{"id":"https://openalex.org/W2805234577","doi":"https://doi.org/10.1101/340653","title":"Bayesian Classification of Microbial Communities Based on 16S rRNA Metagenomic Data","display_name":"Bayesian Classification of Microbial Communities Based on 16S rRNA Metagenomic Data","publication_year":2018,"publication_date":"2018-06-06","ids":{"openalex":"https://openalex.org/W2805234577","doi":"https://doi.org/10.1101/340653","mag":"2805234577"},"language":"en","primary_location":{"id":"doi:10.1101/340653","doi":"https://doi.org/10.1101/340653","is_oa":true,"landing_page_url":"https://doi.org/10.1101/340653","pdf_url":"https://www.biorxiv.org/content/biorxiv/early/2018/06/06/340653.full.pdf","source":{"id":"https://openalex.org/S4306402567","display_name":"bioRxiv (Cold Spring Harbor Laboratory)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I2750212522","host_organization_name":"Cold Spring Harbor Laboratory","host_organization_lineage":["https://openalex.org/I2750212522"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"acceptedVersion","is_accepted":true,"is_published":false,"raw_source_name":"bioRxiv","raw_type":"posted-content"},"volume":null,"type":"preprint","indexed_in":["crossref"],"open_access":{"is_oa":true,"oa_status":"green","oa_url":"https://www.biorxiv.org/content/biorxiv/early/2018/06/06/340653.full.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5088329282","display_name":"Arghavan Bahadorinejad","orcid":null,"observed_orcids":[]},"institutions":[{"id":"https://openalex.org/I91045830","display_name":"Texas A&M University","ror":"https://ror.org/01f5ytq51","country_code":"US","type":"education","lineage":["https://openalex.org/I91045830"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Arghavan Bahadorinejad","raw_affiliation_strings":["Electrical and Computer Engineering Department Texas A&M University, College Station, TX, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Electrical and Computer Engineering Department Texas A&M University, College Station, TX, USA","institution_ids":["https://openalex.org/I91045830"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5079620688","display_name":"Ivan V. Ivanov","orcid":"https://orcid.org/0000-0002-5323-8325","observed_orcids":["https://orcid.org/0000-0002-5323-8325"]},"institutions":[{"id":"https://openalex.org/I91045830","display_name":"Texas A&M University","ror":"https://ror.org/01f5ytq51","country_code":"US","type":"education","lineage":["https://openalex.org/I91045830"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Ivan Ivanov","raw_affiliation_strings":["Veterinary Physiology & Pharmacology Department,Texas A&M University, College Station, TX, USA, College Station, TX, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Veterinary Physiology & Pharmacology Department,Texas A&M University, College Station, TX, USA, College Station, TX, USA","institution_ids":["https://openalex.org/I91045830"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5019716896","display_name":"Johanna W. Lampe","orcid":"https://orcid.org/0000-0003-2717-3780","observed_orcids":["https://orcid.org/0000-0003-2717-3780"]},"institutions":[{"id":"https://openalex.org/I4210089486","display_name":"Fred Hutch Cancer Center","ror":"https://ror.org/007ps6h72","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I4210089486"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Johanna W Lampe","raw_affiliation_strings":["Fred Hutchinson Cancer Center, Seattle, WA, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Fred Hutchinson Cancer Center, Seattle, WA, USA","institution_ids":["https://openalex.org/I4210089486"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5060830421","display_name":"Meredith A.J. Hullar","orcid":"https://orcid.org/0000-0002-5322-9568","observed_orcids":["https://orcid.org/0000-0002-5322-9568"]},"institutions":[{"id":"https://openalex.org/I4210089486","display_name":"Fred Hutch Cancer Center","ror":"https://ror.org/007ps6h72","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I4210089486"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Meredith AJ Hullar","raw_affiliation_strings":["Fred Hutchinson Cancer Center, Seattle, WA, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Fred Hutchinson Cancer Center, Seattle, WA, USA","institution_ids":["https://openalex.org/I4210089486"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5019568866","display_name":"Robert S. Chapkin","orcid":"https://orcid.org/0000-0002-6515-3898","observed_orcids":["https://orcid.org/0000-0002-6515-3898"]},"institutions":[{"id":"https://openalex.org/I91045830","display_name":"Texas A&M University","ror":"https://ror.org/01f5ytq51","country_code":"US","type":"education","lineage":["https://openalex.org/I91045830"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Robert S Chapkin","raw_affiliation_strings":["Nutrition and Food Science Department and the Program in Integrative Nutrition and Complex Diseases, Texas A&M University, College Station, TX, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Nutrition and Food Science Department and the Program in Integrative Nutrition and Complex Diseases, Texas A&M University, College Station, TX, USA","institution_ids":["https://openalex.org/I91045830"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5026990034","display_name":"Ulisses Braga-Neto","orcid":"https://orcid.org/0000-0002-1210-2173","observed_orcids":["https://orcid.org/0000-0002-1210-2173"]},"institutions":[{"id":"https://openalex.org/I91045830","display_name":"Texas A&M University","ror":"https://ror.org/01f5ytq51","country_code":"US","type":"education","lineage":["https://openalex.org/I91045830"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Ulisses M Braga-Neto","raw_affiliation_strings":["Electrical and Computer Engineering Department Texas A&M University, College Station, TX, USA"],"raw_orcid":"https://orcid.org/0000-0002-1210-2173","affiliations":[{"raw_affiliation_string":"Electrical and Computer Engineering Department Texas A&M University, College Station, TX, USA","institution_ids":["https://openalex.org/I91045830"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":null,"apc_paid":null,"fwci":null,"has_fulltext":true,"cited_by_count":2,"citation_normalized_percentile":null,"cited_by_percentile_year":null,"biblio":{"volume":null,"issue":null,"first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.5928000211715698,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},"topics":[{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.5928000211715698,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T11791","display_name":"Microbial Community Ecology and Physiology","score":0.10220000147819519,"subfield":{"id":"https://openalex.org/subfields/2303","display_name":"Ecology"},"field":{"id":"https://openalex.org/fields/23","display_name":"Environmental Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T10885","display_name":"Gene expression and cancer classification","score":0.07240000367164612,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/16s-rrna-metagenomics","display_name":"16S rRNA metagenomics","score":0.925000011920929},{"id":"https://openalex.org/keywords/microbial-community-classification","display_name":"microbial community classification","score":0.8889999985694885},{"id":"https://openalex.org/keywords/bayesian-classifier","display_name":"Bayesian classifier","score":0.7450000047683716},{"id":"https://openalex.org/keywords/small-sample-size","display_name":"small sample size","score":0.6800000071525574},{"id":"https://openalex.org/keywords/high-dimensional-data","display_name":"high-dimensional data","score":0.7400000095367432},{"id":"https://openalex.org/keywords/colorectal-cancer","display_name":"colorectal cancer","score":0.7400000095367432},{"id":"https://openalex.org/keywords/gut-microbiota","display_name":"gut microbiota","score":0.8510000109672546}],"concepts":[{"id":"https://openalex.org/C15151743","wikidata":"https://www.wikidata.org/wiki/Q903778","display_name":"Metagenomics","level":3,"score":0.921364426612854},{"id":"https://openalex.org/C107673813","wikidata":"https://www.wikidata.org/wiki/Q812534","display_name":"Bayesian probability","level":2,"score":0.6109994053840637},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5469980835914612},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.5425283908843994},{"id":"https://openalex.org/C95623464","wikidata":"https://www.wikidata.org/wiki/Q1096149","display_name":"Classifier (UML)","level":2,"score":0.4966195225715637},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.47668004035949707},{"id":"https://openalex.org/C111030470","wikidata":"https://www.wikidata.org/wiki/Q1430460","display_name":"Curse of dimensionality","level":2,"score":0.4648323059082031},{"id":"https://openalex.org/C52001869","wikidata":"https://www.wikidata.org/wiki/Q812530","display_name":"Naive Bayes classifier","level":3,"score":0.4604535698890686},{"id":"https://openalex.org/C177769412","wikidata":"https://www.wikidata.org/wiki/Q278090","display_name":"Prior probability","level":3,"score":0.45468685030937195},{"id":"https://openalex.org/C129848803","wikidata":"https://www.wikidata.org/wiki/Q2564360","display_name":"Sample size determination","level":2,"score":0.42440617084503174},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.3904011845588684},{"id":"https://openalex.org/C153180895","wikidata":"https://www.wikidata.org/wiki/Q7148389","display_name":"Pattern recognition (psychology)","level":2,"score":0.37256449460983276},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.2853200435638428},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.22291266918182373},{"id":"https://openalex.org/C105795698","wikidata":"https://www.wikidata.org/wiki/Q12483","display_name":"Statistics","level":1,"score":0.19340118765830994},{"id":"https://openalex.org/C12267149","wikidata":"https://www.wikidata.org/wiki/Q282453","display_name":"Support vector machine","level":2,"score":0.1415574848651886},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.0},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.0}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.1101/340653","doi":"https://doi.org/10.1101/340653","is_oa":true,"landing_page_url":"https://doi.org/10.1101/340653","pdf_url":"https://www.biorxiv.org/content/biorxiv/early/2018/06/06/340653.full.pdf","source":{"id":"https://openalex.org/S4306402567","display_name":"bioRxiv (Cold Spring Harbor Laboratory)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I2750212522","host_organization_name":"Cold Spring Harbor Laboratory","host_organization_lineage":["https://openalex.org/I2750212522"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"acceptedVersion","is_accepted":true,"is_published":false,"raw_source_name":"bioRxiv","raw_type":"posted-content"}],"best_oa_location":{"id":"doi:10.1101/340653","doi":"https://doi.org/10.1101/340653","is_oa":true,"landing_page_url":"https://doi.org/10.1101/340653","pdf_url":"https://www.biorxiv.org/content/biorxiv/early/2018/06/06/340653.full.pdf","source":{"id":"https://openalex.org/S4306402567","display_name":"bioRxiv (Cold Spring Harbor Laboratory)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I2750212522","host_organization_name":"Cold Spring Harbor Laboratory","host_organization_lineage":["https://openalex.org/I2750212522"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"acceptedVersion","is_accepted":true,"is_published":false,"raw_source_name":"bioRxiv","raw_type":"posted-content"},"sustainable_development_goals":[],"study_designs":[],"awards":[],"funders":[],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2805234577.pdf","grobid_xml":"https://content.openalex.org/works/W2805234577.grobid-xml"},"referenced_works_count":25,"referenced_works":["https://openalex.org/W1598928703","https://openalex.org/W1811186957","https://openalex.org/W1970178155","https://openalex.org/W1985372952","https://openalex.org/W1989889539","https://openalex.org/W2004419591","https://openalex.org/W2011084061","https://openalex.org/W2053801811","https://openalex.org/W2066011810","https://openalex.org/W2089643849","https://openalex.org/W2093891969","https://openalex.org/W2097936772","https://openalex.org/W2114986399","https://openalex.org/W2120240539","https://openalex.org/W2131754626","https://openalex.org/W2133057705","https://openalex.org/W2134717973","https://openalex.org/W2144494558","https://openalex.org/W2149573313","https://openalex.org/W2152885278","https://openalex.org/W2170951896","https://openalex.org/W2525231178","https://openalex.org/W2911964244","https://openalex.org/W2952835781","https://openalex.org/W3123857276"],"related_works":["https://openalex.org/W2008528231","https://openalex.org/W6889327659","https://openalex.org/W2103584973","https://openalex.org/W2612975255","https://openalex.org/W7096422886","https://openalex.org/W2617116853","https://openalex.org/W2775802116","https://openalex.org/W2954377269","https://openalex.org/W2133057705","https://openalex.org/W2045073446"],"abstract_inverted_index":{"Abstract":[0],"We":[1],"propose":[2,172],"a":[3,19,28,173,192],"Bayesian":[4,45,193],"method":[5,132,174,190,224],"for":[6,23,57,70,175,198],"the":[7,24,35,66,93,108,114,117,130,136,144,210,222],"classification":[8,55,74,230],"of":[9,14,79,119,157,179,204,206],"16S":[10,58,184],"rRNA":[11,59,185],"metagenomic":[12,60,86,161,186,218,229],"profiles":[13],"bacterial":[15],"abundance,":[16],"by":[17],"introducing":[18],"Poisson-Dirichlet-Multinomial":[20],"hierarchical":[21],"model":[22],"sequencing":[25],"data,":[26,33,61],"constructing":[27],"prior":[29],"distribution":[30,37],"from":[31],"sample":[32,72,120],"calculating":[34],"posterior":[36],"in":[38,113],"closed":[39],"form;":[40],"and":[41,65,76,84,151,216],"deriving":[42],"an":[43],"Optimal":[44],"Classifier":[46],"(OBC).":[47],"The":[48,89,155,188],"proposed":[49,94,131,189,223],"algorithm":[50],"is":[51,103,124,196],"compared":[52],"to":[53,107,122,209],"state-of-the-art":[54,228],"methods":[56],"including":[62],"Random":[63],"Forests":[64],"phylogeny-based":[67],"Metaphyl":[68],"algorithm,":[69],"varying":[71],"size,":[73],"difficulty,":[75],"dimensionality":[77,123],"(number":[78],"OTUs),":[80],"using":[81,160,213],"both":[82,214],"synthetic":[83,215],"real":[85,217],"data":[87,199,219],"sets.":[88],"results":[90],"demonstrate":[91],"that":[92,129,221],"OBC":[95],"method,":[96],"with":[97,201],"either":[98],"noninformative":[99],"or":[100,105],"constructed":[101],"priors,":[102],"competitive":[104],"superior":[106],"other":[109,227],"methods.":[110],"In":[111,168],"particular,":[112],"case":[115],"where":[116],"ratio":[118],"size":[121],"small,":[125],"it":[126],"was":[127],"observed":[128],"can":[133,225],"vastly":[134],"outperform":[135,226],"others.":[137],"Author":[138],"summary":[139],"Recent":[140],"studies":[141],"have":[142],"highlighted":[143],"interplay":[145],"between":[146],"host":[147],"genetics,":[148],"gut":[149],"microbes,":[150],"colorectal":[152],"tumor":[153],"initiation/progression.":[154],"characterization":[156],"microbial":[158],"communities":[159],"profiling":[162],"has":[163],"therefore":[164],"received":[165],"renewed":[166],"interest.":[167],"this":[169],"paper,":[170],"we":[171],"classification,":[176],"i.e.,":[177],"prediction":[178],"different":[180],"outcomes,":[181],"based":[182],"on":[183],"data.":[187],"employs":[191],"approach,":[194],"which":[195],"suitable":[197],"sets":[200],"small":[202],"ration":[203],"number":[205],"available":[207],"instances":[208],"dimensionality.":[211],"Results":[212],"show":[220],"algorithms.":[231]},"counts_by_year":[{"year":2020,"cited_by_count":1},{"year":2019,"cited_by_count":1}],"updated_date":"2026-10-16T09:59:22.235173","created_date":"2018-06-13T00:00:00"}