{"id":"https://openalex.org/W2967177832","doi":"https://doi.org/10.1093/bioinformatics/btz625","title":"BBKNN: fast batch alignment of single cell transcriptomes","display_name":"BBKNN: fast batch alignment of single cell transcriptomes","publication_year":2019,"publication_date":"2019-08-08","ids":{"openalex":"https://openalex.org/W2967177832","doi":"https://doi.org/10.1093/bioinformatics/btz625","mag":"2967177832","pmid":"https://pubmed.ncbi.nlm.nih.gov/31400197"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btz625","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btz625","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/36/3/964/32369783/btz625.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"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":"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":"hybrid","oa_url":"https://academic.oup.com/bioinformatics/article-pdf/36/3/964/32369783/btz625.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5090126209","display_name":"Krzysztof Pola\u0144ski","orcid":"https://orcid.org/0000-0002-2586-9576"},"institutions":[{"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":"Krzysztof Pola\u0144ski","raw_affiliation_strings":["Cellular Genetics, Wellcome Sanger Institute , Hinxton, Cambridge CB10 1SA, UK"],"affiliations":[{"raw_affiliation_string":"Cellular Genetics, Wellcome Sanger Institute , Hinxton, Cambridge CB10 1SA, UK","institution_ids":["https://openalex.org/I2802476451"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5088977635","display_name":"Matthew D. Young","orcid":"https://orcid.org/0000-0003-0937-5290"},"institutions":[{"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":"Matthew D Young","raw_affiliation_strings":["Cellular Genetics, Wellcome Sanger Institute , Hinxton, Cambridge CB10 1SA, UK"],"affiliations":[{"raw_affiliation_string":"Cellular Genetics, Wellcome Sanger Institute , Hinxton, Cambridge CB10 1SA, UK","institution_ids":["https://openalex.org/I2802476451"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5047497779","display_name":"Zhichao Miao","orcid":"https://orcid.org/0000-0002-5777-9815"},"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":"Zhichao Miao","raw_affiliation_strings":["Cellular Genetics, Wellcome Sanger Institute , Hinxton, Cambridge CB10 1SA, UK","European Molecular Biology Laboratory, European Bioinformatics Institute , Hinxton, Cambridge CB10 1SD, UK"],"affiliations":[{"raw_affiliation_string":"Cellular Genetics, Wellcome Sanger Institute , Hinxton, Cambridge CB10 1SA, UK","institution_ids":["https://openalex.org/I2802476451"]},{"raw_affiliation_string":"European Molecular Biology Laboratory, European Bioinformatics Institute , Hinxton, Cambridge CB10 1SD, UK","institution_ids":["https://openalex.org/I1303153112"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5105457989","display_name":"Kerstin B. Meyer","orcid":"https://orcid.org/0000-0001-5906-1498"},"institutions":[{"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":"Kerstin B Meyer","raw_affiliation_strings":["Cellular Genetics, Wellcome Sanger Institute , Hinxton, Cambridge CB10 1SA, UK"],"affiliations":[{"raw_affiliation_string":"Cellular Genetics, Wellcome Sanger Institute , Hinxton, Cambridge CB10 1SA, UK","institution_ids":["https://openalex.org/I2802476451"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5028596003","display_name":"Sarah A. Teichmann","orcid":"https://orcid.org/0000-0002-6294-6366"},"institutions":[{"id":"https://openalex.org/I241749","display_name":"University of Cambridge","ror":"https://ror.org/013meh722","country_code":"GB","type":"education","lineage":["https://openalex.org/I241749"]},{"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":true,"raw_author_name":"Sarah A Teichmann","raw_affiliation_strings":["Cellular Genetics, Wellcome Sanger Institute , Hinxton, Cambridge CB10 1SA, UK","Theory of Condensed Matter Group, Cavendish Laboratory/Department of Physics, University of Cambridge , Cambridge CB3 0HE, UK"],"affiliations":[{"raw_affiliation_string":"Cellular Genetics, Wellcome Sanger Institute , Hinxton, Cambridge CB10 1SA, UK","institution_ids":["https://openalex.org/I2802476451"]},{"raw_affiliation_string":"Theory of Condensed Matter Group, Cavendish Laboratory/Department of Physics, University of Cambridge , Cambridge CB3 0HE, UK","institution_ids":["https://openalex.org/I241749"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5101701220","display_name":"Jong-Eun Park","orcid":"https://orcid.org/0000-0002-1687-2423"},"institutions":[{"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":true,"raw_author_name":"Jong-Eun Park","raw_affiliation_strings":["Cellular Genetics, Wellcome Sanger Institute , Hinxton, Cambridge CB10 1SA, UK"],"affiliations":[{"raw_affiliation_string":"Cellular Genetics, Wellcome Sanger Institute , Hinxton, Cambridge CB10 1SA, UK","institution_ids":["https://openalex.org/I2802476451"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":6,"corresponding_author_ids":["https://openalex.org/A5028596003","https://openalex.org/A5101701220"],"corresponding_institution_ids":["https://openalex.org/I241749","https://openalex.org/I2802476451"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":{"value":3618,"currency":"USD","value_usd":3618},"fwci":33.0648,"has_fulltext":false,"cited_by_count":964,"citation_normalized_percentile":{"value":0.99867369,"is_in_top_1_percent":true,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":99,"max":100},"biblio":{"volume":"36","issue":"3","first_page":"964","last_page":"965"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11289","display_name":"Single-cell and spatial transcriptomics","score":1.0,"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"}},"topics":[{"id":"https://openalex.org/T11289","display_name":"Single-cell and spatial transcriptomics","score":1.0,"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"}},{"id":"https://openalex.org/T11313","display_name":"Immune cells in cancer","score":0.9624000191688538,"subfield":{"id":"https://openalex.org/subfields/2403","display_name":"Immunology"},"field":{"id":"https://openalex.org/fields/24","display_name":"Immunology and Microbiology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T10981","display_name":"Cytomegalovirus and herpesvirus research","score":0.9510999917984009,"subfield":{"id":"https://openalex.org/subfields/2713","display_name":"Epidemiology"},"field":{"id":"https://openalex.org/fields/27","display_name":"Medicine"},"domain":{"id":"https://openalex.org/domains/4","display_name":"Health Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.7951910495758057},{"id":"https://openalex.org/keywords/benchmark","display_name":"Benchmark (surveying)","score":0.7466439008712769},{"id":"https://openalex.org/keywords/documentation","display_name":"Documentation","score":0.6590128540992737},{"id":"https://openalex.org/keywords/graph","display_name":"Graph","score":0.5299402475357056},{"id":"https://openalex.org/keywords/data-integration","display_name":"Data integration","score":0.5073680281639099},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.4660220146179199},{"id":"https://openalex.org/keywords/scale","display_name":"Scale (ratio)","score":0.4253968298435211},{"id":"https://openalex.org/keywords/theoretical-computer-science","display_name":"Theoretical computer science","score":0.2522115707397461},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.12538611888885498}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7951910495758057},{"id":"https://openalex.org/C185798385","wikidata":"https://www.wikidata.org/wiki/Q1161707","display_name":"Benchmark (surveying)","level":2,"score":0.7466439008712769},{"id":"https://openalex.org/C56666940","wikidata":"https://www.wikidata.org/wiki/Q788790","display_name":"Documentation","level":2,"score":0.6590128540992737},{"id":"https://openalex.org/C132525143","wikidata":"https://www.wikidata.org/wiki/Q141488","display_name":"Graph","level":2,"score":0.5299402475357056},{"id":"https://openalex.org/C72634772","wikidata":"https://www.wikidata.org/wiki/Q386824","display_name":"Data integration","level":2,"score":0.5073680281639099},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.4660220146179199},{"id":"https://openalex.org/C2778755073","wikidata":"https://www.wikidata.org/wiki/Q10858537","display_name":"Scale (ratio)","level":2,"score":0.4253968298435211},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.2522115707397461},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.12538611888885498},{"id":"https://openalex.org/C205649164","wikidata":"https://www.wikidata.org/wiki/Q1071","display_name":"Geography","level":0,"score":0.0},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.0},{"id":"https://openalex.org/C62520636","wikidata":"https://www.wikidata.org/wiki/Q944","display_name":"Quantum mechanics","level":1,"score":0.0},{"id":"https://openalex.org/C13280743","wikidata":"https://www.wikidata.org/wiki/Q131089","display_name":"Geodesy","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D000073359","descriptor_name":"Exome Sequencing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000073359","descriptor_name":"Exome Sequencing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000073359","descriptor_name":"Exome Sequencing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000081246","descriptor_name":"RNA-Seq","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000081246","descriptor_name":"RNA-Seq","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000081246","descriptor_name":"RNA-Seq","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":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":true},{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D051379","descriptor_name":"Mice","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D051379","descriptor_name":"Mice","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D051379","descriptor_name":"Mice","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D059467","descriptor_name":"Transcriptome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D059467","descriptor_name":"Transcriptome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D059467","descriptor_name":"Transcriptome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":3,"locations":[{"id":"doi:10.1093/bioinformatics/btz625","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btz625","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/36/3/964/32369783/btz625.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"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":"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:31400197","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/31400197","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:9883685","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/9883685","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/btz625","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btz625","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/36/3/964/32369783/btz625.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"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":"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":[{"id":"https://metadata.un.org/sdg/9","score":0.5,"display_name":"Industry, innovation and infrastructure"}],"awards":[{"id":"https://openalex.org/G1335143235","display_name":null,"funder_award_id":"108437/Z/15/Z","funder_id":"https://openalex.org/F4320311904","funder_display_name":"Wellcome Trust"},{"id":"https://openalex.org/G2339430666","display_name":null,"funder_award_id":"211276/Z/18/Z","funder_id":"https://openalex.org/F4320311904","funder_display_name":"Wellcome Trust"}],"funders":[{"id":"https://openalex.org/F4320311904","display_name":"Wellcome Trust","ror":"https://ror.org/029chgv08"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2967177832.pdf","grobid_xml":"https://content.openalex.org/works/W2967177832.grobid-xml"},"referenced_works_count":20,"referenced_works":["https://openalex.org/W1979283544","https://openalex.org/W2023887100","https://openalex.org/W2509957998","https://openalex.org/W2741536364","https://openalex.org/W2788348358","https://openalex.org/W2794480084","https://openalex.org/W2794521141","https://openalex.org/W2794765397","https://openalex.org/W2795687816","https://openalex.org/W2796170779","https://openalex.org/W2800392236","https://openalex.org/W2806983506","https://openalex.org/W2894687190","https://openalex.org/W2897249806","https://openalex.org/W2905317377","https://openalex.org/W2942880491","https://openalex.org/W2949067670","https://openalex.org/W2949177718","https://openalex.org/W2984472267","https://openalex.org/W3106188259"],"related_works":["https://openalex.org/W2618286804","https://openalex.org/W2378211422","https://openalex.org/W2329643025","https://openalex.org/W4321353415","https://openalex.org/W2745001401","https://openalex.org/W2002770077","https://openalex.org/W3131163342","https://openalex.org/W2092256833","https://openalex.org/W2142369114","https://openalex.org/W2361728394"],"abstract_inverted_index":{"Supplementary":[0],"data":[1],"are":[2],"available":[3],"at":[4],"Bioinformatics":[5],"online.":[6]},"counts_by_year":[{"year":2026,"cited_by_count":33},{"year":2025,"cited_by_count":174},{"year":2024,"cited_by_count":220},{"year":2023,"cited_by_count":164},{"year":2022,"cited_by_count":145},{"year":2021,"cited_by_count":137},{"year":2020,"cited_by_count":79},{"year":2019,"cited_by_count":10}],"updated_date":"2026-04-09T08:11:56.329763","created_date":"2025-10-10T00:00:00"}