{"id":"https://openalex.org/W4410216266","doi":"https://doi.org/10.3389/fbinf.2025.1556361","title":"micRoclean: an R package for decontaminating low-biomass 16S-rRNA microbiome data","display_name":"micRoclean: an R package for decontaminating low-biomass 16S-rRNA microbiome data","publication_year":2025,"publication_date":"2025-05-08","ids":{"openalex":"https://openalex.org/W4410216266","doi":"https://doi.org/10.3389/fbinf.2025.1556361","pmid":"https://pubmed.ncbi.nlm.nih.gov/40406150"},"language":"en","primary_location":{"id":"doi:10.3389/fbinf.2025.1556361","is_oa":true,"landing_page_url":"https://doi.org/10.3389/fbinf.2025.1556361","pdf_url":"https://www.frontiersin.org/journals/bioinformatics/articles/10.3389/fbinf.2025.1556361/pdf","source":{"id":"https://openalex.org/S4210219554","display_name":"Frontiers in Bioinformatics","issn_l":"2673-7647","issn":["2673-7647"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320527","host_organization_name":"Frontiers Media","host_organization_lineage":["https://openalex.org/P4310320527"],"host_organization_lineage_names":["Frontiers Media"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Frontiers in Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://www.frontiersin.org/journals/bioinformatics/articles/10.3389/fbinf.2025.1556361/pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5117486663","display_name":"Rachel Griffard-Smith","orcid":null},"institutions":[{"id":"https://openalex.org/I4210128618","display_name":"University of Kansas Medical Center","ror":"https://ror.org/036c9yv20","country_code":"US","type":"funder","lineage":["https://openalex.org/I4210128618"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Rachel Griffard-Smith","raw_affiliation_strings":["Department of Biostatistics & Data Science, University of Kansas Medical Center, Kansas City, KS, United States"],"affiliations":[{"raw_affiliation_string":"Department of Biostatistics & Data Science, University of Kansas Medical Center, Kansas City, KS, United States","institution_ids":["https://openalex.org/I4210128618"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5117486664","display_name":"Emily Schueddig","orcid":null},"institutions":[{"id":"https://openalex.org/I4210128618","display_name":"University of Kansas Medical Center","ror":"https://ror.org/036c9yv20","country_code":"US","type":"funder","lineage":["https://openalex.org/I4210128618"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Emily Schueddig","raw_affiliation_strings":["Department of Biostatistics & Data Science, University of Kansas Medical Center, Kansas City, KS, United States"],"affiliations":[{"raw_affiliation_string":"Department of Biostatistics & Data Science, University of Kansas Medical Center, Kansas City, KS, United States","institution_ids":["https://openalex.org/I4210128618"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5001119744","display_name":"Diane E. Mahoney","orcid":"https://orcid.org/0000-0002-9346-0828"},"institutions":[{"id":"https://openalex.org/I4210128618","display_name":"University of Kansas Medical Center","ror":"https://ror.org/036c9yv20","country_code":"US","type":"funder","lineage":["https://openalex.org/I4210128618"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Diane E. Mahoney","raw_affiliation_strings":["School of Nursing, University of Kansas Medical Center, Kansas City, KS, United States"],"affiliations":[{"raw_affiliation_string":"School of Nursing, University of Kansas Medical Center, Kansas City, KS, United States","institution_ids":["https://openalex.org/I4210128618"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5090752431","display_name":"Prabhakar Chalise","orcid":"https://orcid.org/0000-0001-5581-1220"},"institutions":[{"id":"https://openalex.org/I4210128618","display_name":"University of Kansas Medical Center","ror":"https://ror.org/036c9yv20","country_code":"US","type":"funder","lineage":["https://openalex.org/I4210128618"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Prabhakar Chalise","raw_affiliation_strings":["Department of Biostatistics & Data Science, University of Kansas Medical Center, Kansas City, KS, United States"],"affiliations":[{"raw_affiliation_string":"Department of Biostatistics & Data Science, University of Kansas Medical Center, Kansas City, KS, United States","institution_ids":["https://openalex.org/I4210128618"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5046887908","display_name":"Devin C. Koestler","orcid":"https://orcid.org/0000-0002-0598-0146"},"institutions":[{"id":"https://openalex.org/I4210128618","display_name":"University of Kansas Medical Center","ror":"https://ror.org/036c9yv20","country_code":"US","type":"funder","lineage":["https://openalex.org/I4210128618"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Devin C. Koestler","raw_affiliation_strings":["Department of Biostatistics & Data Science, University of Kansas Medical Center, Kansas City, KS, United States"],"affiliations":[{"raw_affiliation_string":"Department of Biostatistics & Data Science, University of Kansas Medical Center, Kansas City, KS, United States","institution_ids":["https://openalex.org/I4210128618"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5010958257","display_name":"Dong Pei","orcid":"https://orcid.org/0000-0001-8937-1913"},"institutions":[{"id":"https://openalex.org/I4210128618","display_name":"University of Kansas Medical Center","ror":"https://ror.org/036c9yv20","country_code":"US","type":"funder","lineage":["https://openalex.org/I4210128618"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Dong Pei","raw_affiliation_strings":["Department of Biostatistics & Data Science, University of Kansas Medical Center, Kansas City, KS, United States"],"affiliations":[{"raw_affiliation_string":"Department of Biostatistics & Data Science, University of Kansas Medical Center, Kansas City, KS, United States","institution_ids":["https://openalex.org/I4210128618"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":6,"corresponding_author_ids":["https://openalex.org/A5010958257"],"corresponding_institution_ids":["https://openalex.org/I4210128618"],"apc_list":{"value":1900,"currency":"USD","value_usd":1900},"apc_paid":{"value":1900,"currency":"USD","value_usd":1900},"fwci":1.4487,"has_fulltext":false,"cited_by_count":2,"citation_normalized_percentile":{"value":0.8098858,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":91,"max":98},"biblio":{"volume":"5","issue":null,"first_page":"1556361","last_page":"1556361"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10066","display_name":"Gut microbiota and health","score":0.9965000152587891,"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":0.9965000152587891,"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":0.9879000186920166,"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/T11970","display_name":"Molecular Biology Techniques and Applications","score":0.9649999737739563,"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":0.8418365716934204},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6480342149734497},{"id":"https://openalex.org/keywords/human-decontamination","display_name":"Human decontamination","score":0.6474615335464478},{"id":"https://openalex.org/keywords/metagenomics","display_name":"Metagenomics","score":0.5275582671165466},{"id":"https://openalex.org/keywords/contamination","display_name":"Contamination","score":0.4953650236129761},{"id":"https://openalex.org/keywords/biochemical-engineering","display_name":"Biochemical engineering","score":0.3524024486541748},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.2042352259159088},{"id":"https://openalex.org/keywords/bioinformatics","display_name":"Bioinformatics","score":0.17417681217193604},{"id":"https://openalex.org/keywords/engineering","display_name":"Engineering","score":0.1360996961593628},{"id":"https://openalex.org/keywords/ecology","display_name":"Ecology","score":0.11057773232460022},{"id":"https://openalex.org/keywords/waste-management","display_name":"Waste management","score":0.07828199863433838}],"concepts":[{"id":"https://openalex.org/C143121216","wikidata":"https://www.wikidata.org/wiki/Q1330402","display_name":"Microbiome","level":2,"score":0.8418365716934204},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6480342149734497},{"id":"https://openalex.org/C107211472","wikidata":"https://www.wikidata.org/wiki/Q284486","display_name":"Human decontamination","level":2,"score":0.6474615335464478},{"id":"https://openalex.org/C15151743","wikidata":"https://www.wikidata.org/wiki/Q903778","display_name":"Metagenomics","level":3,"score":0.5275582671165466},{"id":"https://openalex.org/C112570922","wikidata":"https://www.wikidata.org/wiki/Q60528603","display_name":"Contamination","level":2,"score":0.4953650236129761},{"id":"https://openalex.org/C183696295","wikidata":"https://www.wikidata.org/wiki/Q2487696","display_name":"Biochemical engineering","level":1,"score":0.3524024486541748},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.2042352259159088},{"id":"https://openalex.org/C60644358","wikidata":"https://www.wikidata.org/wiki/Q128570","display_name":"Bioinformatics","level":1,"score":0.17417681217193604},{"id":"https://openalex.org/C127413603","wikidata":"https://www.wikidata.org/wiki/Q11023","display_name":"Engineering","level":0,"score":0.1360996961593628},{"id":"https://openalex.org/C18903297","wikidata":"https://www.wikidata.org/wiki/Q7150","display_name":"Ecology","level":1,"score":0.11057773232460022},{"id":"https://openalex.org/C548081761","wikidata":"https://www.wikidata.org/wiki/Q180388","display_name":"Waste management","level":1,"score":0.07828199863433838},{"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":4,"locations":[{"id":"doi:10.3389/fbinf.2025.1556361","is_oa":true,"landing_page_url":"https://doi.org/10.3389/fbinf.2025.1556361","pdf_url":"https://www.frontiersin.org/journals/bioinformatics/articles/10.3389/fbinf.2025.1556361/pdf","source":{"id":"https://openalex.org/S4210219554","display_name":"Frontiers in Bioinformatics","issn_l":"2673-7647","issn":["2673-7647"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320527","host_organization_name":"Frontiers Media","host_organization_lineage":["https://openalex.org/P4310320527"],"host_organization_lineage_names":["Frontiers Media"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Frontiers in Bioinformatics","raw_type":"journal-article"},{"id":"pmid:40406150","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/40406150","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":"Frontiers in bioinformatics","raw_type":null},{"id":"pmh:oai:doaj.org/article:42d7f25230a04505a563d5b0bea131cc","is_oa":true,"landing_page_url":"https://doaj.org/article/42d7f25230a04505a563d5b0bea131cc","pdf_url":null,"source":{"id":"https://openalex.org/S112646816","display_name":"SHILAP Revista de lepidopterolog\u00eda","issn_l":"0300-5267","issn":["0300-5267","2340-4078"],"is_oa":true,"is_in_doaj":true,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Frontiers in Bioinformatics, Vol 5 (2025)","raw_type":"article"},{"id":"pmh:oai:pubmedcentral.nih.gov:12095030","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/12095030","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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Front Bioinform","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.3389/fbinf.2025.1556361","is_oa":true,"landing_page_url":"https://doi.org/10.3389/fbinf.2025.1556361","pdf_url":"https://www.frontiersin.org/journals/bioinformatics/articles/10.3389/fbinf.2025.1556361/pdf","source":{"id":"https://openalex.org/S4210219554","display_name":"Frontiers in Bioinformatics","issn_l":"2673-7647","issn":["2673-7647"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320527","host_organization_name":"Frontiers Media","host_organization_lineage":["https://openalex.org/P4310320527"],"host_organization_lineage_names":["Frontiers Media"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Frontiers in Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"grobid_xml":false,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4410216266.pdf"},"referenced_works_count":33,"referenced_works":["https://openalex.org/W2002832354","https://openalex.org/W2034285706","https://openalex.org/W2170486072","https://openalex.org/W2493607481","https://openalex.org/W2805310212","https://openalex.org/W2809519941","https://openalex.org/W2903174799","https://openalex.org/W2903670208","https://openalex.org/W2945138421","https://openalex.org/W2952463830","https://openalex.org/W2963276645","https://openalex.org/W2967450000","https://openalex.org/W3007945801","https://openalex.org/W3043062835","https://openalex.org/W3176723750","https://openalex.org/W3214361435","https://openalex.org/W4225335644","https://openalex.org/W4296777868","https://openalex.org/W4309884145","https://openalex.org/W4310957810","https://openalex.org/W4327569177","https://openalex.org/W4361301521","https://openalex.org/W4366090397","https://openalex.org/W4366819920","https://openalex.org/W4388942949","https://openalex.org/W4390839409","https://openalex.org/W4399547459","https://openalex.org/W4399691497","https://openalex.org/W4400390698","https://openalex.org/W4401090344","https://openalex.org/W4401730694","https://openalex.org/W4405016591","https://openalex.org/W4406717199"],"related_works":["https://openalex.org/W2106709734","https://openalex.org/W2388326394","https://openalex.org/W3150814824","https://openalex.org/W3215545042","https://openalex.org/W2903640460","https://openalex.org/W2148959479","https://openalex.org/W4231130575","https://openalex.org/W2347933607","https://openalex.org/W2912009363","https://openalex.org/W3196027678"],"abstract_inverted_index":{"In":[0,149],"16S-rRNA":[1],"microbiome":[2,40,89,119,170,179],"studies,":[3,20],"cross-contamination":[4],"and":[5,36,61,107,113,121,167],"environmental":[6],"contamination":[7,14],"can":[8],"obscure":[9],"true":[10],"biological":[11],"signal.":[12],"This":[13,110,190],"is":[15,44,192],"particularly":[16],"problematic":[17],"in":[18],"low-biomass":[19],"which":[21,95],"are":[22],"characterized":[23],"by":[24],"samples":[25],"with":[26,92,187],"a":[27,131,176],"small":[28],"amount":[29],"of":[30,67,103,125,139,146,156],"microbial":[31],"DNA.":[32],"Although":[33],"multiple":[34],"methods":[35],"packages":[37,117],"for":[38,52,118,123],"decontaminating":[39],"data":[41],"exist,":[42],"there":[43],"no":[45],"consensus":[46],"on":[47,55,94,99,115,141,160],"the":[48,56,65,100,104,137,142,147,154],"most":[49],"appropriate":[50],"tool":[51],"decontamination":[53,90,120,140],"based":[54,98],"individual":[57],"research":[58,105],"study":[59,106,108],"design":[60],"how":[62],"to":[63,71,96,135],"quantify":[64,136],"impact":[66,138],"removing":[68],"identified":[69],"contaminants":[70],"avoid":[72],"over-filtering.":[73],"To":[74],"address":[75],"these":[76],"gaps,":[77],"we":[78,152,173],"introduce":[79],"micRoclean,":[80],"an":[81],"open-source":[82],"R":[83],"package":[84,111,191],"that":[85,164,181],"contains":[86],"two":[87],"distinct":[88],"pipelines":[91],"guidance":[93],"select":[97],"downstream":[101],"goals":[102],"design.":[109],"integrates":[112],"expands":[114],"existing":[116],"analysis":[122],"convenience":[124],"users.":[126],"Furthermore,":[127],"micRoclean":[128,157,165,182],"also":[129],"implements":[130],"filtering":[132],"loss":[133],"statistic":[134],"overall":[143],"covariance":[144],"structure":[145],"data.":[148,171],"this":[150],"paper,":[151],"demonstrate":[153,174],"utility":[155],"through":[158,175],"implementation":[159],"example":[161],"data,":[162],"illustrating":[163],"effectively":[166],"intuitively":[168],"decontaminates":[169],"Further,":[172],"multi-batch":[177],"simulated":[178],"sample":[180],"matches":[183],"or":[184],"outperforms":[185],"tools":[186],"similar":[188],"objectives.":[189],"freely":[193],"available":[194],"from":[195],"GitHub":[196],"repository":[197],"rachelgriffard/micRoclean.":[198]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2025,"cited_by_count":1}],"updated_date":"2026-04-21T08:09:41.155169","created_date":"2025-10-10T00:00:00"}