{"id":"https://openalex.org/W2088592612","doi":"https://doi.org/10.1155/2009/809469","title":"Bridging the Divide between Manual Gating and Bioinformatics with the Bioconductor Package flowFlowJo","display_name":"Bridging the Divide between Manual Gating and Bioinformatics with the Bioconductor Package flowFlowJo","publication_year":2009,"publication_date":"2009-10-07","ids":{"openalex":"https://openalex.org/W2088592612","doi":"https://doi.org/10.1155/2009/809469","mag":"2088592612","pmid":"https://pubmed.ncbi.nlm.nih.gov/19956421"},"language":"en","primary_location":{"id":"doi:10.1155/2009/809469","is_oa":true,"landing_page_url":"https://doi.org/10.1155/2009/809469","pdf_url":"https://downloads.hindawi.com/archive/2009/809469.pdf","source":{"id":"https://openalex.org/S146125958","display_name":"Advances in Bioinformatics","issn_l":"1687-8027","issn":["1687-8027","1687-8035"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319869","host_organization_name":"Hindawi Publishing Corporation","host_organization_lineage":["https://openalex.org/P4310319869"],"host_organization_lineage_names":["Hindawi Publishing Corporation"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Advances in Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","pubmed"],"open_access":{"is_oa":true,"oa_status":"hybrid","oa_url":"https://downloads.hindawi.com/archive/2009/809469.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5078996982","display_name":"John J. Gosink","orcid":"https://orcid.org/0000-0003-0398-0633"},"institutions":[{"id":"https://openalex.org/I1320553840","display_name":"Amgen (United States)","ror":"https://ror.org/03g03ge92","country_code":"US","type":"company","lineage":["https://openalex.org/I1320553840"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"John J. Gosink","raw_affiliation_strings":["Department of Computational Biology, Amgen, 1201 Amgen Court West, Seattle, WA 98119, USA"],"affiliations":[{"raw_affiliation_string":"Department of Computational Biology, Amgen, 1201 Amgen Court West, Seattle, WA 98119, USA","institution_ids":["https://openalex.org/I1320553840"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5113551386","display_name":"Gary Means","orcid":null},"institutions":[{"id":"https://openalex.org/I1320553840","display_name":"Amgen (United States)","ror":"https://ror.org/03g03ge92","country_code":"US","type":"company","lineage":["https://openalex.org/I1320553840"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Gary D. Means","raw_affiliation_strings":["Department of Molecular Sciences, Amgen, 1201 Amgen Court West, Seattle, WA 98119, USA"],"affiliations":[{"raw_affiliation_string":"Department of Molecular Sciences, Amgen, 1201 Amgen Court West, Seattle, WA 98119, USA","institution_ids":["https://openalex.org/I1320553840"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5031718088","display_name":"William A. Rees","orcid":"https://orcid.org/0000-0003-1857-8364"},"institutions":[{"id":"https://openalex.org/I1320553840","display_name":"Amgen (United States)","ror":"https://ror.org/03g03ge92","country_code":"US","type":"company","lineage":["https://openalex.org/I1320553840"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"William A. Rees","raw_affiliation_strings":["Department of Molecular Sciences, Amgen, 1201 Amgen Court West, Seattle, WA 98119, USA"],"affiliations":[{"raw_affiliation_string":"Department of Molecular Sciences, Amgen, 1201 Amgen Court West, Seattle, WA 98119, USA","institution_ids":["https://openalex.org/I1320553840"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5089005621","display_name":"Cheng Su","orcid":"https://orcid.org/0000-0002-8646-2155"},"institutions":[{"id":"https://openalex.org/I1320553840","display_name":"Amgen (United States)","ror":"https://ror.org/03g03ge92","country_code":"US","type":"company","lineage":["https://openalex.org/I1320553840"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Cheng Su","raw_affiliation_strings":["Department of Biostatistics\u2014Medical Sciences, Amgen, 1201 Amgen Court West, Seattle, WA 98119, USA"],"affiliations":[{"raw_affiliation_string":"Department of Biostatistics\u2014Medical Sciences, Amgen, 1201 Amgen Court West, Seattle, WA 98119, USA","institution_ids":["https://openalex.org/I1320553840"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5037593913","display_name":"Hugh Rand","orcid":null},"institutions":[{"id":"https://openalex.org/I1320553840","display_name":"Amgen (United States)","ror":"https://ror.org/03g03ge92","country_code":"US","type":"company","lineage":["https://openalex.org/I1320553840"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Hugh A. Rand","raw_affiliation_strings":["Department of Computational Biology, Amgen, 1201 Amgen Court West, Seattle, WA 98119, USA"],"affiliations":[{"raw_affiliation_string":"Department of Computational Biology, Amgen, 1201 Amgen Court West, Seattle, WA 98119, USA","institution_ids":["https://openalex.org/I1320553840"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":5,"corresponding_author_ids":["https://openalex.org/A5078996982"],"corresponding_institution_ids":["https://openalex.org/I1320553840"],"apc_list":null,"apc_paid":null,"fwci":0.674,"has_fulltext":true,"cited_by_count":6,"citation_normalized_percentile":{"value":0.69662549,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":97},"biblio":{"volume":"2009","issue":null,"first_page":"1","last_page":"8"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11289","display_name":"Single-cell and spatial transcriptomics","score":0.9997000098228455,"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":0.9997000098228455,"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":0.9943000078201294,"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/T10621","display_name":"Gene Regulatory Network Analysis","score":0.988099992275238,"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/bioconductor","display_name":"Bioconductor","score":0.9868289828300476},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.807265043258667},{"id":"https://openalex.org/keywords/r-package","display_name":"R package","score":0.6708639860153198},{"id":"https://openalex.org/keywords/robustness","display_name":"Robustness (evolution)","score":0.6151899099349976},{"id":"https://openalex.org/keywords/gating","display_name":"Gating","score":0.5933343172073364},{"id":"https://openalex.org/keywords/bridging","display_name":"Bridging (networking)","score":0.5160326957702637},{"id":"https://openalex.org/keywords/process","display_name":"Process (computing)","score":0.4846956729888916},{"id":"https://openalex.org/keywords/work-flow","display_name":"Work flow","score":0.47636958956718445},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.4738120138645172},{"id":"https://openalex.org/keywords/raw-data","display_name":"Raw data","score":0.44924068450927734},{"id":"https://openalex.org/keywords/software","display_name":"Software","score":0.42639437317848206},{"id":"https://openalex.org/keywords/software-engineering","display_name":"Software engineering","score":0.35834014415740967},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.13517498970031738},{"id":"https://openalex.org/keywords/industrial-engineering","display_name":"Industrial engineering","score":0.12260812520980835},{"id":"https://openalex.org/keywords/medicine","display_name":"Medicine","score":0.11930897831916809}],"concepts":[{"id":"https://openalex.org/C2779694297","wikidata":"https://www.wikidata.org/wiki/Q2888953","display_name":"Bioconductor","level":3,"score":0.9868289828300476},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.807265043258667},{"id":"https://openalex.org/C2984074130","wikidata":"https://www.wikidata.org/wiki/Q73539779","display_name":"R package","level":2,"score":0.6708639860153198},{"id":"https://openalex.org/C63479239","wikidata":"https://www.wikidata.org/wiki/Q7353546","display_name":"Robustness (evolution)","level":3,"score":0.6151899099349976},{"id":"https://openalex.org/C194544171","wikidata":"https://www.wikidata.org/wiki/Q21105679","display_name":"Gating","level":2,"score":0.5933343172073364},{"id":"https://openalex.org/C174348530","wikidata":"https://www.wikidata.org/wiki/Q188635","display_name":"Bridging (networking)","level":2,"score":0.5160326957702637},{"id":"https://openalex.org/C98045186","wikidata":"https://www.wikidata.org/wiki/Q205663","display_name":"Process (computing)","level":2,"score":0.4846956729888916},{"id":"https://openalex.org/C2985179714","wikidata":"https://www.wikidata.org/wiki/Q627335","display_name":"Work flow","level":2,"score":0.47636958956718445},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.4738120138645172},{"id":"https://openalex.org/C132964779","wikidata":"https://www.wikidata.org/wiki/Q2110223","display_name":"Raw data","level":2,"score":0.44924068450927734},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.42639437317848206},{"id":"https://openalex.org/C115903868","wikidata":"https://www.wikidata.org/wiki/Q80993","display_name":"Software engineering","level":1,"score":0.35834014415740967},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.13517498970031738},{"id":"https://openalex.org/C13736549","wikidata":"https://www.wikidata.org/wiki/Q4489420","display_name":"Industrial engineering","level":1,"score":0.12260812520980835},{"id":"https://openalex.org/C71924100","wikidata":"https://www.wikidata.org/wiki/Q11190","display_name":"Medicine","level":0,"score":0.11930897831916809},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.0},{"id":"https://openalex.org/C42407357","wikidata":"https://www.wikidata.org/wiki/Q521","display_name":"Physiology","level":1,"score":0.0},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.0},{"id":"https://openalex.org/C127413603","wikidata":"https://www.wikidata.org/wiki/Q11023","display_name":"Engineering","level":0,"score":0.0},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.0},{"id":"https://openalex.org/C31258907","wikidata":"https://www.wikidata.org/wiki/Q1301371","display_name":"Computer network","level":1,"score":0.0}],"mesh":[],"locations_count":3,"locations":[{"id":"doi:10.1155/2009/809469","is_oa":true,"landing_page_url":"https://doi.org/10.1155/2009/809469","pdf_url":"https://downloads.hindawi.com/archive/2009/809469.pdf","source":{"id":"https://openalex.org/S146125958","display_name":"Advances in Bioinformatics","issn_l":"1687-8027","issn":["1687-8027","1687-8035"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319869","host_organization_name":"Hindawi Publishing Corporation","host_organization_lineage":["https://openalex.org/P4310319869"],"host_organization_lineage_names":["Hindawi Publishing Corporation"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Advances in Bioinformatics","raw_type":"journal-article"},{"id":"pmid:19956421","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/19956421","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":"Advances in bioinformatics","raw_type":null},{"id":"pmh:oai:pubmedcentral.nih.gov:2775689","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/2775689","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":true,"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":"Adv Bioinformatics","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1155/2009/809469","is_oa":true,"landing_page_url":"https://doi.org/10.1155/2009/809469","pdf_url":"https://downloads.hindawi.com/archive/2009/809469.pdf","source":{"id":"https://openalex.org/S146125958","display_name":"Advances in Bioinformatics","issn_l":"1687-8027","issn":["1687-8027","1687-8035"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319869","host_organization_name":"Hindawi Publishing Corporation","host_organization_lineage":["https://openalex.org/P4310319869"],"host_organization_lineage_names":["Hindawi Publishing Corporation"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Advances in Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[{"score":0.4699999988079071,"display_name":"Industry, innovation and infrastructure","id":"https://metadata.un.org/sdg/9"}],"awards":[],"funders":[{"id":"https://openalex.org/F4320307105","display_name":"Amgen","ror":"https://ror.org/03g03ge92"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2088592612.pdf","grobid_xml":"https://content.openalex.org/works/W2088592612.grobid-xml"},"referenced_works_count":13,"referenced_works":["https://openalex.org/W2009474665","https://openalex.org/W2022710553","https://openalex.org/W2029140107","https://openalex.org/W2034075323","https://openalex.org/W2038482150","https://openalex.org/W2042829929","https://openalex.org/W2047708805","https://openalex.org/W2073307618","https://openalex.org/W2093187991","https://openalex.org/W2104279568","https://openalex.org/W2130167132","https://openalex.org/W2150756255","https://openalex.org/W2154685960"],"related_works":["https://openalex.org/W2982252354","https://openalex.org/W2728564446","https://openalex.org/W3045904767","https://openalex.org/W2161868542","https://openalex.org/W2140163842","https://openalex.org/W3156537409","https://openalex.org/W2747931568","https://openalex.org/W2133055377","https://openalex.org/W2921090651","https://openalex.org/W2287365612"],"abstract_inverted_index":{"In":[0],"flow":[1,33,126],"cytometry,":[2],"different":[3],"cell":[4],"types":[5],"are":[6],"usually":[7],"selected":[8],"or":[9,16],"\"gated\"":[10],"by":[11,110],"a":[12,100,120],"series":[13],"of":[14,20,46,72,137],"1-":[15],"2-dimensional":[17],"geometric":[18],"subsets":[19],"the":[21,44,53,61,70,111,124,138],"measurements":[22],"made":[23],"on":[24],"each":[25],"cell.":[26],"This":[27],"is":[28,38,64],"easily":[29],"accomplished":[30],"in":[31,119,128,140],"commercial":[32,112],"cytometry":[34],"packages":[35,127],"but":[36],"it":[37,142],"difficult":[39],"to":[40,51,69,79],"work":[41,56,116],"computationally":[42],"with":[43,57,117,123],"results":[45,54],"this":[47,95,132],"process.":[48],"The":[49],"ability":[50],"retrieve":[52],"and":[55,60,85,88,115,134],"both":[58],"them":[59,118],"raw":[62],"data":[63,91],"critical;":[65],"our":[66],"experience":[67],"points":[68],"importance":[71],"bioinformatics":[73],"tools":[74],"that":[75,105],"will":[76],"allow":[77],"us":[78],"examine":[80],"gating":[81],"robustness,":[82],"combine":[83],"manual":[84],"automated":[86],"gating,":[87],"perform":[89],"exploratory":[90],"analysis.":[92],"To":[93],"provide":[94],"capability,":[96],"we":[97],"have":[98],"developed":[99],"Bioconductor":[101],"package":[102,113,133],"called":[103],"flowFlowJo":[104],"can":[106,143],"import":[107],"gates":[108],"defined":[109],"FlowJo":[114],"manner":[121],"consistent":[122],"other":[125],"Bioconductor.":[129],"We":[130],"present":[131],"illustrate":[135],"some":[136],"ways":[139],"which":[141],"be":[144],"used.":[145]},"counts_by_year":[{"year":2019,"cited_by_count":1},{"year":2012,"cited_by_count":3}],"updated_date":"2026-04-21T08:09:41.155169","created_date":"2025-10-10T00:00:00"}
