{"id":"https://openalex.org/W7129006512","doi":"https://doi.org/10.1038/s43588-025-00943-1","title":"Toward informed batch correction for single-cell transcriptome integration","display_name":"Toward informed batch correction for single-cell transcriptome integration","publication_year":2026,"publication_date":"2026-02-16","ids":{"openalex":"https://openalex.org/W7129006512","doi":"https://doi.org/10.1038/s43588-025-00943-1","pmid":"https://pubmed.ncbi.nlm.nih.gov/41699077"},"language":"en","primary_location":{"id":"doi:10.1038/s43588-025-00943-1","is_oa":false,"landing_page_url":"https://doi.org/10.1038/s43588-025-00943-1","pdf_url":null,"source":{"id":"https://openalex.org/S4210228084","display_name":"Nature Computational Science","issn_l":"2662-8457","issn":["2662-8457"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319908","host_organization_name":"Nature Portfolio","host_organization_lineage":["https://openalex.org/P4310319908","https://openalex.org/P4310319965"],"host_organization_lineage_names":["Nature Portfolio","Springer Nature"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Nature Computational Science","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","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/A5100415917","display_name":"Shuang Li","orcid":"https://orcid.org/0000-0002-4963-9273"},"institutions":[{"id":"https://openalex.org/I21196054","display_name":"Wellcome/MRC Cambridge Stem Cell Institute","ror":"https://ror.org/05nz0zp31","country_code":"GB","type":"facility","lineage":["https://openalex.org/I21196054","https://openalex.org/I241749","https://openalex.org/I4210087105","https://openalex.org/I87048295","https://openalex.org/I90344618"]},{"id":"https://openalex.org/I2802476451","display_name":"Wellcome Sanger Institute","ror":"https://ror.org/05cy4wa09","country_code":"GB","type":"nonprofit","lineage":["https://openalex.org/I2802476451","https://openalex.org/I87048295"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Shuang Li","raw_affiliation_strings":["Cambridge Stem Cell Institute and Department of Medicine, University of Cambridge, Cambridge, UK","Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK"],"affiliations":[{"raw_affiliation_string":"Cambridge Stem Cell Institute and Department of Medicine, University of Cambridge, Cambridge, UK","institution_ids":["https://openalex.org/I21196054"]},{"raw_affiliation_string":"Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK","institution_ids":["https://openalex.org/I2802476451"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5120517700","display_name":"Malte L\u00fccken","orcid":null},"institutions":[{"id":"https://openalex.org/I3018134672","display_name":"Helmholtz Zentrum M\u00fcnchen","ror":"https://ror.org/00cfam450","country_code":"DE","type":"facility","lineage":["https://openalex.org/I1305996414","https://openalex.org/I3018134672"]},{"id":"https://openalex.org/I4210129183","display_name":"German Center for Lung Research","ror":"https://ror.org/03dx11k66","country_code":"DE","type":"facility","lineage":["https://openalex.org/I4210129183","https://openalex.org/I4405256427"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Malte L\u00fccken","raw_affiliation_strings":["Institute of Computational Biology, Helmholtz Munich, Neuherberg, Germany","Institute of Lung Health and Immunity, Helmholtz Munich, Member of the German Center for Lung Research (DZL), Munich, Germany"],"affiliations":[{"raw_affiliation_string":"Institute of Computational Biology, Helmholtz Munich, Neuherberg, Germany","institution_ids":["https://openalex.org/I3018134672"]},{"raw_affiliation_string":"Institute of Lung Health and Immunity, Helmholtz Munich, Member of the German Center for Lung Research (DZL), Munich, Germany","institution_ids":["https://openalex.org/I4210129183"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5104607587","display_name":"J C Marioni","orcid":null},"institutions":[{"id":"https://openalex.org/I1303153112","display_name":"European Bioinformatics Institute","ror":"https://ror.org/02catss52","country_code":"GB","type":"facility","lineage":["https://openalex.org/I1303153112","https://openalex.org/I4210138560"]},{"id":"https://openalex.org/I2802476451","display_name":"Wellcome Sanger Institute","ror":"https://ror.org/05cy4wa09","country_code":"GB","type":"nonprofit","lineage":["https://openalex.org/I2802476451","https://openalex.org/I87048295"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"John C. Marioni","raw_affiliation_strings":["European Molecular Biology Laboratory European Bioinformatics Institute, Hinxton, Cambridge, UK","Genentech, South San Francisco, CA, USA","Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK"],"affiliations":[{"raw_affiliation_string":"European Molecular Biology Laboratory European Bioinformatics Institute, Hinxton, Cambridge, UK","institution_ids":["https://openalex.org/I1303153112"]},{"raw_affiliation_string":"Genentech, South San Francisco, CA, USA","institution_ids":[]},{"raw_affiliation_string":"Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK","institution_ids":["https://openalex.org/I2802476451"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5048955201","display_name":"Sarah Teichmann","orcid":null},"institutions":[{"id":"https://openalex.org/I109736498","display_name":"Canadian Institute for Advanced Research","ror":"https://ror.org/01sdtdd95","country_code":"CA","type":"facility","lineage":["https://openalex.org/I109736498"]},{"id":"https://openalex.org/I21196054","display_name":"Wellcome/MRC Cambridge Stem Cell Institute","ror":"https://ror.org/05nz0zp31","country_code":"GB","type":"facility","lineage":["https://openalex.org/I21196054","https://openalex.org/I241749","https://openalex.org/I4210087105","https://openalex.org/I87048295","https://openalex.org/I90344618"]}],"countries":["CA","GB"],"is_corresponding":false,"raw_author_name":"Sarah A. Teichmann","raw_affiliation_strings":["CIFAR MacMillan Multi-scale Human Programme, CIFAR, Toronto, Ontario, Canada","Cambridge Stem Cell Institute and Department of Medicine, University of Cambridge, Cambridge, UK"],"affiliations":[{"raw_affiliation_string":"CIFAR MacMillan Multi-scale Human Programme, CIFAR, Toronto, Ontario, Canada","institution_ids":["https://openalex.org/I109736498"]},{"raw_affiliation_string":"Cambridge Stem Cell Institute and Department of Medicine, University of Cambridge, Cambridge, UK","institution_ids":["https://openalex.org/I21196054"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5100688266","display_name":"Peng He","orcid":"https://orcid.org/0000-0002-2457-3554"},"institutions":[{"id":"https://openalex.org/I180670191","display_name":"University of California, San Francisco","ror":"https://ror.org/043mz5j54","country_code":"US","type":"education","lineage":["https://openalex.org/I180670191"]},{"id":"https://openalex.org/I76766440","display_name":"University of San Francisco","ror":"https://ror.org/029m7xn54","country_code":"US","type":"education","lineage":["https://openalex.org/I76766440"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Peng He","raw_affiliation_strings":["Bakar ImmunoX Initiative, University of California, San Francisco, San Francisco, CA, USA. peng.he@ucsf.edu","Department of Pathology, University of California, San Francisco, San Francisco, CA, USA. peng.he@ucsf.edu"],"affiliations":[{"raw_affiliation_string":"Bakar ImmunoX Initiative, University of California, San Francisco, San Francisco, CA, USA. peng.he@ucsf.edu","institution_ids":["https://openalex.org/I76766440"]},{"raw_affiliation_string":"Department of Pathology, University of California, San Francisco, San Francisco, CA, USA. peng.he@ucsf.edu","institution_ids":["https://openalex.org/I180670191","https://openalex.org/I76766440"]}]}],"institutions":[],"countries_distinct_count":4,"institutions_distinct_count":5,"corresponding_author_ids":["https://openalex.org/A5100688266"],"corresponding_institution_ids":["https://openalex.org/I180670191","https://openalex.org/I76766440"],"apc_list":{"value":9750,"currency":"EUR","value_usd":11690},"apc_paid":null,"fwci":30.4237,"has_fulltext":false,"cited_by_count":1,"citation_normalized_percentile":{"value":0.99357974,"is_in_top_1_percent":true,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":97,"max":99},"biblio":{"volume":"6","issue":"2","first_page":"123","last_page":"133"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11289","display_name":"Single-cell and spatial transcriptomics","score":0.9991999864578247,"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/T11289","display_name":"Single-cell and spatial transcriptomics","score":0.9991999864578247,"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/T12859","display_name":"Cell Image Analysis Techniques","score":0.00019999999494757503,"subfield":{"id":"https://openalex.org/subfields/1304","display_name":"Biophysics"},"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":0.0,"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/data-integration","display_name":"Data integration","score":0.5616999864578247},{"id":"https://openalex.org/keywords/transcriptome","display_name":"Transcriptome","score":0.3353999853134155},{"id":"https://openalex.org/keywords/precision-medicine","display_name":"Precision medicine","score":0.2786000072956085},{"id":"https://openalex.org/keywords/noisy-data","display_name":"Noisy data","score":0.26969999074935913}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6129000186920166},{"id":"https://openalex.org/C72634772","wikidata":"https://www.wikidata.org/wiki/Q386824","display_name":"Data integration","level":2,"score":0.5616999864578247},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.42399999499320984},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.39320001006126404},{"id":"https://openalex.org/C2522767166","wikidata":"https://www.wikidata.org/wiki/Q2374463","display_name":"Data science","level":1,"score":0.35510000586509705},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.3537999987602234},{"id":"https://openalex.org/C162317418","wikidata":"https://www.wikidata.org/wiki/Q252857","display_name":"Transcriptome","level":4,"score":0.3353999853134155},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.29910001158714294},{"id":"https://openalex.org/C163763905","wikidata":"https://www.wikidata.org/wiki/Q17075943","display_name":"Precision medicine","level":2,"score":0.2786000072956085},{"id":"https://openalex.org/C2781170535","wikidata":"https://www.wikidata.org/wiki/Q30587856","display_name":"Noisy data","level":2,"score":0.26969999074935913},{"id":"https://openalex.org/C189206191","wikidata":"https://www.wikidata.org/wiki/Q222046","display_name":"Genomics","level":4,"score":0.25459998846054077},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.2515999972820282}],"mesh":[],"locations_count":2,"locations":[{"id":"doi:10.1038/s43588-025-00943-1","is_oa":false,"landing_page_url":"https://doi.org/10.1038/s43588-025-00943-1","pdf_url":null,"source":{"id":"https://openalex.org/S4210228084","display_name":"Nature Computational Science","issn_l":"2662-8457","issn":["2662-8457"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319908","host_organization_name":"Nature Portfolio","host_organization_lineage":["https://openalex.org/P4310319908","https://openalex.org/P4310319965"],"host_organization_lineage_names":["Nature Portfolio","Springer Nature"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Nature Computational Science","raw_type":"journal-article"},{"id":"pmid:41699077","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/41699077","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":"Nature computational science","raw_type":null}],"best_oa_location":null,"sustainable_development_goals":[{"id":"https://metadata.un.org/sdg/9","display_name":"Industry, innovation and infrastructure","score":0.526141345500946}],"awards":[],"funders":[],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":105,"referenced_works":["https://openalex.org/W836672374","https://openalex.org/W2010653277","https://openalex.org/W2025828346","https://openalex.org/W2096192437","https://openalex.org/W2107665951","https://openalex.org/W2114104545","https://openalex.org/W2146512944","https://openalex.org/W2332292689","https://openalex.org/W2343956310","https://openalex.org/W2473258837","https://openalex.org/W2753908609","https://openalex.org/W2762506555","https://openalex.org/W2783644856","https://openalex.org/W2794521141","https://openalex.org/W2901677030","https://openalex.org/W2906625258","https://openalex.org/W2907514116","https://openalex.org/W2942108345","https://openalex.org/W2942880491","https://openalex.org/W2948469692","https://openalex.org/W2949177718","https://openalex.org/W2949237386","https://openalex.org/W2950891712","https://openalex.org/W2951444558","https://openalex.org/W2965552103","https://openalex.org/W2967177832","https://openalex.org/W2968352143","https://openalex.org/W2978541146","https://openalex.org/W2980147288","https://openalex.org/W2984472267","https://openalex.org/W2997280954","https://openalex.org/W3000145506","https://openalex.org/W3002417351","https://openalex.org/W3008278692","https://openalex.org/W3010766518","https://openalex.org/W3019420398","https://openalex.org/W3021272327","https://openalex.org/W3047392293","https://openalex.org/W3078409957","https://openalex.org/W3091491962","https://openalex.org/W3101697142","https://openalex.org/W3113268000","https://openalex.org/W3114078084","https://openalex.org/W3115409560","https://openalex.org/W3117464799","https://openalex.org/W3121168830","https://openalex.org/W3126492421","https://openalex.org/W3134779741","https://openalex.org/W3164156820","https://openalex.org/W3164852867","https://openalex.org/W3173802674","https://openalex.org/W3196650609","https://openalex.org/W3203404644","https://openalex.org/W3203496375","https://openalex.org/W3215181016","https://openalex.org/W4200444229","https://openalex.org/W4205876080","https://openalex.org/W4225598893","https://openalex.org/W4225981439","https://openalex.org/W4280596398","https://openalex.org/W4297094730","https://openalex.org/W4297243391","https://openalex.org/W4307763266","https://openalex.org/W4312018959","https://openalex.org/W4312210380","https://openalex.org/W4328051841","https://openalex.org/W4362521490","https://openalex.org/W4363673883","https://openalex.org/W4378838672","https://openalex.org/W4379879135","https://openalex.org/W4380369163","https://openalex.org/W4381164815","https://openalex.org/W4385638791","https://openalex.org/W4386553577","https://openalex.org/W4387451658","https://openalex.org/W4387569894","https://openalex.org/W4387970385","https://openalex.org/W4389132297","https://openalex.org/W4389136680","https://openalex.org/W4389373718","https://openalex.org/W4390064086","https://openalex.org/W4390880427","https://openalex.org/W4391349656","https://openalex.org/W4392168151","https://openalex.org/W4392356342","https://openalex.org/W4396780660","https://openalex.org/W4398239554","https://openalex.org/W4399387478","https://openalex.org/W4403174218","https://openalex.org/W4404170740","https://openalex.org/W4404566628","https://openalex.org/W4405385270","https://openalex.org/W4405828955","https://openalex.org/W4406108922","https://openalex.org/W4408413441","https://openalex.org/W4409484936","https://openalex.org/W4409566559","https://openalex.org/W4410521040","https://openalex.org/W4411001788","https://openalex.org/W4411111057","https://openalex.org/W4411217022","https://openalex.org/W4411709724","https://openalex.org/W4412150788","https://openalex.org/W4415101863","https://openalex.org/W7118188289"],"related_works":[],"abstract_inverted_index":null,"counts_by_year":[{"year":2026,"cited_by_count":1}],"updated_date":"2026-02-26T06:29:33.603293","created_date":"2026-02-17T00:00:00"}
