{"id":"https://openalex.org/W4362632052","doi":"https://doi.org/10.17615/mg1b-wp07","title":"BZINB Model-Based Pathway Analysis and Module Identification Facilitates Integration of Microbiome and Metabolome Data","display_name":"BZINB Model-Based Pathway Analysis and Module Identification Facilitates Integration of Microbiome and Metabolome Data","publication_year":2023,"publication_date":"2023-04-06","ids":{"openalex":"https://openalex.org/W4362632052","doi":"https://doi.org/10.17615/mg1b-wp07"},"language":"en","primary_location":{"id":"pmh:cdr.lib.unc.edu:fx719x22b","doi":null,"is_oa":false,"landing_page_url":"https://doi.org/10.17615/mg1b-wp07","pdf_url":null,"source":{"id":"https://openalex.org/S4306401075","display_name":"Carolina Digital Repository (University of North Carolina at Chapel Hill)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I114027177","host_organization_name":"University of North Carolina at Chapel Hill","host_organization_lineage":["https://openalex.org/I114027177"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Microorganisms, 11(3)","raw_type":"Article"},"volume":null,"type":"article","indexed_in":["datacite"],"open_access":{"is_oa":true,"oa_status":"green","oa_url":"https://doi.org/10.17615/mg1b-wp07","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5002917649","display_name":"Chengwen Li","orcid":"https://orcid.org/0000-0003-4397-4561","observed_orcids":["https://orcid.org/0000-0003-4397-4561"]},"institutions":[{"id":"https://openalex.org/I114027177","display_name":"University of North Carolina at Chapel Hill","ror":"https://ror.org/0130frc33","country_code":"US","type":"education","lineage":["https://openalex.org/I114027177"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Liu, Chuwen","raw_affiliation_strings":["University of North Carolina at Chapel Hill"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"University of North Carolina at Chapel Hill","institution_ids":["https://openalex.org/I114027177"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5040371459","display_name":"Hunyong Cho","orcid":"https://orcid.org/0000-0002-0087-0079","observed_orcids":["https://orcid.org/0000-0002-0087-0079"]},"institutions":[{"id":"https://openalex.org/I114027177","display_name":"University of North Carolina at Chapel Hill","ror":"https://ror.org/0130frc33","country_code":"US","type":"education","lineage":["https://openalex.org/I114027177"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Cho, Hunyong","raw_affiliation_strings":["University of North Carolina at Chapel Hill"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"University of North Carolina at Chapel Hill","institution_ids":["https://openalex.org/I114027177"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5075626027","display_name":"Kimon Divaris","orcid":"https://orcid.org/0000-0003-1290-7251","observed_orcids":["https://orcid.org/0000-0003-1290-7251"]},"institutions":[{"id":"https://openalex.org/I114027177","display_name":"University of North Carolina at Chapel Hill","ror":"https://ror.org/0130frc33","country_code":"US","type":"education","lineage":["https://openalex.org/I114027177"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Divaris, Kimon","raw_affiliation_strings":["University of North Carolina at Chapel Hill"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"University of North Carolina at Chapel Hill","institution_ids":["https://openalex.org/I114027177"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5022086568","display_name":"Apoena Aguiar Ribeiro","orcid":"https://orcid.org/0000-0001-7702-6178","observed_orcids":["https://orcid.org/0000-0001-7702-6178"]},"institutions":[{"id":"https://openalex.org/I114027177","display_name":"University of North Carolina at Chapel Hill","ror":"https://ror.org/0130frc33","country_code":"US","type":"education","lineage":["https://openalex.org/I114027177"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Ribeiro, Apoena Aguiar","raw_affiliation_strings":["University of North Carolina at Chapel Hill"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"University of North Carolina at Chapel Hill","institution_ids":["https://openalex.org/I114027177"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5013329962","display_name":"Jeffrey M. Roach","orcid":"https://orcid.org/0000-0001-9817-5877","observed_orcids":["https://orcid.org/0000-0001-9817-5877"]},"institutions":[{"id":"https://openalex.org/I114027177","display_name":"University of North Carolina at Chapel Hill","ror":"https://ror.org/0130frc33","country_code":"US","type":"education","lineage":["https://openalex.org/I114027177"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Roach, Jeff","raw_affiliation_strings":["University of North Carolina at Chapel Hill"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"University of North Carolina at Chapel Hill","institution_ids":["https://openalex.org/I114027177"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5013848390","display_name":"Bridget M. Lin","orcid":"https://orcid.org/0000-0002-5313-4171","observed_orcids":["https://orcid.org/0000-0002-5313-4171"]},"institutions":[{"id":"https://openalex.org/I114027177","display_name":"University of North Carolina at Chapel Hill","ror":"https://ror.org/0130frc33","country_code":"US","type":"education","lineage":["https://openalex.org/I114027177"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Lin, Bridget M.","raw_affiliation_strings":["University of North Carolina at Chapel Hill"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"University of North Carolina at Chapel Hill","institution_ids":["https://openalex.org/I114027177"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5113318506","display_name":"Di Wu","orcid":"https://orcid.org/0000-0003-1870-798X","observed_orcids":["https://orcid.org/0000-0003-1870-798X"]},"institutions":[{"id":"https://openalex.org/I114027177","display_name":"University of North Carolina at Chapel Hill","ror":"https://ror.org/0130frc33","country_code":"US","type":"education","lineage":["https://openalex.org/I114027177"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Wu, Di","raw_affiliation_strings":["University of North Carolina at Chapel Hill"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"University of North Carolina at Chapel Hill","institution_ids":["https://openalex.org/I114027177"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":[],"corresponding_institution_ids":["https://openalex.org/I114027177"],"apc_list":null,"apc_paid":null,"fwci":0.0,"has_fulltext":false,"cited_by_count":0,"citation_normalized_percentile":{"value":0.03617442,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"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/T10066","display_name":"Gut microbiota and health","score":0.4530999958515167,"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/T10066","display_name":"Gut microbiota and health","score":0.4530999958515167,"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/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.35910001397132874,"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/T10257","display_name":"Oral microbiology and periodontitis research","score":0.11400000005960464,"subfield":{"id":"https://openalex.org/subfields/3506","display_name":"Periodontics"},"field":{"id":"https://openalex.org/fields/35","display_name":"Dentistry"},"domain":{"id":"https://openalex.org/domains/4","display_name":"Health Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/multi-omics-integration","display_name":"multi-omics integration","score":0.8650000095367432},{"id":"https://openalex.org/keywords/correlation-networks","display_name":"correlation networks","score":0.49300000071525574},{"id":"https://openalex.org/keywords/module-identification","display_name":"module identification","score":0.7689999938011169},{"id":"https://openalex.org/keywords/zero-inflated-count-data","display_name":"zero-inflated count data","score":0.847000002861023},{"id":"https://openalex.org/keywords/early-childhood-caries","display_name":"early childhood caries","score":0.8709999918937683},{"id":"https://openalex.org/keywords/oral-microbiota","display_name":"oral microbiota","score":0.8479999899864197},{"id":"https://openalex.org/keywords/carbohydrate-metabolites","display_name":"carbohydrate metabolites","score":0.8920000195503235}],"concepts":[{"id":"https://openalex.org/C135870905","wikidata":"https://www.wikidata.org/wiki/Q903667","display_name":"Metabolome","level":3,"score":0.9140790104866028},{"id":"https://openalex.org/C116834253","wikidata":"https://www.wikidata.org/wiki/Q2039217","display_name":"Identification (biology)","level":2,"score":0.712415874004364},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.6771140098571777},{"id":"https://openalex.org/C143121216","wikidata":"https://www.wikidata.org/wiki/Q1330402","display_name":"Microbiome","level":2,"score":0.6229782104492188},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.4666716158390045},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.4254686236381531},{"id":"https://openalex.org/C21565614","wikidata":"https://www.wikidata.org/wiki/Q12149006","display_name":"Metabolomics","level":2,"score":0.4169464111328125},{"id":"https://openalex.org/C60644358","wikidata":"https://www.wikidata.org/wiki/Q128570","display_name":"Bioinformatics","level":1,"score":0.2990104556083679},{"id":"https://openalex.org/C18903297","wikidata":"https://www.wikidata.org/wiki/Q7150","display_name":"Ecology","level":1,"score":0.08498546481132507}],"mesh":[],"locations_count":2,"locations":[{"id":"pmh:cdr.lib.unc.edu:fx719x22b","doi":null,"is_oa":false,"landing_page_url":"https://doi.org/10.17615/mg1b-wp07","pdf_url":null,"source":{"id":"https://openalex.org/S4306401075","display_name":"Carolina Digital Repository (University of North Carolina at Chapel Hill)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I114027177","host_organization_name":"University of North Carolina at Chapel Hill","host_organization_lineage":["https://openalex.org/I114027177"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Microorganisms, 11(3)","raw_type":"Article"},{"id":"doi:10.17615/mg1b-wp07","doi":"https://doi.org/10.17615/mg1b-wp07","is_oa":true,"landing_page_url":"https://doi.org/10.17615/mg1b-wp07","pdf_url":null,"source":{"id":"https://openalex.org/S7407051488","display_name":"UNC Libraries","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":null,"is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"article-journal"}],"best_oa_location":{"id":"doi:10.17615/mg1b-wp07","doi":"https://doi.org/10.17615/mg1b-wp07","is_oa":true,"landing_page_url":"https://doi.org/10.17615/mg1b-wp07","pdf_url":null,"source":{"id":"https://openalex.org/S7407051488","display_name":"UNC Libraries","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":null,"is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"article-journal"},"sustainable_development_goals":[{"score":0.5683000087738037,"display_name":"Good health and well-being","id":"https://metadata.un.org/sdg/3"}],"sustainable_development_goals_aurora":[{"score":0.5199999809265137,"display_name":"Zero hunger","id":"https://metadata.un.org/sdg/2"}],"study_designs":[],"awards":[{"id":"https://openalex.org/G1848365825","display_name":"Investigating the microbial basis of early childhood caries via metagenomics and metatranscriptomics analyses","funder_award_id":"R03DE028983","funder_id":"https://openalex.org/F4320337365","funder_display_name":"National Institute of Dental and Craniofacial Research"}],"funders":[{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"},{"id":"https://openalex.org/F4320337365","display_name":"National Institute of Dental and Craniofacial Research","ror":"https://ror.org/004a2wv92"}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":0,"referenced_works":[],"related_works":["https://openalex.org/W6887859100","https://openalex.org/W4405556041","https://openalex.org/W4205342937","https://openalex.org/W3026604541","https://openalex.org/W7134957258","https://openalex.org/W4400586871","https://openalex.org/W2994811958","https://openalex.org/W4206514793","https://openalex.org/W2905487416","https://openalex.org/W2981393809"],"abstract_inverted_index":{"Integration":[0],"of":[1,14,104,121,138,155,166,196,213,249,261],"multi-omics":[2,29,102,262],"data":[3,98,253,263],"is":[4,127,235,256],"a":[5,67,101,236],"challenging":[6],"but":[7],"necessary":[8],"step":[9],"to":[10,27,130,239],"advance":[11],"our":[12],"understanding":[13],"the":[15,54,119,122,140,153,197,201,232,246],"biology":[16],"underlying":[17,141,247],"human":[18],"health":[19,107],"and":[20,32,75,83,96,116,133,146,157,163,173,180,190,223,254,270],"disease":[21],"processes.":[22],"To":[23],"date,":[24],"investigations":[25],"seeking":[26],"integrate":[28],"(e.g.,":[30],"microbiome":[31,47,269],"metabolome)":[33],"employ":[34],"simple":[35],"correlation-based":[36,86],"network":[37,74],"analyses;":[38],"however,":[39],"these":[40,60],"methods":[41],"are":[42],"not":[43,52],"always":[44],"well-suited":[45],"for":[46,244,258],"analyses":[48,260],"because":[49],"they":[50],"do":[51],"accommodate":[53],"excess":[55,91],"zeros":[56],"typically":[57],"present":[58],"in":[59,136,177,200,268],"data.":[61],"In":[62,227],"this":[63,81],"paper,":[64],"we":[65,207,229],"introduce":[66],"bivariate":[68,251],"zero-inflated":[69,250],"negative":[70],"binomial":[71],"(BZINB)":[72],"model-based":[73,124],"module":[76],"analysis":[77],"method":[78,126,199],"that":[79,118,209,231],"addresses":[80],"limitation":[82],"improves":[84],"microbiome\u2013metabolome":[85,205],"model":[87,234],"fitting":[88],"by":[89,170],"accommodating":[90],"zeros.":[92],"We":[93],"use":[94],"real":[95],"simulated":[97],"based":[99],"on":[100],"study":[103,192,204],"childhood":[105,112],"oral":[106],"(ZOE":[108],"2.0;":[109],"investigating":[110],"early":[111],"dental":[113,224],"caries,":[114],"ECC)":[115],"find":[117,230],"accuracy":[120],"BZINB":[123,162,172,233],"correlation":[125,159,178,248],"superior":[128],"compared":[129],"Spearman\u2019s":[131],"rank":[132],"Pearson":[134,242],"correlations":[135,212,243],"terms":[137],"approximating":[139],"relationships":[142],"between":[143,186,221],"microbial":[144,215],"taxa":[145,216],"metabolites.":[147],"The":[148],"new":[149,198],"method,":[150],"BZINB-iMMPath,":[151],"facilitates":[152],"construction":[154],"metabolite\u2013species":[156],"species\u2013species":[158],"networks":[160,179],"using":[161],"identifies":[164],"modules":[165,181],"(i.e.,":[167,188],"correlated)":[168],"species":[169],"combining":[171],"similarity-based":[174],"clustering.":[175],"Perturbations":[176],"can":[182],"be":[183],"efficiently":[184],"tested":[185],"groups":[187],"healthy":[189,222],"diseased":[191],"participants).":[193],"Upon":[194],"application":[195],"ZOE":[202],"2.0":[203],"data,":[206],"identify":[208],"several":[210],"biologically-relevant":[211],"ECC-associated":[214],"with":[217],"carbohydrate":[218],"metabolites":[219],"differ":[220],"caries-affected":[225],"participants.":[226],"sum,":[228],"useful":[237],"alternative":[238],"Spearman":[240],"or":[241],"estimating":[245],"count":[252],"thus":[255],"suitable":[257],"integrative":[259],"such":[264],"as":[265],"those":[266],"encountered":[267],"metabolome":[271],"studies.":[272]},"counts_by_year":[],"updated_date":"2026-10-28T10:33:24.094632","created_date":"2023-04-07T00:00:00"}
