{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,11]],"date-time":"2026-04-11T16:51:16Z","timestamp":1775926276021,"version":"3.50.1"},"reference-count":7,"publisher":"Oxford University Press (OUP)","issue":"23","license":[{"start":{"date-parts":[[2018,5,29]],"date-time":"2018-05-29T00:00:00Z","timestamp":1527552000000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/journals\/pages\/open_access\/funder_policies\/chorus\/standard_publication_model"}],"funder":[{"name":"Ann Schreiber Mentored Investigator Award"},{"DOI":"10.13039\/100001282","name":"Ovarian Cancer Research Fund","doi-asserted-by":"publisher","award":["OCRF 292495"],"award-info":[{"award-number":["OCRF 292495"]}],"id":[{"id":"10.13039\/100001282","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100000024","name":"Canadian Institute of Health Research","doi-asserted-by":"crossref","id":[{"id":"10.13039\/501100000024","id-type":"DOI","asserted-by":"crossref"}]},{"DOI":"10.13039\/501100000024","name":"CIHR","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100000024","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Postdoctoral Fellowship","award":["CIHR 321510"],"award-info":[{"award-number":["CIHR 321510"]}]},{"name":"International Society for Advancement of Cytometry Scholarship"},{"name":"Damon Runyon Cancer Research Foundation Postdoctoral Fellowship","award":["DRG 2190-14"],"award-info":[{"award-number":["DRG 2190-14"]}]},{"name":"March of Dimes Prematurity Research Center at Stanford University"},{"name":"Gates Foundations"},{"name":"Department of Anesthesiology, Perioperative and Pain Medicine"},{"DOI":"10.13039\/100005492","name":"Stanford University","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100005492","id-type":"DOI","asserted-by":"publisher"}]},{"name":"National Institute of Health","award":["T32GM007276"],"award-info":[{"award-number":["T32GM007276"]}]},{"DOI":"10.13039\/100000002","name":"NIH","doi-asserted-by":"publisher","award":["0158GKB065"],"award-info":[{"award-number":["0158GKB065"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000002","name":"NIH","doi-asserted-by":"publisher","award":["1R01CA130826"],"award-info":[{"award-number":["1R01CA130826"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000002","name":"NIH","doi-asserted-by":"publisher","award":["5U54CA143907"],"award-info":[{"award-number":["5U54CA143907"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000002","name":"NIH","doi-asserted-by":"publisher","award":["HHSN272200700038C"],"award-info":[{"award-number":["HHSN272200700038C"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000002","name":"NIH","doi-asserted-by":"publisher","award":["N01-HV-00242"],"award-info":[{"award-number":["N01-HV-00242"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000002","name":"NIH","doi-asserted-by":"publisher","award":["41000411217"],"award-info":[{"award-number":["41000411217"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000002","name":"NIH","doi-asserted-by":"publisher","award":["5-24927"],"award-info":[{"award-number":["5-24927"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000002","name":"NIH","doi-asserted-by":"publisher","award":["P01 CA034233-22A1"],"award-info":[{"award-number":["P01 CA034233-22A1"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000002","name":"NIH","doi-asserted-by":"publisher","award":["P01 CA034233-22A1"],"award-info":[{"award-number":["P01 CA034233-22A1"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000002","name":"NIH","doi-asserted-by":"publisher","award":["PN2EY018228"],"award-info":[{"award-number":["PN2EY018228"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000002","name":"NIH","doi-asserted-by":"publisher","award":["RFA CA 09-009"],"award-info":[{"award-number":["RFA CA 09-009"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000002","name":"NIH","doi-asserted-by":"publisher","award":["RFA CA 09-011"],"award-info":[{"award-number":["RFA CA 09-011"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000002","name":"NIH","doi-asserted-by":"publisher","award":["U19 AI057229"],"award-info":[{"award-number":["U19 AI057229"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000002","name":"NIH","doi-asserted-by":"publisher","award":["U54CA149145"],"award-info":[{"award-number":["U54CA149145"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000900","name":"California Institute for Regenerative Medicine","doi-asserted-by":"publisher","award":["DR1-01477"],"award-info":[{"award-number":["DR1-01477"]}],"id":[{"id":"10.13039\/100000900","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000900","name":"California Institute for Regenerative Medicine","doi-asserted-by":"publisher","award":["RB2-01592"],"award-info":[{"award-number":["RB2-01592"]}],"id":[{"id":"10.13039\/100000900","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100000780","name":"European Commission","doi-asserted-by":"publisher","award":["HEALTH.2010.1.2-1"],"award-info":[{"award-number":["HEALTH.2010.1.2-1"]}],"id":[{"id":"10.13039\/501100000780","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000038","name":"FDA","doi-asserted-by":"publisher","award":["HHSF223201210194C"],"award-info":[{"award-number":["HHSF223201210194C"]}],"id":[{"id":"10.13039\/100000038","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000038","name":"FDA","doi-asserted-by":"publisher","award":["BAA-12-00118"],"award-info":[{"award-number":["BAA-12-00118"]}],"id":[{"id":"10.13039\/100000038","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100006535","name":"Entertainment Industry Foundation","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100006535","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000002","name":"NIH","doi-asserted-by":"publisher","award":["1R33CA183692-01"],"award-info":[{"award-number":["1R33CA183692-01"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100008221","name":"Cure Starts Now Foundation","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100008221","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Terry Fox Foundation Program Project","award":["TFF 122869"],"award-info":[{"award-number":["TFF 122869"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2018,12,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Motivation<\/jats:title>\n                  <jats:p>High-parameter single-cell technologies can reveal novel cell populations of interest, but studying or validating these populations using lower-parameter methods remains challenging.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Results<\/jats:title>\n                  <jats:p>Here, we present GateFinder, an algorithm that enriches high-dimensional cell types with simple, stepwise polygon gates requiring only two markers at a time. A series of case studies of complex cell types illustrates how simplified enrichment strategies can enable more efficient assays, reveal novel biomarkers and clarify underlying biology.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>The GateFinder algorithm is implemented as a free and open-source package for BioConductor: https:\/\/nalab.stanford.edu\/gatefinder.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Supplementary information<\/jats:title>\n                  <jats:p>Supplementary data are available at Bioinformatics online.<\/jats:p>\n               <\/jats:sec>","DOI":"10.1093\/bioinformatics\/bty430","type":"journal-article","created":{"date-parts":[[2018,5,23]],"date-time":"2018-05-23T03:17:21Z","timestamp":1527045441000},"page":"4131-4133","source":"Crossref","is-referenced-by-count":23,"title":["GateFinder: projection-based gating strategy optimization for flow and mass cytometry"],"prefix":"10.1093","volume":"34","author":[{"given":"Nima","family":"Aghaeepour","sequence":"first","affiliation":[{"name":"Baxter Laboratory in Stem Cell Biology"},{"name":"Department of Anesthesiology, Stanford University, Stanford, CA, USA"}]},{"given":"Erin F","family":"Simonds","sequence":"additional","affiliation":[{"name":"Department of Neurology, University of California, San Francisco, CA, USA"}]},{"given":"David J H F","family":"Knapp","sequence":"additional","affiliation":[{"name":"Terry Fox Laboratory, British Columbia Cancer Research Center, Vancouver, BC, Canada"}]},{"given":"Robert V","family":"Bruggner","sequence":"additional","affiliation":[{"name":"Baxter Laboratory in Stem Cell Biology"}]},{"given":"Karen","family":"Sachs","sequence":"additional","affiliation":[{"name":"Baxter Laboratory in Stem Cell Biology"}]},{"given":"Anthony","family":"Culos","sequence":"additional","affiliation":[{"name":"Department of Anesthesiology, Stanford University, Stanford, CA, USA"}]},{"given":"Pier Federico","family":"Gherardini","sequence":"additional","affiliation":[{"name":"Baxter Laboratory in Stem Cell Biology"}]},{"given":"Nikolay","family":"Samusik","sequence":"additional","affiliation":[{"name":"Baxter Laboratory in Stem Cell Biology"}]},{"given":"Gabriela K","family":"Fragiadakis","sequence":"additional","affiliation":[{"name":"Baxter Laboratory in Stem Cell Biology"}]},{"given":"Sean C","family":"Bendall","sequence":"additional","affiliation":[{"name":"Baxter Laboratory in Stem Cell Biology"},{"name":"Department of Pathology"}]},{"given":"Brice","family":"Gaudilliere","sequence":"additional","affiliation":[{"name":"Baxter Laboratory in Stem Cell Biology"},{"name":"Department of Anesthesiology, Stanford University, Stanford, CA, USA"}]},{"given":"Martin S","family":"Angst","sequence":"additional","affiliation":[{"name":"Department of Anesthesiology, Stanford University, Stanford, CA, USA"}]},{"given":"Connie J","family":"Eaves","sequence":"additional","affiliation":[{"name":"Terry Fox Laboratory, British Columbia Cancer Research Center, Vancouver, BC, Canada"}]},{"given":"William A","family":"Weiss","sequence":"additional","affiliation":[{"name":"Department of Neurology, University of California, San Francisco, CA, USA"}]},{"given":"Wendy J","family":"Fantl","sequence":"additional","affiliation":[{"name":"Department of Obstetrics and Gynecology, Stanford University, Stanford, CA, USA"}]},{"given":"Garry P","family":"Nolan","sequence":"additional","affiliation":[{"name":"Baxter Laboratory in Stem Cell Biology"}]}],"member":"286","published-online":{"date-parts":[[2018,5,29]]},"reference":[{"key":"2023012712295680200_bty430-B1","doi-asserted-by":"crossref","first-page":"16","DOI":"10.1002\/cyto.a.22732","article-title":"A benchmark for evaluation of algorithms for identification of cellular correlates of clinical outcomes","volume":"89","author":"Aghaeepour","year":"2016","journal-title":"Cytometry A"},{"key":"2023012712295680200_bty430-B2","doi-asserted-by":"crossref","first-page":"559.","DOI":"10.1186\/s12859-017-1977-1","article-title":"Cell type discovery and representation in the era of high-content single cell phenotyping","volume":"18","author":"Bakken","year":"2017","journal-title":"BMC Bioinformatics"},{"key":"2023012712295680200_bty430-B3","doi-asserted-by":"crossref","first-page":"272","DOI":"10.1086\/649430","article-title":"Immunologic and virologic events in early HIV infection predict subsequent rate of progression","volume":"201","author":"Ganesan","year":"2010","journal-title":"J. Infect. Dis"},{"key":"2023012712295680200_bty430-B4","doi-asserted-by":"crossref","first-page":"346","DOI":"10.1002\/cyto.a.22628","article-title":"Single-cell mass cytometry reveals intracellular survival\/proliferative signaling in FLT3-ITD-mutated AML stem\/progenitor cells","volume":"87","author":"Han","year":"2015","journal-title":"Cytometry A"},{"key":"2023012712295680200_bty430-B5","doi-asserted-by":"crossref","first-page":"337","DOI":"10.1016\/j.ccell.2016.05.018","article-title":"Mutant IDH1 downregulates ATM and alters DNA repair and sensitivity to DNA damage independent of TET2","volume":"30","author":"Inoue","year":"2016","journal-title":"Cancer Cell"},{"key":"2023012712295680200_bty430-B6","doi-asserted-by":"crossref","first-page":"449","DOI":"10.1038\/nri.2016.56","article-title":"Computational flow cytometry: helping to make sense of high-dimensional immunology data","volume":"16","author":"Saeys","year":"2016","journal-title":"Nat. Rev. Immunol"},{"key":"2023012712295680200_bty430-B7","doi-asserted-by":"crossref","first-page":"1084","DOI":"10.1002\/cyto.a.23030","article-title":"Comparison of clustering methods for high-dimensional single-cell flow and mass cytometry data","volume":"89","author":"Weber","year":"2016","journal-title":"Cytometry A"}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/34\/23\/4131\/48920696\/bioinformatics_34_23_4131.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/34\/23\/4131\/48920696\/bioinformatics_34_23_4131.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,1,27]],"date-time":"2023-01-27T13:17:41Z","timestamp":1674825461000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/34\/23\/4131\/5021694"}},"subtitle":[],"editor":[{"given":"Jonathan","family":"Wren","sequence":"additional","affiliation":[]}],"short-title":[],"issued":{"date-parts":[[2018,5,29]]},"references-count":7,"journal-issue":{"issue":"23","published-print":{"date-parts":[[2018,12,1]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/bty430","relation":{},"ISSN":["1367-4803","1367-4811"],"issn-type":[{"value":"1367-4803","type":"print"},{"value":"1367-4811","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2018,12,1]]},"published":{"date-parts":[[2018,5,29]]}}}