{"id":"https://openalex.org/W4407909309","doi":"https://doi.org/10.1093/bioinformatics/btaf084","title":"NPM: latent batch effects correction of omics data by nearest-pair matching","display_name":"NPM: latent batch effects correction of omics data by nearest-pair matching","publication_year":2025,"publication_date":"2025-02-25","ids":{"openalex":"https://openalex.org/W4407909309","doi":"https://doi.org/10.1093/bioinformatics/btaf084","pmid":"https://pubmed.ncbi.nlm.nih.gov/39999010"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btaf084","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btaf084","pdf_url":"https://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btaf084/62168193/btaf084.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":true,"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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btaf084/62168193/btaf084.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5036352419","display_name":"Antonino Zito","orcid":null},"institutions":[{"id":"https://openalex.org/I4210093740","display_name":"Swiss Institute for Regenerative Medicine","ror":"https://ror.org/00g3rdy81","country_code":"CH","type":"nonprofit","lineage":["https://openalex.org/I4210093740"]}],"countries":["CH"],"is_corresponding":true,"raw_author_name":"Antonino Zito","raw_affiliation_strings":["BigOmics Analytics , Via Serafino Balestra 12 , Lugano 6900,","BigOmics Analytics , Lugano, 6900,"],"affiliations":[{"raw_affiliation_string":"BigOmics Analytics , Via Serafino Balestra 12 , Lugano 6900,","institution_ids":["https://openalex.org/I4210093740"]},{"raw_affiliation_string":"BigOmics Analytics , Lugano, 6900,","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5065164931","display_name":"Axel Martinelli","orcid":"https://orcid.org/0000-0003-2662-7162"},"institutions":[{"id":"https://openalex.org/I4210093740","display_name":"Swiss Institute for Regenerative Medicine","ror":"https://ror.org/00g3rdy81","country_code":"CH","type":"nonprofit","lineage":["https://openalex.org/I4210093740"]}],"countries":["CH"],"is_corresponding":false,"raw_author_name":"Axel Martinelli","raw_affiliation_strings":["BigOmics Analytics , Via Serafino Balestra 12 , Lugano 6900,","BigOmics Analytics , Lugano, 6900,"],"affiliations":[{"raw_affiliation_string":"BigOmics Analytics , Via Serafino Balestra 12 , Lugano 6900,","institution_ids":["https://openalex.org/I4210093740"]},{"raw_affiliation_string":"BigOmics Analytics , Lugano, 6900,","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5096068469","display_name":"Mauro Masiero","orcid":null},"institutions":[{"id":"https://openalex.org/I4210093740","display_name":"Swiss Institute for Regenerative Medicine","ror":"https://ror.org/00g3rdy81","country_code":"CH","type":"nonprofit","lineage":["https://openalex.org/I4210093740"]}],"countries":["CH"],"is_corresponding":false,"raw_author_name":"Mauro Masiero","raw_affiliation_strings":["BigOmics Analytics , Via Serafino Balestra 12 , Lugano 6900,","BigOmics Analytics , Lugano, 6900,"],"affiliations":[{"raw_affiliation_string":"BigOmics Analytics , Via Serafino Balestra 12 , Lugano 6900,","institution_ids":["https://openalex.org/I4210093740"]},{"raw_affiliation_string":"BigOmics Analytics , Lugano, 6900,","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5102659395","display_name":"Murat Akhmedov","orcid":null},"institutions":[{"id":"https://openalex.org/I4210093740","display_name":"Swiss Institute for Regenerative Medicine","ror":"https://ror.org/00g3rdy81","country_code":"CH","type":"nonprofit","lineage":["https://openalex.org/I4210093740"]}],"countries":["CH"],"is_corresponding":false,"raw_author_name":"Murodzhon Akhmedov","raw_affiliation_strings":["BigOmics Analytics , Via Serafino Balestra 12 , Lugano 6900,","BigOmics Analytics , Lugano, 6900,"],"affiliations":[{"raw_affiliation_string":"BigOmics Analytics , Via Serafino Balestra 12 , Lugano 6900,","institution_ids":["https://openalex.org/I4210093740"]},{"raw_affiliation_string":"BigOmics Analytics , Lugano, 6900,","institution_ids":[]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5079771818","display_name":"Ivo Kwee","orcid":"https://orcid.org/0000-0002-2751-4218"},"institutions":[{"id":"https://openalex.org/I4210093740","display_name":"Swiss Institute for Regenerative Medicine","ror":"https://ror.org/00g3rdy81","country_code":"CH","type":"nonprofit","lineage":["https://openalex.org/I4210093740"]}],"countries":["CH"],"is_corresponding":false,"raw_author_name":"Ivo Kwee","raw_affiliation_strings":["BigOmics Analytics , Via Serafino Balestra 12 , Lugano 6900,","BigOmics Analytics , Lugano, 6900,"],"affiliations":[{"raw_affiliation_string":"BigOmics Analytics , Via Serafino Balestra 12 , Lugano 6900,","institution_ids":["https://openalex.org/I4210093740"]},{"raw_affiliation_string":"BigOmics Analytics , Lugano, 6900,","institution_ids":[]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":5,"corresponding_author_ids":["https://openalex.org/A5036352419"],"corresponding_institution_ids":["https://openalex.org/I4210093740"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":{"value":3618,"currency":"USD","value_usd":3618},"fwci":0.7498,"has_fulltext":false,"cited_by_count":1,"citation_normalized_percentile":{"value":0.68123015,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":96,"max":98},"biblio":{"volume":"41","issue":"3","first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.9991000294685364,"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/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.9991000294685364,"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":0.9976999759674072,"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/T10621","display_name":"Gene Regulatory Network Analysis","score":0.9926999807357788,"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/computer-science","display_name":"Computer science","score":0.7766062021255493},{"id":"https://openalex.org/keywords/matching","display_name":"Matching (statistics)","score":0.66729336977005},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.6002323031425476},{"id":"https://openalex.org/keywords/noise","display_name":"Noise (video)","score":0.5548518300056458},{"id":"https://openalex.org/keywords/source-code","display_name":"Source code","score":0.5155379772186279},{"id":"https://openalex.org/keywords/r-package","display_name":"R package","score":0.4415375590324402},{"id":"https://openalex.org/keywords/k-nearest-neighbors-algorithm","display_name":"k-nearest neighbors algorithm","score":0.4374352991580963},{"id":"https://openalex.org/keywords/software","display_name":"Software","score":0.41415080428123474},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.2725701332092285},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.21331986784934998},{"id":"https://openalex.org/keywords/statistics","display_name":"Statistics","score":0.09493681788444519},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.07191500067710876}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7766062021255493},{"id":"https://openalex.org/C165064840","wikidata":"https://www.wikidata.org/wiki/Q1321061","display_name":"Matching (statistics)","level":2,"score":0.66729336977005},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.6002323031425476},{"id":"https://openalex.org/C99498987","wikidata":"https://www.wikidata.org/wiki/Q2210247","display_name":"Noise (video)","level":3,"score":0.5548518300056458},{"id":"https://openalex.org/C43126263","wikidata":"https://www.wikidata.org/wiki/Q128751","display_name":"Source code","level":2,"score":0.5155379772186279},{"id":"https://openalex.org/C2984074130","wikidata":"https://www.wikidata.org/wiki/Q73539779","display_name":"R package","level":2,"score":0.4415375590324402},{"id":"https://openalex.org/C113238511","wikidata":"https://www.wikidata.org/wiki/Q1071612","display_name":"k-nearest neighbors algorithm","level":2,"score":0.4374352991580963},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.41415080428123474},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.2725701332092285},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.21331986784934998},{"id":"https://openalex.org/C105795698","wikidata":"https://www.wikidata.org/wiki/Q12483","display_name":"Statistics","level":1,"score":0.09493681788444519},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.07191500067710876},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.0},{"id":"https://openalex.org/C459310","wikidata":"https://www.wikidata.org/wiki/Q117801","display_name":"Computational science","level":1,"score":0.0},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.0},{"id":"https://openalex.org/C115961682","wikidata":"https://www.wikidata.org/wiki/Q860623","display_name":"Image (mathematics)","level":2,"score":0.0}],"mesh":[{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","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":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true}],"locations_count":3,"locations":[{"id":"doi:10.1093/bioinformatics/btaf084","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btaf084","pdf_url":"https://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btaf084/62168193/btaf084.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":true,"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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:39999010","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/39999010","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":"Bioinformatics (Oxford, England)","raw_type":null},{"id":"pmh:oai:pubmedcentral.nih.gov:11925496","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/11925496","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Bioinformatics","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btaf084","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btaf084","pdf_url":"https://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btaf084/62168193/btaf084.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":true,"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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"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/W4407909309.pdf"},"referenced_works_count":30,"referenced_works":["https://openalex.org/W2037796411","https://openalex.org/W2060002238","https://openalex.org/W2062094438","https://openalex.org/W2096192437","https://openalex.org/W2107665951","https://openalex.org/W2116650193","https://openalex.org/W2137499573","https://openalex.org/W2139577967","https://openalex.org/W2146512944","https://openalex.org/W2152849583","https://openalex.org/W2167980479","https://openalex.org/W2295124130","https://openalex.org/W2530292989","https://openalex.org/W2574912984","https://openalex.org/W2793722631","https://openalex.org/W2904124790","https://openalex.org/W2931512726","https://openalex.org/W2951638683","https://openalex.org/W2966871345","https://openalex.org/W3120159706","https://openalex.org/W3144776955","https://openalex.org/W3167525828","https://openalex.org/W3183726003","https://openalex.org/W3196242974","https://openalex.org/W3200079988","https://openalex.org/W3204344878","https://openalex.org/W3204934477","https://openalex.org/W4285405545","https://openalex.org/W4290861579","https://openalex.org/W4386468546"],"related_works":["https://openalex.org/W1972035260","https://openalex.org/W2754214645","https://openalex.org/W2785302227","https://openalex.org/W4301594054","https://openalex.org/W2794488505","https://openalex.org/W3125889879","https://openalex.org/W4225126530","https://openalex.org/W3124422538","https://openalex.org/W4389426664","https://openalex.org/W2295467472"],"abstract_inverted_index":{"NPM":[0],"is":[1],"freely":[2,49],"available":[3,17,45],"on":[4,8,51],"GitHub":[5],"(https://github.com/bigomics/NPM)":[6],"and":[7,38,46],"Omics":[9],"Playground":[10],"(https://bigomics.ch/omics-playground).":[11],"Computer":[12],"codes":[13],"for":[14],"analyses":[15],"are":[16,25,43],"at":[18],"(https://github.com/bigomics/NPM).":[19],"The":[20],"datasets":[21,42],"underlying":[22],"this":[23],"article":[24],"the":[26,52],"following:":[27],"GSE120099,":[28],"GSE82177,":[29],"GSE162760,":[30],"GSE171343,":[31],"GSE153380,":[32],"GSE163214,":[33],"GSE182440,":[34],"GSE163857,":[35],"GSE117970,":[36],"GSE173078,":[37],"GSE10846.":[39],"All":[40],"these":[41],"publicly":[44],"can":[47],"be":[48],"accessed":[50],"Gene":[53],"Expression":[54],"Omnibus":[55],"repository.":[56]},"counts_by_year":[{"year":2026,"cited_by_count":1}],"updated_date":"2026-04-14T08:04:32.555800","created_date":"2025-10-10T00:00:00"}