{"id":"https://openalex.org/W3210537005","doi":"https://doi.org/10.1093/bib/bbab443","title":"MZINBVA: variational approximation for multilevel zero-inflated negative-binomial models for association analysis in microbiome surveys","display_name":"MZINBVA: variational approximation for multilevel zero-inflated negative-binomial models for association analysis in microbiome surveys","publication_year":2021,"publication_date":"2021-09-30","ids":{"openalex":"https://openalex.org/W3210537005","doi":"https://doi.org/10.1093/bib/bbab443","mag":"3210537005","pmid":"https://pubmed.ncbi.nlm.nih.gov/34718406"},"language":"en","primary_location":{"id":"doi:10.1093/bib/bbab443","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bib/bbab443","pdf_url":null,"source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Briefings in Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":false,"oa_status":"closed","oa_url":null,"any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5012107739","display_name":"Tiantian Liu","orcid":"https://orcid.org/0000-0001-6743-6042"},"institutions":[{"id":"https://openalex.org/I183067930","display_name":"Shanghai Jiao Tong University","ror":"https://ror.org/0220qvk04","country_code":"CN","type":"education","lineage":["https://openalex.org/I183067930"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Tiantian Liu","raw_affiliation_strings":["SJTU-Yale Joint Center for Biostatistics and Data Science, Shanghai Jiao Tong University, 800 Dongchuan RD, 200240, Shanghai, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"SJTU-Yale Joint Center for Biostatistics and Data Science, Shanghai Jiao Tong University, 800 Dongchuan RD, 200240, Shanghai, China","institution_ids":["https://openalex.org/I183067930"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5101145240","display_name":"Peirong Xu","orcid":null},"institutions":[{"id":"https://openalex.org/I183067930","display_name":"Shanghai Jiao Tong University","ror":"https://ror.org/0220qvk04","country_code":"CN","type":"education","lineage":["https://openalex.org/I183067930"]},{"id":"https://openalex.org/I2800570007","display_name":"Renji Hospital","ror":"https://ror.org/03ypbx660","country_code":"CN","type":"healthcare","lineage":["https://openalex.org/I2800570007"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Peirong Xu","raw_affiliation_strings":["Department of Breast Surgery, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, 200127, Shanghai, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Breast Surgery, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, 200127, Shanghai, China","institution_ids":["https://openalex.org/I183067930","https://openalex.org/I2800570007"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5006099817","display_name":"Yueyao Du","orcid":"https://orcid.org/0000-0001-8630-0028"},"institutions":[{"id":"https://openalex.org/I183067930","display_name":"Shanghai Jiao Tong University","ror":"https://ror.org/0220qvk04","country_code":"CN","type":"education","lineage":["https://openalex.org/I183067930"]},{"id":"https://openalex.org/I32971472","display_name":"Yale University","ror":"https://ror.org/03v76x132","country_code":"US","type":"education","lineage":["https://openalex.org/I32971472"]}],"countries":["CN","US"],"is_corresponding":false,"raw_author_name":"Yueyao Du","raw_affiliation_strings":["Department of Biostatistics, Yale University, 60 College Stree, CT 06520, New Haven, USA","MoE Key Lab of Artificial Intelligence, AI Institute, Shanghai Jiao Tong University, 800 Dongchuan RD, 200240, Shanghai, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Biostatistics, Yale University, 60 College Stree, CT 06520, New Haven, USA","institution_ids":["https://openalex.org/I32971472"]},{"raw_affiliation_string":"MoE Key Lab of Artificial Intelligence, AI Institute, Shanghai Jiao Tong University, 800 Dongchuan RD, 200240, Shanghai, China","institution_ids":["https://openalex.org/I183067930"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100716955","display_name":"Hui L\u00fc","orcid":"https://orcid.org/0000-0001-8347-0830"},"institutions":[{"id":"https://openalex.org/I183067930","display_name":"Shanghai Jiao Tong University","ror":"https://ror.org/0220qvk04","country_code":"CN","type":"education","lineage":["https://openalex.org/I183067930"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Hui Lu","raw_affiliation_strings":["SJTU-Yale Joint Center for Biostatistics and Data Science, Shanghai Jiao Tong University, 800 Dongchuan RD, 200240, Shanghai, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"SJTU-Yale Joint Center for Biostatistics and Data Science, Shanghai Jiao Tong University, 800 Dongchuan RD, 200240, Shanghai, China","institution_ids":["https://openalex.org/I183067930"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5074828414","display_name":"Hongyu Zhao","orcid":"https://orcid.org/0000-0003-1195-9607"},"institutions":[{"id":"https://openalex.org/I32971472","display_name":"Yale University","ror":"https://ror.org/03v76x132","country_code":"US","type":"education","lineage":["https://openalex.org/I32971472"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Hongyu Zhao","raw_affiliation_strings":["Department of Biostatistics, Yale University, 60 College Stree, CT 06520, New Haven, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Biostatistics, Yale University, 60 College Stree, CT 06520, New Haven, USA","institution_ids":["https://openalex.org/I32971472"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5023727941","display_name":"Tao Wang","orcid":"https://orcid.org/0000-0002-1218-4017"},"institutions":[{"id":"https://openalex.org/I183067930","display_name":"Shanghai Jiao Tong University","ror":"https://ror.org/0220qvk04","country_code":"CN","type":"education","lineage":["https://openalex.org/I183067930"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Tao Wang","raw_affiliation_strings":["SJTU-Yale Joint Center for Biostatistics and Data Science, Shanghai Jiao Tong University, 800 Dongchuan RD, 200240, Shanghai, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"SJTU-Yale Joint Center for Biostatistics and Data Science, Shanghai Jiao Tong University, 800 Dongchuan RD, 200240, Shanghai, China","institution_ids":["https://openalex.org/I183067930"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5023727941"],"corresponding_institution_ids":["https://openalex.org/I183067930"],"apc_list":{"value":4011,"currency":"USD","value_usd":4011},"apc_paid":null,"fwci":0.9087,"has_fulltext":false,"cited_by_count":7,"citation_normalized_percentile":{"value":0.77117164,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":98},"biblio":{"volume":"23","issue":"1","first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10594","display_name":"Genetic and phenotypic traits in livestock","score":0.9995999932289124,"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"}},"topics":[{"id":"https://openalex.org/T10594","display_name":"Genetic and phenotypic traits in livestock","score":0.9995999932289124,"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"}},{"id":"https://openalex.org/T10066","display_name":"Gut microbiota and health","score":0.996399998664856,"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/T11226","display_name":"Milk Quality and Mastitis in Dairy Cows","score":0.9944000244140625,"subfield":{"id":"https://openalex.org/subfields/1102","display_name":"Agronomy and Crop Science"},"field":{"id":"https://openalex.org/fields/11","display_name":"Agricultural and Biological Sciences"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/zero","display_name":"Zero (linguistics)","score":0.6917304396629333},{"id":"https://openalex.org/keywords/negative-binomial-distribution","display_name":"Negative binomial distribution","score":0.6401171088218689},{"id":"https://openalex.org/keywords/binomial","display_name":"Binomial (polynomial)","score":0.5442635416984558},{"id":"https://openalex.org/keywords/association","display_name":"Association (psychology)","score":0.5269085764884949},{"id":"https://openalex.org/keywords/statistics","display_name":"Statistics","score":0.4577987492084503},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.4334834814071655},{"id":"https://openalex.org/keywords/applied-mathematics","display_name":"Applied mathematics","score":0.4179019033908844},{"id":"https://openalex.org/keywords/count-data","display_name":"Count data","score":0.4131152629852295},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.3877829313278198},{"id":"https://openalex.org/keywords/econometrics","display_name":"Econometrics","score":0.3569490909576416},{"id":"https://openalex.org/keywords/psychology","display_name":"Psychology","score":0.22143781185150146},{"id":"https://openalex.org/keywords/poisson-distribution","display_name":"Poisson distribution","score":0.1867026388645172},{"id":"https://openalex.org/keywords/linguistics","display_name":"Linguistics","score":0.07255515456199646}],"concepts":[{"id":"https://openalex.org/C2780813799","wikidata":"https://www.wikidata.org/wiki/Q3274237","display_name":"Zero (linguistics)","level":2,"score":0.6917304396629333},{"id":"https://openalex.org/C199335787","wikidata":"https://www.wikidata.org/wiki/Q743364","display_name":"Negative binomial distribution","level":3,"score":0.6401171088218689},{"id":"https://openalex.org/C2781315470","wikidata":"https://www.wikidata.org/wiki/Q193623","display_name":"Binomial (polynomial)","level":2,"score":0.5442635416984558},{"id":"https://openalex.org/C142853389","wikidata":"https://www.wikidata.org/wiki/Q744778","display_name":"Association (psychology)","level":2,"score":0.5269085764884949},{"id":"https://openalex.org/C105795698","wikidata":"https://www.wikidata.org/wiki/Q12483","display_name":"Statistics","level":1,"score":0.4577987492084503},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.4334834814071655},{"id":"https://openalex.org/C28826006","wikidata":"https://www.wikidata.org/wiki/Q33521","display_name":"Applied mathematics","level":1,"score":0.4179019033908844},{"id":"https://openalex.org/C33643355","wikidata":"https://www.wikidata.org/wiki/Q5176731","display_name":"Count data","level":3,"score":0.4131152629852295},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.3877829313278198},{"id":"https://openalex.org/C149782125","wikidata":"https://www.wikidata.org/wiki/Q160039","display_name":"Econometrics","level":1,"score":0.3569490909576416},{"id":"https://openalex.org/C15744967","wikidata":"https://www.wikidata.org/wiki/Q9418","display_name":"Psychology","level":0,"score":0.22143781185150146},{"id":"https://openalex.org/C100906024","wikidata":"https://www.wikidata.org/wiki/Q205692","display_name":"Poisson distribution","level":2,"score":0.1867026388645172},{"id":"https://openalex.org/C41895202","wikidata":"https://www.wikidata.org/wiki/Q8162","display_name":"Linguistics","level":1,"score":0.07255515456199646},{"id":"https://openalex.org/C138885662","wikidata":"https://www.wikidata.org/wiki/Q5891","display_name":"Philosophy","level":0,"score":0.0},{"id":"https://openalex.org/C542102704","wikidata":"https://www.wikidata.org/wiki/Q183257","display_name":"Psychotherapist","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","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":"D012107","descriptor_name":"Research Design","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012107","descriptor_name":"Research Design","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012107","descriptor_name":"Research Design","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015233","descriptor_name":"Models, Statistical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015233","descriptor_name":"Models, Statistical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015233","descriptor_name":"Models, Statistical","qualifier_ui":null,"qualifier_name":null,"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":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":2,"locations":[{"id":"doi:10.1093/bib/bbab443","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bib/bbab443","pdf_url":null,"source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Briefings in Bioinformatics","raw_type":"journal-article"},{"id":"pmid:34718406","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/34718406","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":"Briefings in bioinformatics","raw_type":null}],"best_oa_location":null,"sustainable_development_goals":[{"score":0.41999998688697815,"display_name":"Life in Land","id":"https://metadata.un.org/sdg/15"}],"awards":[],"funders":[],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":60,"referenced_works":["https://openalex.org/W1490768654","https://openalex.org/W1601795611","https://openalex.org/W1983865742","https://openalex.org/W2004014148","https://openalex.org/W2026006003","https://openalex.org/W2027235406","https://openalex.org/W2029761439","https://openalex.org/W2056279562","https://openalex.org/W2059424427","https://openalex.org/W2100318919","https://openalex.org/W2106985417","https://openalex.org/W2142802314","https://openalex.org/W2144673831","https://openalex.org/W2150785952","https://openalex.org/W2171571559","https://openalex.org/W2179438025","https://openalex.org/W2210190562","https://openalex.org/W2225156818","https://openalex.org/W2318878471","https://openalex.org/W2325994949","https://openalex.org/W2342540743","https://openalex.org/W2346233234","https://openalex.org/W2398800349","https://openalex.org/W2581853214","https://openalex.org/W2591708767","https://openalex.org/W2612481336","https://openalex.org/W2761069142","https://openalex.org/W2762290518","https://openalex.org/W2768617299","https://openalex.org/W2769209214","https://openalex.org/W2786358356","https://openalex.org/W2791901931","https://openalex.org/W2803457956","https://openalex.org/W2883602574","https://openalex.org/W2891344912","https://openalex.org/W2894973120","https://openalex.org/W2938573248","https://openalex.org/W2949004447","https://openalex.org/W2953228655","https://openalex.org/W2963049513","https://openalex.org/W2963831345","https://openalex.org/W2990249310","https://openalex.org/W2994811958","https://openalex.org/W3000337788","https://openalex.org/W3007722513","https://openalex.org/W3016855559","https://openalex.org/W3023665135","https://openalex.org/W3041436284","https://openalex.org/W3097964496","https://openalex.org/W3100759574","https://openalex.org/W3101380508","https://openalex.org/W3101584830","https://openalex.org/W3104810320","https://openalex.org/W3135985405","https://openalex.org/W3152171186","https://openalex.org/W4241635929","https://openalex.org/W4399579631","https://openalex.org/W6674816313","https://openalex.org/W6732982888","https://openalex.org/W6868975981"],"related_works":["https://openalex.org/W2599805416","https://openalex.org/W3210390693","https://openalex.org/W2971731486","https://openalex.org/W2974887920","https://openalex.org/W4214644238","https://openalex.org/W3135460725","https://openalex.org/W2338849605","https://openalex.org/W3122903216","https://openalex.org/W2556931687","https://openalex.org/W2095810391"],"abstract_inverted_index":{"As":[0],"our":[1,186],"understanding":[2],"of":[3,12,25,39,61,113,164,167,185],"the":[4,10,23,40,56,66,75,81,111,154,165,183,196,208,215],"microbiome":[5,45,62,77,132],"has":[6,9],"expanded,":[7],"so":[8],"recognition":[11],"its":[13],"critical":[14],"role":[15],"in":[16,74,131],"human":[17,76],"health":[18],"and":[19,50,58,65,115,144,156,170,181,192],"disease,":[20],"thereby":[21],"emphasizing":[22],"importance":[24],"testing":[26],"whether":[27],"microbes":[28],"are":[29,89,97],"associated":[30],"with":[31],"environmental":[32],"factors":[33],"or":[34],"clinical":[35],"outcomes.":[36],"However,":[37],"many":[38],"fundamental":[41],"challenges":[42],"that":[43],"concern":[44],"surveys":[46],"arise":[47],"from":[48,214],"statistical":[49,117],"experimental":[51],"design":[52],"issues,":[53],"such":[54],"as":[55],"sparse":[57],"overdispersed":[59],"nature":[60],"count":[63],"data":[64],"complex":[67],"correlation":[68],"structure":[69],"among":[70],"samples.":[71],"For":[72],"example,":[73],"project":[78],"(HMP)":[79],"dataset,":[80],"repeated":[82],"observations":[83],"across":[84],"time":[85],"points":[86],"(level":[87,94,102],"1)":[88],"nested":[90,99],"within":[91,100],"body":[92],"sites":[93],"2),":[95],"which":[96,211],"further":[98],"subjects":[101],"3).":[103],"Therefore,":[104],"there":[105],"is":[106,212],"a":[107,136,161,172],"great":[108],"need":[109],"for":[110,128,140,176],"development":[112],"specialized":[114],"sophisticated":[116],"tests.":[118],"In":[119],"this":[120],"paper,":[121],"we":[122],"propose":[123],"multilevel":[124],"zero-inflated":[125],"negative-binomial":[126],"models":[127],"association":[129,177],"analysis":[130],"surveys.":[133],"We":[134,179,199],"develop":[135],"variational":[137],"approximation":[138],"method":[139,187],"maximum":[141],"likelihood":[142],"estimation":[143],"inference.":[145],"It":[146],"uses":[147],"optimization,":[148],"rather":[149],"than":[150],"sampling,":[151],"to":[152,195,206],"approximate":[153],"log-likelihood":[155],"compute":[157],"parameter":[158,168],"estimates,":[159],"provides":[160],"robust":[162],"estimate":[163],"covariance":[166],"estimates":[169],"constructs":[171],"Wald-type":[173],"test":[174],"statistic":[175],"testing.":[178],"evaluate":[180],"demonstrate":[182],"performance":[184],"using":[188],"extensive":[189],"simulation":[190],"studies":[191],"an":[193,202],"application":[194],"HMP":[197],"dataset.":[198],"have":[200],"developed":[201],"R":[203],"package":[204],"MZINBVA":[205],"implement":[207],"proposed":[209],"method,":[210],"available":[213],"GitHub":[216],"repository":[217],"https://github.com/liudoubletian/MZINBVA.":[218]},"counts_by_year":[{"year":2025,"cited_by_count":1},{"year":2024,"cited_by_count":4},{"year":2023,"cited_by_count":1},{"year":2022,"cited_by_count":1}],"updated_date":"2026-07-22T07:51:19.307946","created_date":"2025-10-10T00:00:00"}
