{"id":"https://openalex.org/W2950017555","doi":"https://doi.org/10.1186/s12918-019-0690-2","title":"Ultrafast clustering of single-cell flow cytometry data using FlowGrid","display_name":"Ultrafast clustering of single-cell flow cytometry data using FlowGrid","publication_year":2019,"publication_date":"2019-04-01","ids":{"openalex":"https://openalex.org/W2950017555","doi":"https://doi.org/10.1186/s12918-019-0690-2","mag":"2950017555","pmid":"https://pubmed.ncbi.nlm.nih.gov/30953498"},"language":"en","primary_location":{"id":"doi:10.1186/s12918-019-0690-2","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12918-019-0690-2","pdf_url":"https://bmcsystbiol.biomedcentral.com/track/pdf/10.1186/s12918-019-0690-2","source":{"id":"https://openalex.org/S92363890","display_name":"BMC Systems Biology","issn_l":"1752-0509","issn":["1752-0509"],"is_oa":true,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319900","host_organization_name":"Springer Science+Business Media","host_organization_lineage":["https://openalex.org/P4310319900","https://openalex.org/P4310319965"],"host_organization_lineage_names":["Springer Science+Business Media","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Systems Biology","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"diamond","oa_url":"https://bmcsystbiol.biomedcentral.com/track/pdf/10.1186/s12918-019-0690-2","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5035543778","display_name":"Xiaoxin Ye","orcid":"https://orcid.org/0009-0005-1795-9175"},"institutions":[{"id":"https://openalex.org/I19514445","display_name":"Victor Chang Cardiac Research Institute","ror":"https://ror.org/03trvqr13","country_code":"AU","type":"funder","lineage":["https://openalex.org/I19514445"]},{"id":"https://openalex.org/I31746571","display_name":"UNSW Sydney","ror":"https://ror.org/03r8z3t63","country_code":"AU","type":"education","lineage":["https://openalex.org/I31746571"]}],"countries":["AU"],"is_corresponding":true,"raw_author_name":"Xiaoxin Ye","raw_affiliation_strings":["University of New South Wales, Sydney, Australia","Victor Chang Cardiac Research Institute, Sydney, Australia"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"University of New South Wales, Sydney, Australia","institution_ids":["https://openalex.org/I31746571"]},{"raw_affiliation_string":"Victor Chang Cardiac Research Institute, Sydney, Australia","institution_ids":["https://openalex.org/I19514445"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5028008500","display_name":"Joshua W. K. Ho","orcid":"https://orcid.org/0000-0003-2331-7011"},"institutions":[{"id":"https://openalex.org/I19514445","display_name":"Victor Chang Cardiac Research Institute","ror":"https://ror.org/03trvqr13","country_code":"AU","type":"funder","lineage":["https://openalex.org/I19514445"]}],"countries":["AU"],"is_corresponding":false,"raw_author_name":"Joshua W. K. Ho","raw_affiliation_strings":["School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong. jwkho@hku.hk","University of New South Wales, Sydney, Australia. jwkho@hku.hk","Victor Chang Cardiac Research Institute, Sydney, Australia. jwkho@hku.hk","Victor Chang Cardiac Research Institute, Sydney, Australia"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong. jwkho@hku.hk","institution_ids":[]},{"raw_affiliation_string":"University of New South Wales, Sydney, Australia. jwkho@hku.hk","institution_ids":[]},{"raw_affiliation_string":"Victor Chang Cardiac Research Institute, Sydney, Australia. jwkho@hku.hk","institution_ids":[]},{"raw_affiliation_string":"Victor Chang Cardiac Research Institute, Sydney, Australia","institution_ids":["https://openalex.org/I19514445"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5035543778"],"corresponding_institution_ids":["https://openalex.org/I19514445","https://openalex.org/I31746571"],"apc_list":null,"apc_paid":null,"fwci":1.9659,"has_fulltext":true,"cited_by_count":40,"citation_normalized_percentile":{"value":0.86860548,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":94,"max":99},"biblio":{"volume":"13","issue":"S2","first_page":"35","last_page":"35"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11289","display_name":"Single-cell and spatial transcriptomics","score":0.9779000282287598,"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":0.9779000282287598,"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":0.013100000098347664,"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":0.0010000000474974513,"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/cluster-analysis","display_name":"Cluster analysis","score":0.8640574216842651},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.765260636806488},{"id":"https://openalex.org/keywords/mass-cytometry","display_name":"Mass cytometry","score":0.6121231317520142},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.538274347782135},{"id":"https://openalex.org/keywords/scalability","display_name":"Scalability","score":0.5223042368888855},{"id":"https://openalex.org/keywords/python","display_name":"Python (programming language)","score":0.5156823396682739},{"id":"https://openalex.org/keywords/population","display_name":"Population","score":0.5101049542427063},{"id":"https://openalex.org/keywords/dbscan","display_name":"DBSCAN","score":0.42435771226882935},{"id":"https://openalex.org/keywords/correlation-clustering","display_name":"Correlation clustering","score":0.4016456604003906},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.38750314712524414},{"id":"https://openalex.org/keywords/cure-data-clustering-algorithm","display_name":"CURE data clustering algorithm","score":0.3448665142059326},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.2270784080028534},{"id":"https://openalex.org/keywords/database","display_name":"Database","score":0.16820228099822998},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.10837754607200623}],"concepts":[{"id":"https://openalex.org/C73555534","wikidata":"https://www.wikidata.org/wiki/Q622825","display_name":"Cluster analysis","level":2,"score":0.8640574216842651},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.765260636806488},{"id":"https://openalex.org/C2778015335","wikidata":"https://www.wikidata.org/wiki/Q17051163","display_name":"Mass cytometry","level":4,"score":0.6121231317520142},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.538274347782135},{"id":"https://openalex.org/C48044578","wikidata":"https://www.wikidata.org/wiki/Q727490","display_name":"Scalability","level":2,"score":0.5223042368888855},{"id":"https://openalex.org/C519991488","wikidata":"https://www.wikidata.org/wiki/Q28865","display_name":"Python (programming language)","level":2,"score":0.5156823396682739},{"id":"https://openalex.org/C2908647359","wikidata":"https://www.wikidata.org/wiki/Q2625603","display_name":"Population","level":2,"score":0.5101049542427063},{"id":"https://openalex.org/C46576248","wikidata":"https://www.wikidata.org/wiki/Q1114630","display_name":"DBSCAN","level":5,"score":0.42435771226882935},{"id":"https://openalex.org/C94641424","wikidata":"https://www.wikidata.org/wiki/Q5172845","display_name":"Correlation clustering","level":3,"score":0.4016456604003906},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.38750314712524414},{"id":"https://openalex.org/C33704608","wikidata":"https://www.wikidata.org/wiki/Q5014717","display_name":"CURE data clustering algorithm","level":4,"score":0.3448665142059326},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.2270784080028534},{"id":"https://openalex.org/C77088390","wikidata":"https://www.wikidata.org/wiki/Q8513","display_name":"Database","level":1,"score":0.16820228099822998},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.10837754607200623},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.0},{"id":"https://openalex.org/C149923435","wikidata":"https://www.wikidata.org/wiki/Q37732","display_name":"Demography","level":1,"score":0.0},{"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/C144024400","wikidata":"https://www.wikidata.org/wiki/Q21201","display_name":"Sociology","level":0,"score":0.0},{"id":"https://openalex.org/C127716648","wikidata":"https://www.wikidata.org/wiki/Q104053","display_name":"Phenotype","level":3,"score":0.0},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.0}],"mesh":[{"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":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D002452","descriptor_name":"Cell Count","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D002452","descriptor_name":"Cell Count","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D002452","descriptor_name":"Cell Count","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D005434","descriptor_name":"Flow Cytometry","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D005434","descriptor_name":"Flow Cytometry","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D005434","descriptor_name":"Flow Cytometry","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D013997","descriptor_name":"Time Factors","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D013997","descriptor_name":"Time Factors","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D013997","descriptor_name":"Time Factors","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016000","descriptor_name":"Cluster Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016000","descriptor_name":"Cluster Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016000","descriptor_name":"Cluster Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D059010","descriptor_name":"Single-Cell Analysis","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D059010","descriptor_name":"Single-Cell Analysis","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D059010","descriptor_name":"Single-Cell Analysis","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false}],"locations_count":4,"locations":[{"id":"doi:10.1186/s12918-019-0690-2","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12918-019-0690-2","pdf_url":"https://bmcsystbiol.biomedcentral.com/track/pdf/10.1186/s12918-019-0690-2","source":{"id":"https://openalex.org/S92363890","display_name":"BMC Systems Biology","issn_l":"1752-0509","issn":["1752-0509"],"is_oa":true,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319900","host_organization_name":"Springer Science+Business Media","host_organization_lineage":["https://openalex.org/P4310319900","https://openalex.org/P4310319965"],"host_organization_lineage_names":["Springer Science+Business Media","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Systems Biology","raw_type":"journal-article"},{"id":"pmid:30953498","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/30953498","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":"BMC systems biology","raw_type":null},{"id":"pmh:oai:doaj.org/article:90f8f776a4e049e89acfa7765c1bb83c","is_oa":false,"landing_page_url":"https://doaj.org/article/90f8f776a4e049e89acfa7765c1bb83c","pdf_url":null,"source":{"id":"https://openalex.org/S4306401280","display_name":"DOAJ (DOAJ: Directory of Open Access Journals)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"BMC Systems Biology, Vol 13, Iss S2, Pp 1-8 (2019)","raw_type":"article"},{"id":"pmh:oai:europepmc.org:5447091","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/6449887","pdf_url":null,"source":{"id":"https://openalex.org/S4306400806","display_name":"Europe PMC (PubMed Central)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1303153112","host_organization_name":"European Bioinformatics Institute","host_organization_lineage":["https://openalex.org/I1303153112"],"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":null,"raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1186/s12918-019-0690-2","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12918-019-0690-2","pdf_url":"https://bmcsystbiol.biomedcentral.com/track/pdf/10.1186/s12918-019-0690-2","source":{"id":"https://openalex.org/S92363890","display_name":"BMC Systems Biology","issn_l":"1752-0509","issn":["1752-0509"],"is_oa":true,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319900","host_organization_name":"Springer Science+Business Media","host_organization_lineage":["https://openalex.org/P4310319900","https://openalex.org/P4310319965"],"host_organization_lineage_names":["Springer Science+Business Media","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Systems Biology","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G5208258750","display_name":null,"funder_award_id":"1105271","funder_id":"https://openalex.org/F4320334705","funder_display_name":"National Health and Medical Research Council"}],"funders":[{"id":"https://openalex.org/F4320309614","display_name":"Victor Chang Cardiac Research Institute","ror":"https://ror.org/03trvqr13"},{"id":"https://openalex.org/F4320325396","display_name":"NSW Ministry of Health","ror":null},{"id":"https://openalex.org/F4320334626","display_name":"Medical Research Council","ror":"https://ror.org/03x94j517"},{"id":"https://openalex.org/F4320334705","display_name":"National Health and Medical Research Council","ror":"https://ror.org/011kf5r70"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2950017555.pdf","grobid_xml":"https://content.openalex.org/works/W2950017555.grobid-xml"},"referenced_works_count":11,"referenced_works":["https://openalex.org/W1673310716","https://openalex.org/W1815640012","https://openalex.org/W1989838792","https://openalex.org/W1993835819","https://openalex.org/W2101038583","https://openalex.org/W2112493011","https://openalex.org/W2238214435","https://openalex.org/W2461073387","https://openalex.org/W2761095749","https://openalex.org/W2951566836","https://openalex.org/W4235169531"],"related_works":["https://openalex.org/W2394193399","https://openalex.org/W3134385809","https://openalex.org/W2559422900","https://openalex.org/W2392255773","https://openalex.org/W2054669762","https://openalex.org/W2387373525","https://openalex.org/W2809859387","https://openalex.org/W2353158678","https://openalex.org/W2604015980","https://openalex.org/W2377732725"],"abstract_inverted_index":{"BACKGROUND:":[0],"Flow":[1],"cytometry":[2,217],"is":[3,32,57,60,122,133,174,208,222],"a":[4,33,99,178,182],"popular":[5],"technology":[6],"for":[7,36,63,213],"quantitative":[8],"single-cell":[9,215],"profiling":[10],"of":[11,19,21,28,79,107,115,144,151,185],"cell":[12,22,38,42,52],"surface":[13,23],"markers.":[14],"It":[15,31],"enables":[16],"expression":[17],"measurement":[18],"tens":[20],"protein":[24],"markers":[25],"in":[26,124,189],"millions":[27],"single":[29],"cells.":[30,94,145],"powerful":[34],"tool":[35],"discovering":[37],"sub-populations":[39],"and":[40,59,136,158],"quantifying":[41],"population":[43],"heterogeneity.":[44],"Traditionally,":[45],"scientists":[46],"use":[47],"manual":[48],"gating":[49],"to":[50,73,84,141,176],"identify":[51],"types,":[53],"but":[54,77,166],"the":[55,105,113,142,149],"process":[56],"subjective":[58],"not":[61,82],"effective":[62],"large":[64,86,214],"multidimensional":[65],"data.":[66,218],"Many":[67],"clustering":[68,101,109,120,156,164,179,211],"algorithms":[69,196],"have":[70,147],"been":[71],"developed":[72],"analyse":[74],"these":[75],"data":[76,87,183],"most":[78],"them":[80],"are":[81],"scalable":[83],"very":[85],"sets":[88],"with":[89,112,139,167],"more":[90,198],"than":[91,191,199],"ten":[92],"million":[93,187],"RESULTS:":[95],"Here,":[96],"we":[97],"present":[98],"new":[100,119],"algorithm":[102,110,121,212],"that":[103,160],"combines":[104],"advantages":[106],"density-based":[108],"DBSCAN":[111],"scalability":[114],"grid-based":[116],"clustering.":[117],"This":[118],"implemented":[123],"python":[125],"as":[126],"an":[127,209],"open":[128],"source":[129,220],"package,":[130],"FlowGrid.":[131],"FlowGrid":[132,152,161,173,207],"memory":[134],"efficient":[135],"scales":[137],"linearly":[138],"respect":[140],"number":[143],"We":[146],"evaluated":[148],"performance":[150],"against":[153],"other":[154,195],"state-of-the-art":[155],"programs":[157],"found":[159],"produces":[162],"similar":[163],"results":[165],"substantially":[168],"less":[169,190],"time.":[170],"For":[171],"example,":[172],"able":[175],"complete":[177],"task":[180],"on":[181],"set":[184],"23.6":[186],"cells":[188],"12":[192],"seconds,":[193],"while":[194],"take":[197],"500":[200],"seconds":[201],"or":[202],"get":[203],"into":[204],"error.":[205],"CONCLUSIONS:":[206],"ultrafast":[210],"flow":[216],"The":[219],"code":[221],"available":[223],"at":[224],"https://github.com/VCCRI/FlowGrid":[225],".":[226]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2025,"cited_by_count":3},{"year":2024,"cited_by_count":7},{"year":2023,"cited_by_count":6},{"year":2022,"cited_by_count":5},{"year":2021,"cited_by_count":9},{"year":2020,"cited_by_count":7},{"year":2019,"cited_by_count":2}],"updated_date":"2026-05-06T08:25:59.206177","created_date":"2025-10-10T00:00:00"}