{"id":"https://openalex.org/W4406260002","doi":"https://doi.org/10.1109/bibm62325.2024.10822371","title":"RMComBat: A Batch Effect Correction Algorithm for Repeated Measurement Sequencing Data to Prevent Overcorrection","display_name":"RMComBat: A Batch Effect Correction Algorithm for Repeated Measurement Sequencing Data to Prevent Overcorrection","publication_year":2024,"publication_date":"2024-12-03","ids":{"openalex":"https://openalex.org/W4406260002","doi":"https://doi.org/10.1109/bibm62325.2024.10822371"},"language":"en","primary_location":{"id":"doi:10.1109/bibm62325.2024.10822371","is_oa":false,"landing_page_url":"https://doi.org/10.1109/bibm62325.2024.10822371","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2024 IEEE International Conference on Bioinformatics and Biomedicine (BIBM)","raw_type":"proceedings-article"},"type":"article","indexed_in":["crossref"],"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/A5088818118","display_name":"Yuqian Liu","orcid":"https://orcid.org/0000-0001-8536-0854"},"institutions":[{"id":"https://openalex.org/I87445476","display_name":"Xi'an Jiaotong University","ror":"https://ror.org/017zhmm22","country_code":"CN","type":"education","lineage":["https://openalex.org/I87445476"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Yuqian Liu","raw_affiliation_strings":["Xi&#x2019;an Jiaotong University,School of Computer Science and Technology,Xi&#x2019;an,China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Xi&#x2019;an Jiaotong University,School of Computer Science and Technology,Xi&#x2019;an,China","institution_ids":["https://openalex.org/I87445476"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5103757362","display_name":"Zhenfang Wei","orcid":null},"institutions":[{"id":"https://openalex.org/I87445476","display_name":"Xi'an Jiaotong University","ror":"https://ror.org/017zhmm22","country_code":"CN","type":"education","lineage":["https://openalex.org/I87445476"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Zhaoxing Wei","raw_affiliation_strings":["Xi&#x2019;an Jiaotong University,School of Computer Science and Technology,Xi&#x2019;an,China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Xi&#x2019;an Jiaotong University,School of Computer Science and Technology,Xi&#x2019;an,China","institution_ids":["https://openalex.org/I87445476"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5027360778","display_name":"Jiayin Wang","orcid":"https://orcid.org/0000-0002-3862-6557"},"institutions":[{"id":"https://openalex.org/I87445476","display_name":"Xi'an Jiaotong University","ror":"https://ror.org/017zhmm22","country_code":"CN","type":"education","lineage":["https://openalex.org/I87445476"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Jiayin Wang","raw_affiliation_strings":["Xi&#x2019;an Jiaotong University,School of Computer Science and Technology,Xi&#x2019;an,China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Xi&#x2019;an Jiaotong University,School of Computer Science and Technology,Xi&#x2019;an,China","institution_ids":["https://openalex.org/I87445476"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100452966","display_name":"Xiaoyan Zhu","orcid":"https://orcid.org/0000-0001-5361-6691"},"institutions":[{"id":"https://openalex.org/I87445476","display_name":"Xi'an Jiaotong University","ror":"https://ror.org/017zhmm22","country_code":"CN","type":"education","lineage":["https://openalex.org/I87445476"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Xiaoyan Zhu","raw_affiliation_strings":["Xi&#x2019;an Jiaotong University,School of Computer Science and Technology,Xi&#x2019;an,China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Xi&#x2019;an Jiaotong University,School of Computer Science and Technology,Xi&#x2019;an,China","institution_ids":["https://openalex.org/I87445476"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100716157","display_name":"Ruo-Yu Liu","orcid":"https://orcid.org/0000-0003-1576-0961"},"institutions":[{"id":"https://openalex.org/I4210131893","display_name":"Second Affiliated Hospital of Xi'an Jiaotong University","ror":"https://ror.org/03aq7kf18","country_code":"CN","type":"healthcare","lineage":["https://openalex.org/I4210131893"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Ruoyu Liu","raw_affiliation_strings":["The Second Affiliated Hospital of Xi&#x2019;an Jiaotong University,Department of Respiratory and Critical Care Medicine,Xi&#x2019;an,China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"The Second Affiliated Hospital of Xi&#x2019;an Jiaotong University,Department of Respiratory and Critical Care Medicine,Xi&#x2019;an,China","institution_ids":["https://openalex.org/I4210131893"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5054657033","display_name":"Xuwen Wang","orcid":"https://orcid.org/0000-0003-3022-6513"},"institutions":[{"id":"https://openalex.org/I4210131893","display_name":"Second Affiliated Hospital of Xi'an Jiaotong University","ror":"https://ror.org/03aq7kf18","country_code":"CN","type":"healthcare","lineage":["https://openalex.org/I4210131893"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Xuwen Wang","raw_affiliation_strings":["The Second Affiliated Hospital of Xi&#x2019;an Jiaotong University,Department of Respiratory and Critical Care Medicine,Xi&#x2019;an,China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"The Second Affiliated Hospital of Xi&#x2019;an Jiaotong University,Department of Respiratory and Critical Care Medicine,Xi&#x2019;an,China","institution_ids":["https://openalex.org/I4210131893"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5115694725","display_name":"Shenjie Wang","orcid":null},"institutions":[{"id":"https://openalex.org/I87445476","display_name":"Xi'an Jiaotong University","ror":"https://ror.org/017zhmm22","country_code":"CN","type":"education","lineage":["https://openalex.org/I87445476"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Shenjie Wang","raw_affiliation_strings":["Xi&#x2019;an Jiaotong University,School of Computer Science and Technology,Xi&#x2019;an,China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Xi&#x2019;an Jiaotong University,School of Computer Science and Technology,Xi&#x2019;an,China","institution_ids":["https://openalex.org/I87445476"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5047344339","display_name":"Xin Lai","orcid":"https://orcid.org/0000-0003-3850-5680"},"institutions":[{"id":"https://openalex.org/I87445476","display_name":"Xi'an Jiaotong University","ror":"https://ror.org/017zhmm22","country_code":"CN","type":"education","lineage":["https://openalex.org/I87445476"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Xin Lai","raw_affiliation_strings":["Xi&#x2019;an Jiaotong University,School of Computer Science and Technology,Xi&#x2019;an,China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Xi&#x2019;an Jiaotong University,School of Computer Science and Technology,Xi&#x2019;an,China","institution_ids":["https://openalex.org/I87445476"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":8,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":null,"apc_paid":null,"fwci":0.0,"has_fulltext":false,"cited_by_count":0,"citation_normalized_percentile":{"value":0.21717317,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":null,"issue":null,"first_page":"5387","last_page":"5394"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10215","display_name":"Semantic Web and Ontologies","score":0.7556999921798706,"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/T10215","display_name":"Semantic Web and Ontologies","score":0.7556999921798706,"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/T11719","display_name":"Data Quality and Management","score":0.6635000109672546,"subfield":{"id":"https://openalex.org/subfields/1803","display_name":"Management Science and Operations Research"},"field":{"id":"https://openalex.org/fields/18","display_name":"Decision Sciences"},"domain":{"id":"https://openalex.org/domains/2","display_name":"Social Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.6414583325386047},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5697558522224426}],"concepts":[{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.6414583325386047},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5697558522224426}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.1109/bibm62325.2024.10822371","is_oa":false,"landing_page_url":"https://doi.org/10.1109/bibm62325.2024.10822371","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2024 IEEE International Conference on Bioinformatics and Biomedicine (BIBM)","raw_type":"proceedings-article"}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[],"funders":[{"id":"https://openalex.org/F4320321001","display_name":"National Natural Science Foundation of China","ror":"https://ror.org/01h0zpd94"}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":21,"referenced_works":["https://openalex.org/W1518016665","https://openalex.org/W1987971958","https://openalex.org/W2049446938","https://openalex.org/W2096192437","https://openalex.org/W2107665951","https://openalex.org/W2118489472","https://openalex.org/W2120865735","https://openalex.org/W2137499573","https://openalex.org/W2138879180","https://openalex.org/W2139345901","https://openalex.org/W2148541040","https://openalex.org/W2168175751","https://openalex.org/W2555502666","https://openalex.org/W2603756957","https://openalex.org/W2791018867","https://openalex.org/W2883544453","https://openalex.org/W2984472267","https://openalex.org/W3002417351","https://openalex.org/W3038220767","https://openalex.org/W4213135642","https://openalex.org/W4235169531"],"related_works":["https://openalex.org/W4391375266","https://openalex.org/W2899084033","https://openalex.org/W2748952813","https://openalex.org/W2051487156","https://openalex.org/W2073681303","https://openalex.org/W2390279801","https://openalex.org/W4391913857","https://openalex.org/W2358668433","https://openalex.org/W4396701345","https://openalex.org/W2376932109"],"abstract_inverted_index":{"Batch":[0],"effects,":[1,165],"caused":[2],"by":[3,103],"non-biological":[4],"variations":[5],"such":[6],"as":[7,56],"differences":[8],"in":[9,22,59,182,193],"laboratory":[10],"conditions,":[11],"reagent":[12],"lots,":[13],"or":[14],"personnel,":[15],"are":[16,45,53],"a":[17,82,110,186,200],"substantial":[18],"source":[19],"of":[20,39,84,94,128,173,207],"noise":[21],"gene":[23,144,208],"expression":[24,145,209],"data.":[25],"Accurately":[26],"correcting":[27],"these":[28],"effects":[29],"is":[30,65],"crucial":[31],"for":[32,121,203],"valid":[33],"biological":[34,86,129,176],"inferences.":[35],"However,":[36],"the":[37,95,105,126,171,205],"majority":[38],"existing":[40],"batch":[41,164],"effect":[42],"correction":[43,192],"algorithms":[44,137,161],"prone":[46],"to":[47,71,81,119],"overcorrection,":[48,184],"where":[49,63],"biologically":[50,77,190],"meaningful":[51],"signals":[52],"mistakenly":[54],"identified":[55],"noise,":[57],"especially":[58],"repeated":[60,142,194],"measurement":[61,143,195],"studies":[62],"time":[64],"confounded":[66],"with":[67,109],"batch.":[68],"The":[69],"failure":[70],"accurately":[72],"distinguish":[73],"between":[74],"batch-related":[75],"and":[76,124,134,140,153,189],"relevant":[78],"variation":[79],"leads":[80],"loss":[83],"critical":[85],"information.":[87],"This":[88],"paper":[89],"presents":[90],"RMComBat,":[91],"an":[92],"enhancement":[93],"widely-used":[96],"ComBat":[97],"framework,":[98],"which":[99],"addresses":[100],"this":[101],"limitation":[102],"replacing":[104],"general":[106],"linear":[107,111],"model":[108],"mixed-effects":[112],"model.":[113],"RMComBat":[114,133,178],"incorporates":[115],"subject-specific":[116],"random":[117],"intercepts":[118],"correct":[120],"sample":[122],"correlation":[123],"enhance":[125],"preservation":[127],"signals.":[130,177],"We":[131],"tested":[132],"several":[135],"popular":[136],"on":[138],"simulated":[139],"real":[141],"datasets,":[146],"evaluating":[147],"their":[148],"performance":[149,181],"through":[150],"visual":[151],"inspections":[152],"quantitative":[154],"metrics.":[155],"Results":[156],"indicate":[157],"that":[158],"although":[159],"most":[160],"can":[162],"reduce":[163],"they":[166],"often":[167],"do":[168],"so":[169,197],"at":[170],"cost":[172],"removing":[174],"true":[175],"demonstrates":[179],"superior":[180],"preventing":[183],"providing":[185],"more":[187],"balanced":[188],"informative":[191],"studies,":[196],"making":[198],"it":[199],"valuable":[201],"tool":[202],"improving":[204],"accuracy":[206],"analyses.":[210]},"counts_by_year":[],"updated_date":"2026-06-11T09:08:48.828518","created_date":"2025-10-10T00:00:00"}
