techniques, and challenges","volume":"19","author":"Hamady","year":"2009","journal-title":"Genome Res."},{"key":"2023012511314394700_B12","doi-asserted-by":"crossref","first-page":"747","DOI":"10.1079\/BJN19930170","article-title":"Ileal pH and apparent absorption of magnesium in rats fed on diets containing either lactose or lactulose","volume":"70","author":"Heijnen","year":"1993","journal-title":"Br. J. Nutr."},{"key":"2023012511314394700_B13","doi-asserted-by":"crossref","first-page":"481","DOI":"10.1038\/455481a","article-title":"Microbiology: metagenomics","volume":"455","author":"Hugenholtz","year":"2008","journal-title":"Nature"},{"key":"2023012511314394700_B14","doi-asserted-by":"crossref","first-page":"681","DOI":"10.1093\/ajcn\/28.7.681","article-title":"Effects of dietary lactose and lactase preparation on the intestinal absorption of calcium and magnesium in normal infants","volume":"28","author":"Kobayashi","year":"1975","journal-title":"Am. J. Clin. Nutr."},{"key":"2023012511314394700_B15","doi-asserted-by":"crossref","first-page":"2144","DOI":"10.1101\/gr.094508.109","article-title":"Windshield splatter analysis with the Galaxy metagenomic pipeline","volume":"19","author":"Kosakovsky Pond","year":"2009","journal-title":"Genome Res."},{"key":"2023012511314394700_B16","doi-asserted-by":"crossref","first-page":"2737","DOI":"10.1093\/bioinformatics\/btp508","article-title":"ShotgunFunctionalizeR: an R-package for functional comparison of metagenomes","volume":"25","author":"Kristiansson","year":"2009","journal-title":"Bioinformatics"},{"key":"2023012511314394700_B17","doi-asserted-by":"crossref","first-page":"169","DOI":"10.1093\/dnares\/dsm018","article-title":"Comparative metagenomics revealed commonly enriched gene sets in human gut microbiomes","volume":"14","author":"Kurokawa","year":"2007","journal-title":"DNA Res."},{"key":"2023012511314394700_B18","doi-asserted-by":"crossref","first-page":"1022","DOI":"10.1038\/4441022a","article-title":"Microbial ecology: human gut microbes associated with obesity","volume":"444","author":"Ley","year":"2006","journal-title":"Nature"},{"key":"2023012511314394700_B19","doi-asserted-by":"crossref","first-page":"359","DOI":"10.1186\/1471-2105-10-359","article-title":"Analysis and comparison of very large metagenomes with fast clustering and functional annotation","volume":"10","author":"Li","year":"2009","journal-title":"BMC Bioinformatics"},{"key":"2023012511314394700_B20","doi-asserted-by":"crossref","DOI":"10.1007\/978-94-015-7358-0","volume-title":"Ecological Diversity and Its Measurement.","author":"Magurran","year":"1988"},{"key":"2023012511314394700_B21","doi-asserted-by":"crossref","first-page":"D534","DOI":"10.1093\/nar\/gkm869","article-title":"IMG\/M: a data management and analysis system for metagenomes","volume":"36","author":"Markowitz","year":"2008","journal-title":"Nucleic Acids Res."},{"key":"2023012511314394700_B22","doi-asserted-by":"crossref","first-page":"495","DOI":"10.1038\/nmeth1043","article-title":"Use of simulated data sets to evaluate the fidelity of metagenomic processing methods","volume":"4","author":"Mavromatis","year":"2007","journal-title":"Nat. Methods"},{"key":"2023012511314394700_B23","doi-asserted-by":"crossref","first-page":"1849","DOI":"10.1093\/bioinformatics\/btp341","article-title":"Visual and statistical comparison of metagenomes","volume":"25","author":"Mitra","year":"2009","journal-title":"Bioinformatics"},{"key":"2023012511314394700_B24","doi-asserted-by":"crossref","first-page":"715","DOI":"10.1093\/bioinformatics\/btq041","article-title":"Identifying biologically relevant differences between metagenomic communities","volume":"26","author":"Parks","year":"2010","journal-title":"Bioinformatics"},{"key":"2023012511314394700_B25","doi-asserted-by":"crossref","first-page":"162","DOI":"10.1186\/1471-2105-7-162","article-title":"An application of statistics to comparative metagenomics","volume":"7","author":"Rodriguez-Brito","year":"2006","journal-title":"BMC Bioinformatics"},{"key":"2023012511314394700_B26","doi-asserted-by":"crossref","first-page":"e77","DOI":"10.1371\/journal.pbio.0050077","article-title":"The Sorcerer II Global Ocean Sampling expedition: northwest Atlantic through eastern tropical Pacific","volume":"5","author":"Rusch","year":"2007","journal-title":"PLoS Biol."},{"key":"2023012511314394700_B27","doi-asserted-by":"crossref","first-page":"480","DOI":"10.1038\/nature07540","article-title":"A core gut microbiome in obese and lean twins","volume":"457","author":"Turnbaugh","year":"2009","journal-title":"Nature"},{"key":"2023012511314394700_B28","doi-asserted-by":"crossref","first-page":"77","DOI":"10.1007\/112_2006_0607","article-title":"Physiology of epithelial Ca2+and Mg2+transport","volume":"158","author":"van de Graaf","year":"2007","journal-title":"Rev. Physiol. Biochem. Pharmacol."},{"key":"2023012511314394700_B29","doi-asserted-by":"crossref","first-page":"e1000352","DOI":"10.1371\/journal.pcbi.1000352","article-title":"Statistical methods for detecting differentially abundant features in clinical metagenomic samples","volume":"5","author":"White","year":"2009","journal-title":"PLoS Comput. Biol."},{"key":"2023012511314394700_B30","doi-asserted-by":"crossref","first-page":"71","DOI":"10.1007\/s11390-010-9306-4","article-title":"Metagenomics: facts and artifacts, and computational challenges","volume":"25","author":"Wooley","year":"2010","journal-title":"J. Comput. Sci. Technol."},{"key":"2023012511314394700_B31","doi-asserted-by":"crossref","first-page":"e1000667","DOI":"10.1371\/journal.pcbi.1000667","article-title":"A primer on metagenomics","volume":"6","author":"Wooley","year":"2010","journal-title":"PLoS Comput. Biol."},{"key":"2023012511314394700_B32","doi-asserted-by":"crossref","first-page":"2365","DOI":"10.1073\/pnas.0812600106","article-title":"Human gut microbiota in obesity and after gastric bypass","volume":"106","author":"Zhang","year":"2009","journal-title":"Proc. Natl Acad. Sci. USA"},{"key":"2023012511314394700_B33","doi-asserted-by":"crossref","first-page":"288","DOI":"10.1097\/00005176-198305000-00012","article-title":"Lactose enhances mineral absorption in infancy","volume":"2","author":"Ziegler","year":"1983","journal-title":"J. Pediatr. Gastroenterol. Nutr."}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/27\/24\/3341\/48862244\/bioinformatics_27_24_3341.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/27\/24\/3341\/48862244\/bioinformatics_27_24_3341.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,1,25]],"date-time":"2023-01-25T11:32:17Z","timestamp":1674646337000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/27\/24\/3341\/306451"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2011,10,20]]},"references-count":33,"journal-issue":{"issue":"24","published-print":{"date-parts":[[2011,12,15]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btr583","relation":{},"ISSN":["1367-4811","1367-4803"],"issn-type":[{"value":"1367-4811","type":"electronic"},{"value":"1367-4803","type":"print"}],"subject":[],"published-other":{"date-parts":[[2011,12,15]]},"published":{"date-parts":[[2011,10,20]]}}}