{"id":"https://openalex.org/W4408061531","doi":"https://doi.org/10.1186/s12859-025-06078-4","title":"Analyzing microbiome data with taxonomic misclassification using a zero-inflated Dirichlet-multinomial model","display_name":"Analyzing microbiome data with taxonomic misclassification using a zero-inflated Dirichlet-multinomial model","publication_year":2025,"publication_date":"2025-02-27","ids":{"openalex":"https://openalex.org/W4408061531","doi":"https://doi.org/10.1186/s12859-025-06078-4","pmid":"https://pubmed.ncbi.nlm.nih.gov/40016656"},"language":"en","primary_location":{"id":"doi:10.1186/s12859-025-06078-4","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-025-06078-4","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/s12859-025-06078-4","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by-nc-nd","license_id":"https://openalex.org/licenses/cc-by-nc-nd","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/s12859-025-06078-4","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5054995850","display_name":"Matthew D. Koslovsky","orcid":"https://orcid.org/0000-0001-5144-2042"},"institutions":[{"id":"https://openalex.org/I92446798","display_name":"Colorado State University","ror":"https://ror.org/03k1gpj17","country_code":"US","type":"education","lineage":["https://openalex.org/I92446798"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Matthew D. Koslovsky","raw_affiliation_strings":["Department of Statistics, Colorado State University, Fort Collins, CO, USA. matt.koslovsky@colostate.edu","Department of Statistics, Colorado State University, Fort Collins, CO, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Statistics, Colorado State University, Fort Collins, CO, USA. matt.koslovsky@colostate.edu","institution_ids":[]},{"raw_affiliation_string":"Department of Statistics, Colorado State University, Fort Collins, CO, USA","institution_ids":["https://openalex.org/I92446798"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5054995850"],"corresponding_institution_ids":["https://openalex.org/I92446798"],"apc_list":{"value":1690,"currency":"GBP","value_usd":2072},"apc_paid":{"value":1690,"currency":"GBP","value_usd":2072},"fwci":2.0776,"has_fulltext":false,"cited_by_count":1,"citation_normalized_percentile":{"value":0.86960654,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":91,"max":95},"biblio":{"volume":"26","issue":"1","first_page":"69","last_page":"69"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11901","display_name":"Bayesian Methods and Mixture Models","score":0.9934999942779541,"subfield":{"id":"https://openalex.org/subfields/1702","display_name":"Artificial Intelligence"},"field":{"id":"https://openalex.org/fields/17","display_name":"Computer Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},"topics":[{"id":"https://openalex.org/T11901","display_name":"Bayesian Methods and Mixture Models","score":0.9934999942779541,"subfield":{"id":"https://openalex.org/subfields/1702","display_name":"Artificial Intelligence"},"field":{"id":"https://openalex.org/fields/17","display_name":"Computer Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T10066","display_name":"Gut microbiota and health","score":0.9670000076293945,"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/T10594","display_name":"Genetic and phenotypic traits in livestock","score":0.958299994468689,"subfield":{"id":"https://openalex.org/subfields/1311","display_name":"Genetics"},"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/multinomial-distribution","display_name":"Multinomial distribution","score":0.6602784395217896},{"id":"https://openalex.org/keywords/microbiome","display_name":"Microbiome","score":0.4171789586544037},{"id":"https://openalex.org/keywords/dna-microarray","display_name":"DNA microarray","score":0.41566282510757446},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.4134121537208557},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.38430723547935486},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.37857621908187866},{"id":"https://openalex.org/keywords/statistics","display_name":"Statistics","score":0.3545766770839691},{"id":"https://openalex.org/keywords/bioinformatics","display_name":"Bioinformatics","score":0.294177770614624},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.24043062329292297},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.21656230092048645}],"concepts":[{"id":"https://openalex.org/C192065140","wikidata":"https://www.wikidata.org/wiki/Q1147928","display_name":"Multinomial distribution","level":2,"score":0.6602784395217896},{"id":"https://openalex.org/C143121216","wikidata":"https://www.wikidata.org/wiki/Q1330402","display_name":"Microbiome","level":2,"score":0.4171789586544037},{"id":"https://openalex.org/C95371953","wikidata":"https://www.wikidata.org/wiki/Q591745","display_name":"DNA microarray","level":4,"score":0.41566282510757446},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.4134121537208557},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.38430723547935486},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.37857621908187866},{"id":"https://openalex.org/C105795698","wikidata":"https://www.wikidata.org/wiki/Q12483","display_name":"Statistics","level":1,"score":0.3545766770839691},{"id":"https://openalex.org/C60644358","wikidata":"https://www.wikidata.org/wiki/Q128570","display_name":"Bioinformatics","level":1,"score":0.294177770614624},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.24043062329292297},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.21656230092048645},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.0},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.0}],"mesh":[{"descriptor_ui":"D000069196","descriptor_name":"Gastrointestinal Microbiome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000069196","descriptor_name":"Gastrointestinal Microbiome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000069196","descriptor_name":"Gastrointestinal Microbiome","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D000069196","descriptor_name":"Gastrointestinal Microbiome","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D000069196","descriptor_name":"Gastrointestinal Microbiome","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D002648","descriptor_name":"Child","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D002648","descriptor_name":"Child","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D002648","descriptor_name":"Child","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D002648","descriptor_name":"Child","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D002648","descriptor_name":"Child","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D009765","descriptor_name":"Obesity","qualifier_ui":"Q000382","qualifier_name":"microbiology","is_major_topic":false},{"descriptor_ui":"D009765","descriptor_name":"Obesity","qualifier_ui":"Q000382","qualifier_name":"microbiology","is_major_topic":false},{"descriptor_ui":"D009765","descriptor_name":"Obesity","qualifier_ui":"Q000382","qualifier_name":"microbiology","is_major_topic":false},{"descriptor_ui":"D009765","descriptor_name":"Obesity","qualifier_ui":"Q000382","qualifier_name":"microbiology","is_major_topic":false},{"descriptor_ui":"D009765","descriptor_name":"Obesity","qualifier_ui":"Q000382","qualifier_name":"microbiology","is_major_topic":false},{"descriptor_ui":"D064307","descriptor_name":"Microbiota","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D064307","descriptor_name":"Microbiota","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D064307","descriptor_name":"Microbiota","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D064307","descriptor_name":"Microbiota","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D064307","descriptor_name":"Microbiota","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true}],"locations_count":4,"locations":[{"id":"doi:10.1186/s12859-025-06078-4","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-025-06078-4","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/s12859-025-06078-4","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by-nc-nd","license_id":"https://openalex.org/licenses/cc-by-nc-nd","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},{"id":"pmid:40016656","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/40016656","pdf_url":null,"source":{"id":"https://openalex.org/S4306525036","display_name":"PubMed","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC bioinformatics","raw_type":null},{"id":"pmh:oai:doaj.org/article:2e7a33d686144c79b24ae45980cf1e42","is_oa":false,"landing_page_url":"https://doaj.org/article/2e7a33d686144c79b24ae45980cf1e42","pdf_url":null,"source":{"id":"https://openalex.org/S4306401280","display_name":"DOAJ (DOAJ: Directory of Open Access Journals)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"BMC Bioinformatics, Vol 26, Iss 1, Pp 1-19 (2025)","raw_type":"article"},{"id":"pmh:oai:pubmedcentral.nih.gov:11869466","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/11869466","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"BMC Bioinformatics","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1186/s12859-025-06078-4","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-025-06078-4","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/s12859-025-06078-4","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by-nc-nd","license_id":"https://openalex.org/licenses/cc-by-nc-nd","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[{"score":0.4399999976158142,"display_name":"Zero hunger","id":"https://metadata.un.org/sdg/2"}],"awards":[{"id":"https://openalex.org/G5537619824","display_name":null,"funder_award_id":"DMS-2245492","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"}],"funders":[{"id":"https://openalex.org/F4320306076","display_name":"National Science Foundation","ror":"https://ror.org/021nxhr62"}],"has_content":{"grobid_xml":false,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4408061531.pdf"},"referenced_works_count":69,"referenced_works":["https://openalex.org/W755741475","https://openalex.org/W1847253990","https://openalex.org/W1979087912","https://openalex.org/W2035378093","https://openalex.org/W2055354074","https://openalex.org/W2088833470","https://openalex.org/W2099878672","https://openalex.org/W2115921802","https://openalex.org/W2116895571","https://openalex.org/W2124053577","https://openalex.org/W2124351063","https://openalex.org/W2152885278","https://openalex.org/W2157859776","https://openalex.org/W2159325249","https://openalex.org/W2159954944","https://openalex.org/W2167460663","https://openalex.org/W2279382301","https://openalex.org/W2401404581","https://openalex.org/W2413207665","https://openalex.org/W2564980658","https://openalex.org/W2580388630","https://openalex.org/W2589893834","https://openalex.org/W2592367925","https://openalex.org/W2593591803","https://openalex.org/W2769542288","https://openalex.org/W2771045365","https://openalex.org/W2786335128","https://openalex.org/W2790152383","https://openalex.org/W2888566822","https://openalex.org/W2901939432","https://openalex.org/W2904250115","https://openalex.org/W2962733802","https://openalex.org/W2963276645","https://openalex.org/W2967355384","https://openalex.org/W2969310263","https://openalex.org/W2971140038","https://openalex.org/W2977990342","https://openalex.org/W2980353637","https://openalex.org/W2981045456","https://openalex.org/W2994811958","https://openalex.org/W3000732706","https://openalex.org/W3003302501","https://openalex.org/W3013091147","https://openalex.org/W3017376615","https://openalex.org/W3036120216","https://openalex.org/W3089053458","https://openalex.org/W3097964496","https://openalex.org/W3103113059","https://openalex.org/W3117714294","https://openalex.org/W3120414327","https://openalex.org/W3144187446","https://openalex.org/W3147003035","https://openalex.org/W3164872214","https://openalex.org/W3167389373","https://openalex.org/W3173323489","https://openalex.org/W3186247356","https://openalex.org/W3186741412","https://openalex.org/W3186747227","https://openalex.org/W3189665086","https://openalex.org/W4206080966","https://openalex.org/W4206912861","https://openalex.org/W4220826128","https://openalex.org/W4225778031","https://openalex.org/W4310422387","https://openalex.org/W4320176016","https://openalex.org/W4323805312","https://openalex.org/W4387723511","https://openalex.org/W4393846917","https://openalex.org/W4396552876"],"related_works":["https://openalex.org/W2955220190","https://openalex.org/W2052791731","https://openalex.org/W2604155846","https://openalex.org/W4320168697","https://openalex.org/W4390658901","https://openalex.org/W2117588607","https://openalex.org/W2305090462","https://openalex.org/W3121185202","https://openalex.org/W4393043634","https://openalex.org/W3020516445"],"abstract_inverted_index":{"The":[0],"human":[1,29,137],"microbiome":[2,19,41,72,104,138,171],"is":[3,21,61,90,106],"the":[4,23,32,40,65,83,120,136],"collection":[5],"of":[6,12,18,34,86,102,119,135],"microorganisms":[7],"living":[8],"on":[9],"and":[10,58,70,127,161,176,189,198],"inside":[11],"our":[13,132],"bodies.":[14],"A":[15],"major":[16],"aim":[17],"research":[20],"understanding":[22],"role":[24],"microbial":[25,95,194],"communities":[26],"play":[27],"in":[28,124,153,192],"health":[30],"with":[31,131,173],"goal":[33],"designing":[35],"personalized":[36],"interventions":[37],"that":[38,107],"modulate":[39],"to":[42,51,54,68,93,112,158],"treat":[43,94],"or":[44],"prevent":[45],"disease.":[46],"Microbiome":[47],"data":[48,105,172],"are":[49,110],"challenging":[50],"analyze":[52],"due":[53],"their":[55],"high-dimensionality,":[56],"overdispersion,":[57],"zero-inflation.":[59],"Analysis":[60],"further":[62],"complicated":[63],"by":[64],"steps":[66],"taken":[67],"collect":[69],"process":[71],"samples.":[73],"For":[74],"example,":[75],"sequencing":[76,125],"instruments":[77],"have":[78,139],"a":[79,166],"fixed":[80],"capacity":[81],"for":[82,170],"total":[84],"number":[85],"reads":[87],"delivered.":[88],"It":[89],"therefore":[91],"essential":[92],"samples":[96],"as":[97],"compositional.":[98],"Another":[99],"complicating":[100],"factor":[101],"modeling":[103,168],"taxa":[108],"counts":[109],"subject":[111],"measurement":[113,121,144,147],"error":[114,148],"introduced":[115],"at":[116],"various":[117],"stages":[118],"protocol.":[122],"Advances":[123],"technology":[126],"preprocessing":[128],"pipelines":[129],"coupled":[130],"growing":[133],"knowledge":[134],"reduced,":[140],"but":[141],"not":[142],"eliminated,":[143],"error.":[145],"Ignoring":[146],"during":[149],"analysis,":[150],"though":[151],"common":[152],"practice,":[154],"can":[155],"then":[156],"lead":[157],"biased":[159],"inference":[160],"curb":[162],"reproducibility.":[163],"We":[164,180],"propose":[165],"Dirichlet-multinomial":[167],"framework":[169],"excess":[174],"zeros":[175],"potential":[177],"taxonomic":[178,184],"misclassification.":[179],"demonstrate":[181],"how":[182],"accommodating":[183],"misclassification":[185],"improves":[186],"estimation":[187],"performance":[188],"investigate":[190],"differences":[191],"gut":[193],"composition":[195],"between":[196],"healthy":[197],"obese":[199],"children.":[200]},"counts_by_year":[{"year":2025,"cited_by_count":1}],"updated_date":"2026-05-06T08:25:59.206177","created_date":"2025-10-10T00:00:00"}