{"id":"https://openalex.org/W2991615383","doi":"https://doi.org/10.1093/bib/bbz105","title":"Managing batch effects in microbiome data","display_name":"Managing batch effects in microbiome data","publication_year":2019,"publication_date":"2019-10-10","ids":{"openalex":"https://openalex.org/W2991615383","doi":"https://doi.org/10.1093/bib/bbz105","mag":"2991615383","pmid":"https://pubmed.ncbi.nlm.nih.gov/31776547"},"language":"en","primary_location":{"id":"doi:10.1093/bib/bbz105","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bib/bbz105","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/A5100383451","display_name":"Yiwen Wang","orcid":"https://orcid.org/0000-0002-7067-9093"},"institutions":[{"id":"https://openalex.org/I165779595","display_name":"University of Melbourne","ror":"https://ror.org/01ej9dk98","country_code":"AU","type":"education","lineage":["https://openalex.org/I165779595"]},{"id":"https://openalex.org/I4210166212","display_name":"Melbourne Genomics Health Alliance","ror":"https://ror.org/05rwzhy90","country_code":"AU","type":"nonprofit","lineage":["https://openalex.org/I4210166212"]}],"countries":["AU"],"is_corresponding":false,"raw_author_name":"Yiwen Wang","raw_affiliation_strings":["Melbourne Integrative Genomics, School of Mathematics and Statistics, University of Melbourne, Melbourne, VIC, 3052, Australia"],"affiliations":[{"raw_affiliation_string":"Melbourne Integrative Genomics, School of Mathematics and Statistics, University of Melbourne, Melbourne, VIC, 3052, Australia","institution_ids":["https://openalex.org/I4210166212","https://openalex.org/I165779595"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5091163780","display_name":"Kim\u2010Anh L\u00ea Cao","orcid":"https://orcid.org/0000-0003-3923-1116"},"institutions":[{"id":"https://openalex.org/I4210166212","display_name":"Melbourne Genomics Health Alliance","ror":"https://ror.org/05rwzhy90","country_code":"AU","type":"nonprofit","lineage":["https://openalex.org/I4210166212"]},{"id":"https://openalex.org/I165779595","display_name":"University of Melbourne","ror":"https://ror.org/01ej9dk98","country_code":"AU","type":"education","lineage":["https://openalex.org/I165779595"]}],"countries":["AU"],"is_corresponding":true,"raw_author_name":"Kim-Anh L\u00eaCao","raw_affiliation_strings":["Melbourne Integrative Genomics, School of Mathematics and Statistics, University of Melbourne, Melbourne, VIC, 3052, Australia"],"affiliations":[{"raw_affiliation_string":"Melbourne Integrative Genomics, School of Mathematics and Statistics, University of Melbourne, Melbourne, VIC, 3052, Australia","institution_ids":["https://openalex.org/I4210166212","https://openalex.org/I165779595"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5091163780"],"corresponding_institution_ids":["https://openalex.org/I165779595","https://openalex.org/I4210166212"],"apc_list":{"value":4011,"currency":"USD","value_usd":4011},"apc_paid":null,"fwci":4.2945,"has_fulltext":false,"cited_by_count":127,"citation_normalized_percentile":{"value":0.95393877,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":98,"max":100},"biblio":{"volume":"21","issue":"6","first_page":"1954","last_page":"1970"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10066","display_name":"Gut microbiota and health","score":0.9990000128746033,"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":0.9990000128746033,"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/T10836","display_name":"Metabolomics and Mass Spectrometry Studies","score":0.9822999835014343,"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/T10885","display_name":"Gene expression and cancer classification","score":0.942799985408783,"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/microbiome","display_name":"Microbiome","score":0.703691840171814},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.49037694931030273},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.4747738540172577},{"id":"https://openalex.org/keywords/data-science","display_name":"Data science","score":0.3839631676673889},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.25626105070114136},{"id":"https://openalex.org/keywords/bioinformatics","display_name":"Bioinformatics","score":0.21217989921569824}],"concepts":[{"id":"https://openalex.org/C143121216","wikidata":"https://www.wikidata.org/wiki/Q1330402","display_name":"Microbiome","level":2,"score":0.703691840171814},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.49037694931030273},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.4747738540172577},{"id":"https://openalex.org/C2522767166","wikidata":"https://www.wikidata.org/wiki/Q2374463","display_name":"Data science","level":1,"score":0.3839631676673889},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.25626105070114136},{"id":"https://openalex.org/C60644358","wikidata":"https://www.wikidata.org/wiki/Q128570","display_name":"Bioinformatics","level":1,"score":0.21217989921569824}],"mesh":[{"descriptor_ui":"D000078332","descriptor_name":"Data Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000078332","descriptor_name":"Data Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000078332","descriptor_name":"Data Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","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},{"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/bbz105","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bib/bbz105","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:31776547","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/31776547","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":[],"awards":[{"id":"https://openalex.org/G376703877","display_name":null,"funder_award_id":"GNT1159458","funder_id":"https://openalex.org/F4320334705","funder_display_name":"National Health and Medical Research Council"}],"funders":[{"id":"https://openalex.org/F4320322725","display_name":"China Scholarship Council","ror":"https://ror.org/04atp4p48"},{"id":"https://openalex.org/F4320334705","display_name":"National Health and Medical Research Council","ror":"https://ror.org/011kf5r70"}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":77,"referenced_works":["https://openalex.org/W190205155","https://openalex.org/W1772250503","https://openalex.org/W1967075719","https://openalex.org/W1975102735","https://openalex.org/W1975470942","https://openalex.org/W1987971958","https://openalex.org/W2004014148","https://openalex.org/W2026006003","https://openalex.org/W2028582941","https://openalex.org/W2029607409","https://openalex.org/W2036827408","https://openalex.org/W2037540915","https://openalex.org/W2061219514","https://openalex.org/W2078112764","https://openalex.org/W2096192437","https://openalex.org/W2098762803","https://openalex.org/W2107665951","https://openalex.org/W2113925621","https://openalex.org/W2113977541","https://openalex.org/W2116650193","https://openalex.org/W2117065897","https://openalex.org/W2137499573","https://openalex.org/W2142942734","https://openalex.org/W2146512944","https://openalex.org/W2147013674","https://openalex.org/W2147525367","https://openalex.org/W2148103005","https://openalex.org/W2148541040","https://openalex.org/W2150542002","https://openalex.org/W2156975150","https://openalex.org/W2157159562","https://openalex.org/W2163903604","https://openalex.org/W2166549811","https://openalex.org/W2170486072","https://openalex.org/W2173778819","https://openalex.org/W2181471414","https://openalex.org/W2270456711","https://openalex.org/W2381894708","https://openalex.org/W2398836226","https://openalex.org/W2404939443","https://openalex.org/W2462800864","https://openalex.org/W2601727535","https://openalex.org/W2603756957","https://openalex.org/W2608404326","https://openalex.org/W2612222797","https://openalex.org/W2630017261","https://openalex.org/W2763540102","https://openalex.org/W2769542288","https://openalex.org/W2784066249","https://openalex.org/W2792384777","https://openalex.org/W2794061371","https://openalex.org/W2794987222","https://openalex.org/W2805044645","https://openalex.org/W2866587047","https://openalex.org/W2887429082","https://openalex.org/W2888566822","https://openalex.org/W2889638535","https://openalex.org/W2890655424","https://openalex.org/W2892875286","https://openalex.org/W2942108345","https://openalex.org/W3203034578","https://openalex.org/W4299542564","https://openalex.org/W6660191130","https://openalex.org/W6665630873","https://openalex.org/W6677216342","https://openalex.org/W6678086366","https://openalex.org/W6702985903","https://openalex.org/W6703209079","https://openalex.org/W6733428306","https://openalex.org/W6733869555","https://openalex.org/W6737356329","https://openalex.org/W6745735992","https://openalex.org/W6749977808","https://openalex.org/W6751898389","https://openalex.org/W6754297202","https://openalex.org/W6776535907","https://openalex.org/W6802197981"],"related_works":["https://openalex.org/W4391375266","https://openalex.org/W2899084033","https://openalex.org/W2748952813","https://openalex.org/W2604155846","https://openalex.org/W4390658901","https://openalex.org/W3121185202","https://openalex.org/W4393043634","https://openalex.org/W4206185765","https://openalex.org/W2900546243","https://openalex.org/W3020516445"],"abstract_inverted_index":{"Microbial":[0],"communities":[1],"have":[2,133],"been":[3],"increasingly":[4],"studied":[5],"in":[6,13,35,120,172],"recent":[7],"years":[8],"to":[9,21,63,74,101,140,167],"investigate":[10],"their":[11],"role":[12],"ecological":[14],"habitats.":[15],"However,":[16,81],"microbiome":[17,83,144],"studies":[18],"are":[19,33,60,72,136],"difficult":[20],"reproduce":[22,168],"or":[23,42,76,104],"replicate":[24],"as":[25,52],"they":[26],"may":[27],"suffer":[28],"from":[29,39],"confounding":[30,57],"factors":[31,58,65],"that":[32,59,117,135],"unavoidable":[34],"practice":[36],"and":[37,69,89,94,160,163],"originate":[38],"biological,":[40],"technical":[41],"computational":[43],"sources.":[44],"In":[45],"this":[46,173],"review,":[47],"we":[48,118],"define":[49],"batch":[50,79,97,107,115],"effects":[51,116],"unwanted":[53],"variation":[54],"introduced":[55],"by":[56],"not":[61,137],"related":[62],"any":[64],"of":[66,96,114,128,143,154],"interest.":[67],"Computational":[68],"analytical":[70],"methods":[71,100,156],"required":[73],"remove":[75],"account":[77,103],"for":[78,106,150],"effects.":[80,108],"inherent":[82],"data":[84],"characteristics":[85],"(e.g.":[86],"sparse,":[87],"compositional":[88],"multivariate)":[90],"challenge":[91],"the":[92,126,141,152,155,169],"development":[93],"application":[95],"effect":[98],"adjustment":[99],"either":[102],"correct":[105],"We":[109,124,146],"present":[110],"commonly":[111],"encountered":[112],"sources":[113],"illustrate":[119],"several":[121],"case":[122],"studies.":[123],"discuss":[125],"limitations":[127],"current":[129],"methods,":[130],"which":[131],"often":[132],"assumptions":[134],"met":[138],"due":[139],"peculiarities":[142],"data.":[145],"provide":[147],"practical":[148],"guidelines":[149],"assessing":[151],"efficiency":[153],"based":[157],"on":[158],"visual":[159],"numerical":[161],"outputs":[162],"a":[164],"thorough":[165],"tutorial":[166],"analyses":[170],"conducted":[171],"review.":[174]},"counts_by_year":[{"year":2026,"cited_by_count":9},{"year":2025,"cited_by_count":19},{"year":2024,"cited_by_count":21},{"year":2023,"cited_by_count":28},{"year":2022,"cited_by_count":27},{"year":2021,"cited_by_count":16},{"year":2020,"cited_by_count":7}],"updated_date":"2026-04-16T08:26:57.006410","created_date":"2025-10-10T00:00:00"}
