<?xml version="1.0" encoding="utf-8"?>
<TEI xmlns="http://www.tei-c.org/ns/1.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xmlns:hal="http://hal.archives-ouvertes.fr/" xmlns:gml="http://www.opengis.net/gml/3.3/" xmlns:gmlce="http://www.opengis.net/gml/3.3/ce" version="1.1" xsi:schemaLocation="http://www.tei-c.org/ns/1.0 http://api.archives-ouvertes.fr/documents/aofr-sword.xsd">
  <teiHeader>
    <fileDesc>
      <titleStmt>
        <title>HAL TEI export of hal-03161874v2</title>
      </titleStmt>
      <publicationStmt>
        <distributor>CCSD</distributor>
        <availability status="restricted">
          <licence target="https://creativecommons.org/publicdomain/zero/1.0/">CC0 1.0 - Universal</licence>
        </availability>
        <date when="2026-05-25T04:36:05+02:00"/>
      </publicationStmt>
      <sourceDesc>
        <p part="N">HAL API Platform</p>
      </sourceDesc>
    </fileDesc>
  </teiHeader>
  <text>
    <body>
      <listBibl>
        <biblFull>
          <titleStmt>
            <title xml:lang="en">cytometree: A binary tree algorithm for automatic gating in cytometry analysis</title>
            <author role="aut">
              <persName>
                <forename type="first">Daniel</forename>
                <surname>Commenges</surname>
              </persName>
              <email type="md5">103005b79db5cad1459d2c3e50e1a69d</email>
              <email type="domain">isped.u-bordeaux2.fr</email>
              <idno type="idhal" notation="numeric">838345</idno>
              <idno type="halauthorid" notation="string">129220-838345</idno>
              <affiliation ref="#struct-55677"/>
              <affiliation ref="#struct-219689"/>
              <affiliation ref="#struct-476572"/>
            </author>
            <author role="aut">
              <persName>
                <forename type="first">Chariff</forename>
                <surname>Alkhassim</surname>
              </persName>
              <idno type="halauthorid">1214525-0</idno>
              <affiliation ref="#struct-220073"/>
              <affiliation ref="#struct-219689"/>
              <affiliation ref="#struct-476572"/>
            </author>
            <author role="aut">
              <persName>
                <forename type="first">Raphael</forename>
                <surname>Gottardo</surname>
              </persName>
              <email type="md5">5c1725ce4dfbab3673bebed59a5d0eca</email>
              <email type="domain">fhcrc.org</email>
              <idno type="idhal" notation="numeric">895681</idno>
              <idno type="halauthorid" notation="string">352565-895681</idno>
              <affiliation ref="#struct-41823"/>
            </author>
            <author role="aut">
              <persName>
                <forename type="first">Boris P.</forename>
                <surname>Hejblum</surname>
              </persName>
              <email type="md5">00e5ae285f2288acc3ba52b6b4c3ff1b</email>
              <email type="domain">u-bordeaux.fr</email>
              <idno type="idhal" notation="string">boris-hejblum</idno>
              <idno type="idhal" notation="numeric">10465</idno>
              <idno type="halauthorid" notation="string">29388-10465</idno>
              <idno type="ARXIV">https://arxiv.org/a/hejblum_b_1</idno>
              <idno type="ORCID">https://orcid.org/0000-0003-0646-452X</idno>
              <idno type="GOOGLE SCHOLAR">https://scholar.google.com/citations?user=xU72YmYAAAAJ</idno>
              <idno type="IDREF">https://www.idref.fr/189970316</idno>
              <affiliation ref="#struct-219689"/>
              <affiliation ref="#struct-220073"/>
              <affiliation ref="#struct-259761"/>
              <affiliation ref="#struct-476572"/>
            </author>
            <author role="aut">
              <persName>
                <forename type="first">Rodolphe</forename>
                <surname>Thiébaut</surname>
              </persName>
              <email type="md5">242f217052cdd1b15e9288ab507c175b</email>
              <email type="domain">u-bordeaux.fr</email>
              <idno type="idhal" notation="string">rodolphe-thiebaut</idno>
              <idno type="idhal" notation="numeric">175125</idno>
              <idno type="halauthorid" notation="string">32082-175125</idno>
              <idno type="ORCID">https://orcid.org/0000-0002-5235-3962</idno>
              <idno type="IDREF">https://www.idref.fr/071580735</idno>
              <affiliation ref="#struct-219689"/>
              <affiliation ref="#struct-220073"/>
              <affiliation ref="#struct-476572"/>
            </author>
            <editor role="depositor">
              <persName>
                <forename>Boris</forename>
                <surname>Hejblum</surname>
              </persName>
              <email type="md5">00e5ae285f2288acc3ba52b6b4c3ff1b</email>
              <email type="domain">u-bordeaux.fr</email>
            </editor>
            <funder ref="#projanr-37855"/>
          </titleStmt>
          <editionStmt>
            <edition n="v2" type="current">
              <date type="whenSubmitted">2018-10-06 10:38:27</date>
              <date type="whenModified">2026-04-28 12:34:58</date>
              <date type="whenReleased">2018-10-08 08:25:20</date>
              <date type="whenProduced">2018</date>
              <date type="whenEndEmbargoed">2018-10-06</date>
              <ref type="file" target="https://inria.hal.science/hal-03161874v2/document">
                <date notBefore="2018-10-06"/>
              </ref>
              <ref type="file" subtype="author" n="1" target="https://inria.hal.science/hal-03161874v2/file/335554.full.pdf" id="file-1889344-1919404">
                <date notBefore="2018-10-06"/>
              </ref>
              <ref type="externalLink" target="https://onlinelibrary.wiley.com/doi/pdfdirect/10.1002/cyto.a.23601"/>
            </edition>
            <edition n="v1">
              <date type="whenSubmitted">2021-03-08 10:23:58</date>
            </edition>
            <respStmt>
              <resp>contributor</resp>
              <name key="557959">
                <persName>
                  <forename>Boris</forename>
                  <surname>Hejblum</surname>
                </persName>
                <email type="md5">00e5ae285f2288acc3ba52b6b4c3ff1b</email>
                <email type="domain">u-bordeaux.fr</email>
              </name>
            </respStmt>
          </editionStmt>
          <publicationStmt>
            <distributor>CCSD</distributor>
            <idno type="halId">hal-03161874</idno>
            <idno type="halUri">https://inria.hal.science/hal-03161874</idno>
            <idno type="halBibtex">commenges:hal-03161874</idno>
            <idno type="halRefHtml">&lt;i&gt;Cytometry Part A&lt;/i&gt;, 2018, 93 (11), pp.1132-1140. &lt;a target="_blank" href="https://dx.doi.org/10.1002/cyto.a.23601"&gt;&amp;#x27E8;10.1002/cyto.a.23601&amp;#x27E9;&lt;/a&gt;</idno>
            <idno type="halRef">Cytometry Part A, 2018, 93 (11), pp.1132-1140. &amp;#x27E8;10.1002/cyto.a.23601&amp;#x27E9;</idno>
            <availability status="restricted">
              <licence target="https://about.hal.science/hal-authorisation-v1/">HAL Authorization<ref corresp="#file-1889344-1919404"/></licence>
            </availability>
          </publicationStmt>
          <seriesStmt>
            <idno type="stamp" n="INRIA">INRIA - Institut National de Recherche en Informatique et en Automatique</idno>
            <idno type="stamp" n="INRIA-BORDEAUX">INRIA Bordeaux - Sud-Ouest</idno>
            <idno type="stamp" n="INRIA_TEST">INRIA - Institut National de Recherche en Informatique et en Automatique</idno>
            <idno type="stamp" n="UPEC" corresp="CV_UPEC">Université Paris-Est Créteil Val-de-Marne</idno>
            <idno type="stamp" n="TESTALAIN1">TESTALAIN1</idno>
            <idno type="stamp" n="TESTBORDEAUX">TESTBORDEAUX</idno>
            <idno type="stamp" n="INRIA2">INRIA 2</idno>
            <idno type="stamp" n="ANR">ANR</idno>
            <idno type="stamp" n="U1219" corresp="INSERM">Bordeaux Population Health</idno>
            <idno type="stamp" n="INRIAARTDOI">INRIAARTDOI</idno>
            <idno type="stamp" n="INRIA-ETATSUNIS">Copublications Inria-Etats-Unis</idno>
            <idno type="stamp" n="UNIVERSITE-BORDEAUX">Université de Bordeaux</idno>
            <idno type="stamp" n="TEST-UPEC-ODD" corresp="UPEC">TEST UPEC ODD</idno>
          </seriesStmt>
          <notesStmt>
            <note type="commentary">bioRxiv 335554</note>
            <note type="audience" n="2">International</note>
            <note type="popular" n="0">No</note>
            <note type="peer" n="1">Yes</note>
          </notesStmt>
          <sourceDesc>
            <biblStruct>
              <analytic>
                <title xml:lang="en">cytometree: A binary tree algorithm for automatic gating in cytometry analysis</title>
                <author role="aut">
                  <persName>
                    <forename type="first">Daniel</forename>
                    <surname>Commenges</surname>
                  </persName>
                  <email type="md5">103005b79db5cad1459d2c3e50e1a69d</email>
                  <email type="domain">isped.u-bordeaux2.fr</email>
                  <idno type="idhal" notation="numeric">838345</idno>
                  <idno type="halauthorid" notation="string">129220-838345</idno>
                  <affiliation ref="#struct-55677"/>
                  <affiliation ref="#struct-219689"/>
                  <affiliation ref="#struct-476572"/>
                </author>
                <author role="aut">
                  <persName>
                    <forename type="first">Chariff</forename>
                    <surname>Alkhassim</surname>
                  </persName>
                  <idno type="halauthorid">1214525-0</idno>
                  <affiliation ref="#struct-220073"/>
                  <affiliation ref="#struct-219689"/>
                  <affiliation ref="#struct-476572"/>
                </author>
                <author role="aut">
                  <persName>
                    <forename type="first">Raphael</forename>
                    <surname>Gottardo</surname>
                  </persName>
                  <email type="md5">5c1725ce4dfbab3673bebed59a5d0eca</email>
                  <email type="domain">fhcrc.org</email>
                  <idno type="idhal" notation="numeric">895681</idno>
                  <idno type="halauthorid" notation="string">352565-895681</idno>
                  <affiliation ref="#struct-41823"/>
                </author>
                <author role="aut">
                  <persName>
                    <forename type="first">Boris P.</forename>
                    <surname>Hejblum</surname>
                  </persName>
                  <email type="md5">00e5ae285f2288acc3ba52b6b4c3ff1b</email>
                  <email type="domain">u-bordeaux.fr</email>
                  <idno type="idhal" notation="string">boris-hejblum</idno>
                  <idno type="idhal" notation="numeric">10465</idno>
                  <idno type="halauthorid" notation="string">29388-10465</idno>
                  <idno type="ARXIV">https://arxiv.org/a/hejblum_b_1</idno>
                  <idno type="ORCID">https://orcid.org/0000-0003-0646-452X</idno>
                  <idno type="GOOGLE SCHOLAR">https://scholar.google.com/citations?user=xU72YmYAAAAJ</idno>
                  <idno type="IDREF">https://www.idref.fr/189970316</idno>
                  <affiliation ref="#struct-219689"/>
                  <affiliation ref="#struct-220073"/>
                  <affiliation ref="#struct-259761"/>
                  <affiliation ref="#struct-476572"/>
                </author>
                <author role="aut">
                  <persName>
                    <forename type="first">Rodolphe</forename>
                    <surname>Thiébaut</surname>
                  </persName>
                  <email type="md5">242f217052cdd1b15e9288ab507c175b</email>
                  <email type="domain">u-bordeaux.fr</email>
                  <idno type="idhal" notation="string">rodolphe-thiebaut</idno>
                  <idno type="idhal" notation="numeric">175125</idno>
                  <idno type="halauthorid" notation="string">32082-175125</idno>
                  <idno type="ORCID">https://orcid.org/0000-0002-5235-3962</idno>
                  <idno type="IDREF">https://www.idref.fr/071580735</idno>
                  <affiliation ref="#struct-219689"/>
                  <affiliation ref="#struct-220073"/>
                  <affiliation ref="#struct-476572"/>
                </author>
              </analytic>
              <monogr>
                <idno type="halJournalId" status="VALID">12354</idno>
                <idno type="issn">1552-4922</idno>
                <idno type="eissn">1552-4930</idno>
                <title level="j">Cytometry Part A</title>
                <imprint>
                  <publisher>Wiley</publisher>
                  <biblScope unit="volume">93</biblScope>
                  <biblScope unit="issue">11</biblScope>
                  <biblScope unit="pp">1132-1140</biblScope>
                  <date type="datePub">2018</date>
                  <date type="dateEpub">2018-10-02</date>
                </imprint>
              </monogr>
              <idno type="doi">10.1002/cyto.a.23601</idno>
              <ref target="https://doi.org/10.1101/335554" type="seeAlso"/>
            </biblStruct>
          </sourceDesc>
          <profileDesc>
            <langUsage>
              <language ident="en">English</language>
            </langUsage>
            <textClass>
              <keywords scheme="author">
                <term xml:lang="en">Automated gating</term>
                <term xml:lang="en">Mixture of distributions</term>
                <term xml:lang="en">Flow cytometry</term>
                <term xml:lang="en">Binary tree</term>
              </keywords>
              <classCode scheme="halDomain" n="stat.ml">Statistics [stat]/Machine Learning [stat.ML]</classCode>
              <classCode scheme="halDomain" n="stat.ap">Statistics [stat]/Applications [stat.AP]</classCode>
              <classCode scheme="halDomain" n="sdv.imm.vac">Life Sciences [q-bio]/Immunology/Vaccinology</classCode>
              <classCode scheme="halDomain" n="sdv.bibs">Life Sciences [q-bio]/Quantitative Methods [q-bio.QM]</classCode>
              <classCode scheme="halTypology" n="ART">Journal articles</classCode>
              <classCode scheme="halOldTypology" n="ART">Journal articles</classCode>
              <classCode scheme="halTreeTypology" n="ART">Journal articles</classCode>
            </textClass>
            <abstract xml:lang="en">
              <p>Motivation: Flow cytometry is a powerful technology that allows the high-throughput quantification of dozens of surface and intracellular proteins at the single-cell level. It has become the most widely used technology for immunophenotyping of cells over the past three decades. Due to the increasing complexity of cytometry experiments (more cells and more markers), traditional manual flow cytometry data analysis has become untenable due to its subjectivity and time-consuming nature. Results: We present a new unsupervised algorithm called "cytometree" to perform automated population discovery (aka gating) in flow cytometry. cytometree is based on the construction of a binary tree, the nodes of which are subpopulations of cells. At each node, the marker distributions are modeled by mixtures of normal distribution. Node splitting is done according to a normalized difference of Akaike information criteria (AIC) between the two models. Post-processing of the tree structure and derived populations allows us to complete the annotation of the derived populations. The algorithm is shown to perform better than the state-of-the-art unsupervised algorithms previously proposed on panels introduced by the Flow Cytometry: Critical Assessment of Population Identification Methods (FlowCAP I) project. The algorithm is also applied to a T-cell panel proposed by the Human Immunology Project Consortium (HIPC) program; it also outperforms the best unsupervised open-source available algorithm while requiring the shortest computation time. Availability: An R package named "cytometree" is available on the CRAN repository.</p>
            </abstract>
          </profileDesc>
        </biblFull>
      </listBibl>
    </body>
    <back>
      <listOrg type="structures">
        <org type="laboratory" xml:id="struct-55677" status="OLD">
          <orgName>Epidémiologie et Biostatistique [Bordeaux]</orgName>
          <desc>
            <address>
              <addrLine>146, rue Léo-Saignat 33076 Bordeaux</addrLine>
              <country key="FR"/>
            </address>
          </desc>
          <listRelation>
            <relation active="#struct-91134" type="direct"/>
            <relation name="U897" active="#struct-303623" type="direct"/>
          </listRelation>
        </org>
        <org type="researchteam" xml:id="struct-219689" status="VALID">
          <idno type="RNSR">201321095C</idno>
          <idno type="ROR">https://ror.org/026t7px13</idno>
          <orgName>Statistics In System biology and Translational Medicine</orgName>
          <orgName type="acronym">SISTM</orgName>
          <date type="start">2016-01-01</date>
          <date type="end">2027-12-31</date>
          <desc>
            <address>
              <addrLine>200, avenue de la Vieille Tour 33405 Talence cedex 146 Rue Léo Saignat33076 Bordeaux cedex</addrLine>
              <country key="FR"/>
            </address>
            <ref type="url">http://www.inria.fr/equipes/sistm</ref>
          </desc>
          <listRelation>
            <relation active="#struct-104751" type="direct"/>
            <relation active="#struct-300009" type="indirect"/>
            <relation active="#struct-476572" type="direct"/>
            <relation active="#struct-259761" type="indirect"/>
            <relation active="#struct-302259" type="indirect"/>
            <relation name="U1219" active="#struct-303623" type="indirect"/>
          </listRelation>
        </org>
        <org type="laboratory" xml:id="struct-476572" status="VALID">
          <idno type="IdRef">197398162</idno>
          <idno type="RNSR">201622170H</idno>
          <idno type="ROR">https://ror.org/00xzzba89</idno>
          <orgName>Bordeaux population health</orgName>
          <orgName type="acronym">BPH</orgName>
          <desc>
            <address>
              <addrLine>Université de Bordeaux - Case 11 - 146 rue Léo Saignat  33076 Bordeaux cedex</addrLine>
              <country key="FR"/>
            </address>
          </desc>
          <listRelation>
            <relation active="#struct-259761" type="direct"/>
            <relation active="#struct-302259" type="direct"/>
            <relation name="U1219" active="#struct-303623" type="direct"/>
          </listRelation>
        </org>
        <org type="laboratory" xml:id="struct-220073" status="VALID">
          <orgName>Vaccine Research Institute [Créteil, France]</orgName>
          <orgName type="acronym">VRI</orgName>
          <desc>
            <address>
              <addrLine>61 avenue du Général de Gaulle 94010 Créteil Cedex France</addrLine>
              <country key="FR"/>
            </address>
            <ref type="url">http://www.recherche-vaccinvih.fr/</ref>
          </desc>
          <listRelation>
            <relation active="#struct-420786" type="direct"/>
          </listRelation>
        </org>
        <org type="institution" xml:id="struct-41823" status="VALID">
          <orgName>Fred Hutchinson Cancer Research Center [Seattle]</orgName>
          <orgName type="acronym">FHCRC</orgName>
          <desc>
            <address>
              <addrLine>1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109</addrLine>
              <country key="US"/>
            </address>
            <ref type="url">http://www.fhcrc.org/</ref>
          </desc>
        </org>
        <org type="institution" xml:id="struct-259761" status="VALID">
          <idno type="IdRef">175206562</idno>
          <idno type="ROR">https://ror.org/057qpr032</idno>
          <orgName>Université de Bordeaux</orgName>
          <orgName type="acronym">UB</orgName>
          <desc>
            <address>
              <addrLine>35, place Pey Berland - 33076 Bordeaux</addrLine>
              <country key="FR"/>
            </address>
            <ref type="url">http://www.u-bordeaux.fr/</ref>
          </desc>
        </org>
        <org type="institution" xml:id="struct-91134" status="OLD">
          <orgName>Université Bordeaux Segalen - Bordeaux 2</orgName>
          <desc>
            <address>
              <addrLine>146 rue Léo Saignat - 33076 Bordeaux cedex</addrLine>
              <country key="FR"/>
            </address>
            <ref type="url">http://www.univ-bordeauxsegalen.fr/</ref>
          </desc>
        </org>
        <org type="institution" xml:id="struct-303623" status="VALID">
          <idno type="IdRef">026388278</idno>
          <idno type="ROR">https://ror.org/02vjkv261</idno>
          <orgName>Institut National de la Santé et de la Recherche Médicale</orgName>
          <orgName type="acronym">INSERM</orgName>
          <desc>
            <address>
              <addrLine>101, rue de Tolbiac, 75013 Paris</addrLine>
              <country key="FR"/>
            </address>
            <ref type="url">http://www.inserm.fr</ref>
          </desc>
        </org>
        <org type="laboratory" xml:id="struct-104751" status="VALID">
          <idno type="RNSR">200818243Z</idno>
          <idno type="ROR">https://ror.org/03tjcj052</idno>
          <orgName>Centre Inria de l'Université de Bordeaux</orgName>
          <desc>
            <address>
              <addrLine>200, avenue de la Vieille Tour, 33405 Talence</addrLine>
              <country key="FR"/>
            </address>
            <ref type="url">http://www.inria.fr/bordeaux/</ref>
          </desc>
          <listRelation>
            <relation active="#struct-300009" type="direct"/>
          </listRelation>
        </org>
        <org type="institution" xml:id="struct-300009" status="VALID">
          <idno type="ROR">https://ror.org/02kvxyf05</idno>
          <orgName>Institut National de Recherche en Informatique et en Automatique</orgName>
          <orgName type="acronym">Inria</orgName>
          <desc>
            <address>
              <addrLine>Domaine de VoluceauRocquencourt - BP 10578153 Le Chesnay Cedex</addrLine>
              <country key="FR"/>
            </address>
            <ref type="url">http://www.inria.fr/en/</ref>
          </desc>
        </org>
        <org type="institution" xml:id="struct-302259" status="VALID">
          <orgName>Institut de Santé Publique, d'Épidémiologie et de Développement (ISPED)</orgName>
          <desc>
            <address>
              <country key="FR"/>
            </address>
          </desc>
        </org>
        <org type="institution" xml:id="struct-420786" status="VALID">
          <idno type="IdRef">028021037</idno>
          <idno type="ISNI">0000000121497878</idno>
          <idno type="ROR">https://ror.org/05ggc9x40</idno>
          <orgName>Université Paris-Est Créteil Val-de-Marne - Paris 12</orgName>
          <orgName type="acronym">UPEC UP12</orgName>
          <date type="start">1970-01-01</date>
          <desc>
            <address>
              <addrLine>61 avenue du Général de Gaulle - 94010 Créteil cedex</addrLine>
              <country key="FR"/>
            </address>
            <ref type="url">http://www.u-pec.fr/</ref>
          </desc>
        </org>
      </listOrg>
      <listOrg type="projects">
        <org type="anrProject" xml:id="projanr-37855" status="VALID">
          <idno type="anr">ANR-10-LABX-0077</idno>
          <idno type="program">Laboratoires d'excellence</idno>
          <orgName>VRI</orgName>
          <desc>Initiative for the creation of a Vaccine Research Institute</desc>
          <date type="start">2010</date>
        </org>
      </listOrg>
    </back>
  </text>
</TEI>