<?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-04765771</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="2026-05-13T12:07:21+02:00"/>
      </publicationStmt>
      <sourceDesc>
        <p part="N">HAL API Platform</p>
      </sourceDesc>
    </fileDesc>
  </teiHeader>
  <text>
    <body>
      <listBibl>
        <biblFull>
          <titleStmt>
            <title xml:lang="en">Transipedia.org: k-mer-based exploration of large RNA sequencing datasets and application to cancer data</title>
            <author role="aut">
              <persName>
                <forename type="first">Chloé</forename>
                <surname>Bessière</surname>
              </persName>
              <idno type="halauthorid">1334441-0</idno>
              <affiliation ref="#struct-1100747"/>
              <affiliation ref="#struct-511697"/>
            </author>
            <author role="aut">
              <persName>
                <forename type="first">Haoliang</forename>
                <surname>Xue</surname>
              </persName>
              <idno type="halauthorid">2033438-0</idno>
              <affiliation ref="#struct-414518"/>
            </author>
            <author role="aut">
              <persName>
                <forename type="first">Benoit</forename>
                <surname>Guibert</surname>
              </persName>
              <idno type="halauthorid">1002242-0</idno>
              <affiliation ref="#struct-1100747"/>
            </author>
            <author role="aut">
              <persName>
                <forename type="first">Anthony</forename>
                <surname>Boureux</surname>
              </persName>
              <idno type="halauthorid">3622-0</idno>
              <affiliation ref="#struct-1100747"/>
            </author>
            <author role="aut">
              <persName>
                <forename type="first">Florence</forename>
                <surname>Rufflé</surname>
              </persName>
              <idno type="halauthorid">14745-0</idno>
              <affiliation ref="#struct-1100747"/>
            </author>
            <author role="aut">
              <persName>
                <forename type="first">Julien</forename>
                <surname>Viot</surname>
              </persName>
              <idno type="halauthorid">2375870-0</idno>
              <affiliation ref="#struct-417758"/>
              <affiliation ref="#struct-182215"/>
            </author>
            <author role="aut">
              <persName>
                <forename type="first">Rayan</forename>
                <surname>Chikhi</surname>
              </persName>
              <email type="md5">74a33c964087563eac21514df380edee</email>
              <email type="domain">ens-cachan.org</email>
              <idno type="idhal" notation="string">rayan-chikhi</idno>
              <idno type="idhal" notation="numeric">14839</idno>
              <idno type="halauthorid" notation="string">16383-14839</idno>
              <idno type="ORCID">https://orcid.org/0000-0003-1099-8735</idno>
              <idno type="IDREF">https://www.idref.fr/16546769X</idno>
              <affiliation ref="#struct-300027"/>
            </author>
            <author role="aut">
              <persName>
                <forename type="first">Mikaël</forename>
                <surname>Salson</surname>
              </persName>
              <idno type="halauthorid">13468-0</idno>
              <affiliation ref="#struct-410272"/>
            </author>
            <author role="aut">
              <persName>
                <forename type="first">Camille</forename>
                <surname>Marchet</surname>
              </persName>
              <idno type="halauthorid">23457-0</idno>
              <affiliation ref="#struct-410272"/>
            </author>
            <author role="crp">
              <persName>
                <forename type="first">Thérèse</forename>
                <surname>Commes</surname>
              </persName>
              <email type="md5">e0e2e6bc09a0b0a2f52b66bf8ba7adb4</email>
              <email type="domain">umontpellier.fr</email>
              <idno type="idhal" notation="string">therese-commes</idno>
              <idno type="idhal" notation="numeric">743232</idno>
              <idno type="halauthorid" notation="string">183874-743232</idno>
              <idno type="ORCID">https://orcid.org/0000-0002-7918-0176</idno>
              <idno type="IDREF">https://www.idref.fr/112246419</idno>
              <affiliation ref="#struct-1100747"/>
            </author>
            <author role="crp">
              <persName>
                <forename type="first">Daniel</forename>
                <surname>Gautheret</surname>
              </persName>
              <email type="md5">662cb0646bef13f7155138d648b2b8fa</email>
              <email type="domain">universite-paris-saclay.fr</email>
              <idno type="idhal" notation="numeric">1077926</idno>
              <idno type="halauthorid" notation="string">149541-1077926</idno>
              <affiliation ref="#struct-414518"/>
            </author>
            <editor role="depositor">
              <persName>
                <forename>Camille</forename>
                <surname>MARCHET</surname>
              </persName>
              <email type="md5">3fbd206738ae75eb3c313381de849eef</email>
              <email type="domain">univ-lille.fr</email>
            </editor>
            <funder ref="#projanr-48817"/>
            <funder ref="#projanr-72323"/>
            <funder ref="#projanr-53312"/>
            <funder ref="#projanr-47681"/>
            <funder ref="#projanr-50388"/>
            <funder ref="#projanr-110004"/>
            <funder ref="#projeurop-714051"/>
            <funder ref="#projeurop-714357"/>
            <funder>Agence Nationale de la Recherche grants ANR-18-CE45-0020, ANR-22-CE45-0007, ANR-19-CE45-0008, PIA/ANR16-CONV-0005, ANR-19-P3IA-0001. Immun4Cure IHU “Institute for innovative immunotherapies in autoimmune diseases” (France 2030 / ANR-23-IHUA-0009). European Union’s Horizon 2020 research and innovation program, Marie Skłodowska-Curie grant agreements No. 872539 and 956229.</funder>
          </titleStmt>
          <editionStmt>
            <edition n="v1" type="current">
              <date type="whenSubmitted">2024-11-04 16:13:24</date>
              <date type="whenModified">2026-05-13 03:17:57</date>
              <date type="whenReleased">2024-11-05 13:51:47</date>
              <date type="whenProduced">2024-10-10</date>
              <date type="whenEndEmbargoed">2024-11-04</date>
              <ref type="file" target="https://hal.science/hal-04765771v1/document">
                <date notBefore="2024-11-04"/>
              </ref>
              <ref type="file" subtype="author" n="1" target="https://hal.science/hal-04765771v1/file/s13059-024-03413-5.pdf" id="file-4765771-4151457">
                <date notBefore="2024-11-04"/>
              </ref>
              <ref type="externalLink" target="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11468207"/>
            </edition>
            <respStmt>
              <resp>contributor</resp>
              <name key="304025">
                <persName>
                  <forename>Camille</forename>
                  <surname>MARCHET</surname>
                </persName>
                <email type="md5">3fbd206738ae75eb3c313381de849eef</email>
                <email type="domain">univ-lille.fr</email>
              </name>
            </respStmt>
          </editionStmt>
          <publicationStmt>
            <distributor>CCSD</distributor>
            <idno type="halId">hal-04765771</idno>
            <idno type="halUri">https://hal.science/hal-04765771</idno>
            <idno type="halBibtex">bessiere:hal-04765771</idno>
            <idno type="halRefHtml">&lt;i&gt;Genome Biology&lt;/i&gt;, 2024, 25 (1), pp.266. &lt;a target="_blank" href="https://dx.doi.org/10.1186/s13059-024-03413-5"&gt;&amp;#x27E8;10.1186/s13059-024-03413-5&amp;#x27E9;&lt;/a&gt;</idno>
            <idno type="halRef">Genome Biology, 2024, 25 (1), pp.266. &amp;#x27E8;10.1186/s13059-024-03413-5&amp;#x27E9;</idno>
            <availability status="restricted">
              <licence target="https://creativecommons.org/licenses/by/4.0/">CC BY 4.0 - Attribution<ref corresp="#file-4765771-4151457"/></licence>
            </availability>
          </publicationStmt>
          <seriesStmt>
            <idno type="stamp" n="PASTEUR">Institut Pasteur</idno>
            <idno type="stamp" n="CEA">CEA - Commissariat à l'énergie atomique</idno>
            <idno type="stamp" n="UNIV-TLSE3">Université de Toulouse</idno>
            <idno type="stamp" n="CNRS">CNRS - Centre national de la recherche scientifique</idno>
            <idno type="stamp" n="OPENAIRE">OpenAIRE</idno>
            <idno type="stamp" n="CRISTAL">Centre de Recherche en Informatique, Signal et Automatique de Lille (CRISTAL)</idno>
            <idno type="stamp" n="CRISTAL-BONSAI" corresp="CRISTAL">CRISTAL-BONSAI</idno>
            <idno type="stamp" n="CEA-UPSAY" corresp="CEA">CEA - Université Paris-Saclay</idno>
            <idno type="stamp" n="I2BC">I2BC</idno>
            <idno type="stamp" n="UNIV-PARIS-SACLAY">Université Paris-Saclay</idno>
            <idno type="stamp" n="UNIV-MONTPELLIER">Université de Montpellier</idno>
            <idno type="stamp" n="JOLIOT" corresp="CEA">Institut des Sciences du Vivant Frédéric JOLIOT</idno>
            <idno type="stamp" n="CEA-DRF" corresp="CEA">Direction de Recherche Fondamentale</idno>
            <idno type="stamp" n="UNIV-LILLE">Université de Lille</idno>
            <idno type="stamp" n="PNRIA">Programme National de Recherche en IA</idno>
            <idno type="stamp" n="UNIVERSITE-PARIS-SACLAY" corresp="UNIV-PARIS-SACLAY">Université Paris-Saclay</idno>
            <idno type="stamp" n="ANR">ANR</idno>
            <idno type="stamp" n="PRAIRIE-IA">PaRis AI Research InstitutE</idno>
            <idno type="stamp" n="GS-BIOSPHERA">Graduate School Biologie, Société, Ecologie &amp; Environnement, Ressources, Agriculture &amp; Alimentation</idno>
            <idno type="stamp" n="GS-LIFE-SCIENCES-HEALTH" corresp="UNIVERSITE-PARIS-SACLAY">Graduate School Life Sciences and Health</idno>
            <idno type="stamp" n="GS-HEALTH-DRUG-SCIENCES">Graduate School Health and Drug Sciences</idno>
            <idno type="stamp" n="INSTITUT-SCIENCES-LUMIERE">Institut des Sciences de la Lumière</idno>
            <idno type="stamp" n="UNIV-UT3">Université Toulouse 3</idno>
            <idno type="stamp" n="UT3-INP">Université de Toulouse / Toulouse INP</idno>
            <idno type="stamp" n="UT3-TOULOUSEINP">Université de Toulouse / Toulouse INP</idno>
            <idno type="stamp" n="UM-2015-2021" corresp="UNIV-MONTPELLIER">Université de Montpellier (2015-2021)</idno>
            <idno type="stamp" n="UM-EPE" corresp="UNIV-MONTPELLIER">Université de Montpellier - EPE</idno>
            <idno type="stamp" n="CRCT">CRCT</idno>
            <idno type="stamp" n="PSACLAY-TEST">Université Paris-Saclay - Collection pour tests</idno>
            <idno type="stamp" n="APT_TEST">APT_TEST</idno>
            <idno type="stamp" n="ANR-IA-19" corresp="ANR-IA">ANR-IA-19</idno>
            <idno type="stamp" n="ANR-IA">ANR-IA</idno>
          </seriesStmt>
          <notesStmt>
            <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">Transipedia.org: k-mer-based exploration of large RNA sequencing datasets and application to cancer data</title>
                <author role="aut">
                  <persName>
                    <forename type="first">Chloé</forename>
                    <surname>Bessière</surname>
                  </persName>
                  <idno type="halauthorid">1334441-0</idno>
                  <affiliation ref="#struct-1100747"/>
                  <affiliation ref="#struct-511697"/>
                </author>
                <author role="aut">
                  <persName>
                    <forename type="first">Haoliang</forename>
                    <surname>Xue</surname>
                  </persName>
                  <idno type="halauthorid">2033438-0</idno>
                  <affiliation ref="#struct-414518"/>
                </author>
                <author role="aut">
                  <persName>
                    <forename type="first">Benoit</forename>
                    <surname>Guibert</surname>
                  </persName>
                  <idno type="halauthorid">1002242-0</idno>
                  <affiliation ref="#struct-1100747"/>
                </author>
                <author role="aut">
                  <persName>
                    <forename type="first">Anthony</forename>
                    <surname>Boureux</surname>
                  </persName>
                  <idno type="halauthorid">3622-0</idno>
                  <affiliation ref="#struct-1100747"/>
                </author>
                <author role="aut">
                  <persName>
                    <forename type="first">Florence</forename>
                    <surname>Rufflé</surname>
                  </persName>
                  <idno type="halauthorid">14745-0</idno>
                  <affiliation ref="#struct-1100747"/>
                </author>
                <author role="aut">
                  <persName>
                    <forename type="first">Julien</forename>
                    <surname>Viot</surname>
                  </persName>
                  <idno type="halauthorid">2375870-0</idno>
                  <affiliation ref="#struct-417758"/>
                  <affiliation ref="#struct-182215"/>
                </author>
                <author role="aut">
                  <persName>
                    <forename type="first">Rayan</forename>
                    <surname>Chikhi</surname>
                  </persName>
                  <email type="md5">74a33c964087563eac21514df380edee</email>
                  <email type="domain">ens-cachan.org</email>
                  <idno type="idhal" notation="string">rayan-chikhi</idno>
                  <idno type="idhal" notation="numeric">14839</idno>
                  <idno type="halauthorid" notation="string">16383-14839</idno>
                  <idno type="ORCID">https://orcid.org/0000-0003-1099-8735</idno>
                  <idno type="IDREF">https://www.idref.fr/16546769X</idno>
                  <affiliation ref="#struct-300027"/>
                </author>
                <author role="aut">
                  <persName>
                    <forename type="first">Mikaël</forename>
                    <surname>Salson</surname>
                  </persName>
                  <idno type="halauthorid">13468-0</idno>
                  <affiliation ref="#struct-410272"/>
                </author>
                <author role="aut">
                  <persName>
                    <forename type="first">Camille</forename>
                    <surname>Marchet</surname>
                  </persName>
                  <idno type="halauthorid">23457-0</idno>
                  <affiliation ref="#struct-410272"/>
                </author>
                <author role="crp">
                  <persName>
                    <forename type="first">Thérèse</forename>
                    <surname>Commes</surname>
                  </persName>
                  <email type="md5">e0e2e6bc09a0b0a2f52b66bf8ba7adb4</email>
                  <email type="domain">umontpellier.fr</email>
                  <idno type="idhal" notation="string">therese-commes</idno>
                  <idno type="idhal" notation="numeric">743232</idno>
                  <idno type="halauthorid" notation="string">183874-743232</idno>
                  <idno type="ORCID">https://orcid.org/0000-0002-7918-0176</idno>
                  <idno type="IDREF">https://www.idref.fr/112246419</idno>
                  <affiliation ref="#struct-1100747"/>
                </author>
                <author role="crp">
                  <persName>
                    <forename type="first">Daniel</forename>
                    <surname>Gautheret</surname>
                  </persName>
                  <email type="md5">662cb0646bef13f7155138d648b2b8fa</email>
                  <email type="domain">universite-paris-saclay.fr</email>
                  <idno type="idhal" notation="numeric">1077926</idno>
                  <idno type="halauthorid" notation="string">149541-1077926</idno>
                  <affiliation ref="#struct-414518"/>
                </author>
              </analytic>
              <monogr>
                <idno type="halJournalId" status="VALID">13604</idno>
                <idno type="issn">1465-6906</idno>
                <idno type="eissn">1474-760X</idno>
                <title level="j">Genome Biology</title>
                <imprint>
                  <publisher>BioMed Central</publisher>
                  <biblScope unit="volume">25</biblScope>
                  <biblScope unit="issue">1</biblScope>
                  <biblScope unit="pp">266</biblScope>
                  <date type="datePub">2024-10-10</date>
                </imprint>
              </monogr>
              <idno type="doi">10.1186/s13059-024-03413-5</idno>
              <idno type="pubmed">39390592</idno>
              <idno type="pubmedcentral">PMC11468207</idno>
            </biblStruct>
          </sourceDesc>
          <profileDesc>
            <langUsage>
              <language ident="en">English</language>
            </langUsage>
            <textClass>
              <keywords scheme="author">
                <term xml:lang="en">RNA-seq</term>
                <term xml:lang="en">Transcriptomics</term>
                <term xml:lang="en">Bioinformatics</term>
                <term xml:lang="en">RNA-processing</term>
                <term xml:lang="en">Non-coding RNA †</term>
              </keywords>
              <classCode scheme="halDomain" n="info.info-bi">Computer Science [cs]/Bioinformatics [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>Indexing techniques relying on k-mers have proven effective in searching for RNA sequences across thousands of RNA-seq libraries, but without enabling direct RNA quantification. We show here that arbitrary RNA sequences can be quantified in seconds through their decomposition into k-mers, with a precision akin to that of conventional RNA quantification methods. Using an index of the Cancer Cell Line Encyclopedia (CCLE) collection consisting of 1019 RNA-seq samples, we show that k-mer indexing offers a powerful means to reveal non-reference sequences, and variant RNAs induced by specific gene alterations, for instance in splicing factors.</p>
            </abstract>
          </profileDesc>
        </biblFull>
      </listBibl>
    </body>
    <back>
      <listOrg type="structures">
        <org type="laboratory" xml:id="struct-1100747" status="VALID">
          <idno type="RNSR">200716494C</idno>
          <idno type="ROR">https://ror.org/00b8mh310</idno>
          <orgName>Cellules Souches, Plasticité Cellulaire, Médecine Régénératrice et Immunothérapies (IRMB)</orgName>
          <date type="start">2022-01-01</date>
          <desc>
            <address>
              <addrLine>Institute for Regenerative Medicine and Biotherapy  - 80 rue Augustin Fliche 34295 Montpellier - Cedex 5</addrLine>
              <country key="FR"/>
            </address>
          </desc>
          <listRelation>
            <relation active="#struct-258773" type="direct"/>
            <relation name="U1183" active="#struct-303623" type="direct"/>
            <relation active="#struct-1100589" type="direct"/>
          </listRelation>
        </org>
        <org type="laboratory" xml:id="struct-511697" status="OLD">
          <idno type="IdRef">168095661</idno>
          <idno type="ISNI">0000000477733907</idno>
          <idno type="RNSR">201119444S</idno>
          <idno type="ROR">https://ror.org/003412r28</idno>
          <orgName>Centre de Recherches en Cancérologie de Toulouse</orgName>
          <orgName type="acronym">CRCT</orgName>
          <date type="start">2011-01-01</date>
          <date type="end">2025-01-01</date>
          <desc>
            <address>
              <addrLine>Centre de Recherches en Cancérologie de Toulouse2 Avenue Hubert Curien31037 Toulouse Cedex 1FRANCE</addrLine>
              <country key="FR"/>
            </address>
            <ref type="url">https://www.crct-inserm.fr/</ref>
          </desc>
          <listRelation>
            <relation active="#struct-217752" type="direct"/>
            <relation active="#struct-443875" type="indirect"/>
            <relation name="U1037" active="#struct-303623" type="direct"/>
            <relation name="UMR5071 / ERL5294" active="#struct-441569" type="direct"/>
          </listRelation>
        </org>
        <org type="laboratory" xml:id="struct-414518" status="VALID">
          <idno type="RNSR">201521299R</idno>
          <idno type="ROR">01fftxe08</idno>
          <orgName>Institut de Biologie Intégrative de la Cellule</orgName>
          <orgName type="acronym">I2BC</orgName>
          <date type="start">2015-01-01</date>
          <desc>
            <address>
              <addrLine>Bâtiment 21, 1 avenue de la Terrasse, 91198 Gif/Yvette cedex</addrLine>
              <country key="FR"/>
            </address>
            <ref type="url">http://www.i2bc.paris-saclay.fr</ref>
          </desc>
          <listRelation>
            <relation name="DRF/I2BC" active="#struct-300016" type="direct"/>
            <relation active="#struct-419361" type="direct"/>
            <relation name="UMR9198" active="#struct-441569" type="direct"/>
          </listRelation>
        </org>
        <org type="laboratory" xml:id="struct-417758" status="VALID">
          <orgName>Service d'Oncologie Médicale [CHRU Besançon]</orgName>
          <desc>
            <address>
              <addrLine>1 Rue Claude Goudimel 25000 Besançon</addrLine>
              <country key="FR"/>
            </address>
          </desc>
          <listRelation>
            <relation active="#struct-300165" type="direct"/>
            <relation active="#struct-458810" type="direct"/>
            <relation active="#struct-426438" type="indirect"/>
          </listRelation>
        </org>
        <org type="laboratory" xml:id="struct-182215" status="VALID">
          <idno type="IdRef">166218421</idno>
          <orgName>Interactions hôte-greffon-tumeur, ingénierie cellulaire et génique - UFC (UMR INSERM 1098)</orgName>
          <orgName type="acronym">RIGHT</orgName>
          <desc>
            <address>
              <addrLine>I.B.C.T. Bâtiment Inserm 240 Route de Dole/Rue F. Dolto 25000 Besançon</addrLine>
              <country key="FR"/>
            </address>
            <ref type="url">http://www.univ-fcomte.fr/pages/fr/menu1/recherche/la-recherche-a-l-ufc/umr-1098---relation-hote-greffon-18229-8143.html</ref>
          </desc>
          <listRelation>
            <relation name="UMR INSERM 1098" active="#struct-303623" type="direct"/>
            <relation active="#struct-439502" type="direct"/>
            <relation active="#struct-199980" type="indirect"/>
            <relation active="#struct-458810" type="direct"/>
            <relation active="#struct-426438" type="indirect"/>
          </listRelation>
        </org>
        <org type="institution" xml:id="struct-300027" status="VALID">
          <idno type="IdRef">027936643</idno>
          <idno type="ISNI">0000 0001 2353 6535</idno>
          <idno type="ROR">https://ror.org/0495fxg12</idno>
          <orgName>Institut Pasteur [Paris]</orgName>
          <orgName type="acronym">IP</orgName>
          <date type="start">1887-06-04</date>
          <desc>
            <address>
              <addrLine>25-28, rue du docteur Roux, 75724 Paris cedex 15</addrLine>
              <country key="FR"/>
            </address>
            <ref type="url">https://www.pasteur.fr</ref>
          </desc>
        </org>
        <org type="laboratory" xml:id="struct-410272" status="VALID">
          <idno type="IdRef">18388695X</idno>
          <idno type="RNSR">201521249L</idno>
          <idno type="ROR">https://ror.org/05vrs3189</idno>
          <idno type="Wikidata">Q116959497</idno>
          <orgName>Centre de Recherche en Informatique, Signal et Automatique de Lille - UMR 9189</orgName>
          <orgName type="acronym">CRIStAL</orgName>
          <date type="start">2015-01-01</date>
          <desc>
            <address>
              <addrLine>Université de Lille - Campus scientifique - Bâtiment ESPRIT - Avenue Henri Poincaré - 59655 Villeneuve d’Ascq</addrLine>
              <country key="FR"/>
            </address>
            <ref type="url">https://www.cristal.univ-lille.fr/</ref>
          </desc>
          <listRelation>
            <relation name="UMR9189" active="#struct-120930" type="direct"/>
            <relation name="UMR9189" active="#struct-374570" type="direct"/>
            <relation name="UMR9189" active="#struct-441569" type="direct"/>
          </listRelation>
        </org>
        <org type="regroupinstitution" xml:id="struct-258773" status="VALID">
          <idno type="ISNI">000000009961060X</idno>
          <idno type="ROR">https://ror.org/04m6sq715</idno>
          <orgName>Centre Hospitalier Régional Universitaire [Montpellier]</orgName>
          <orgName type="acronym">CHRU Montpellier</orgName>
          <desc>
            <address>
              <addrLine>191 avenue du doyen Gaston Giraud 34295 Montpellier</addrLine>
              <country key="FR"/>
            </address>
            <ref type="url">https://www.chu-montpellier.fr/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="regroupinstitution" xml:id="struct-1100589" status="VALID">
          <idno type="ROR">https://ror.org/051escj72</idno>
          <orgName>Université de Montpellier</orgName>
          <orgName type="acronym">UM</orgName>
          <date type="start">2022-01-01</date>
          <desc>
            <address>
              <addrLine>163 rue Auguste Broussonnet - 34090 Montpellier</addrLine>
              <country key="FR"/>
            </address>
            <ref type="url">http://www.umontpellier.fr/</ref>
          </desc>
        </org>
        <org type="institution" xml:id="struct-217752" status="OLD">
          <idno type="IdRef">026404672</idno>
          <idno type="ISNI">0000000121617331</idno>
          <idno type="ROR">https://ror.org/02v6kpv12</idno>
          <idno type="Wikidata">Q1273188</idno>
          <orgName>Université Toulouse III - Paul Sabatier</orgName>
          <orgName type="acronym">UT3</orgName>
          <date type="end">2025-01-01</date>
          <desc>
            <address>
              <addrLine>118 route de Narbonne - 31062 Toulouse</addrLine>
              <country key="FR"/>
            </address>
            <ref type="url">http://www.univ-tlse3.fr/</ref>
          </desc>
          <listRelation>
            <relation active="#struct-443875" type="direct"/>
          </listRelation>
        </org>
        <org type="regroupinstitution" xml:id="struct-443875" status="VALID">
          <idno type="ROR">https://ror.org/017tgbk05</idno>
          <orgName>Communauté d'universités et établissements de Toulouse</orgName>
          <orgName type="acronym">Comue de Toulouse</orgName>
          <desc>
            <address>
              <addrLine>41 Allée Jules Guesde, 31000 Toulouse</addrLine>
              <country key="FR"/>
            </address>
            <ref type="url">https://www.univ-toulouse.fr/</ref>
          </desc>
        </org>
        <org type="regroupinstitution" xml:id="struct-441569" status="VALID">
          <idno type="IdRef">02636817X</idno>
          <idno type="ISNI">0000000122597504</idno>
          <idno type="ROR">https://ror.org/02feahw73</idno>
          <orgName>Centre National de la Recherche Scientifique</orgName>
          <orgName type="acronym">CNRS</orgName>
          <date type="start">1939-10-19</date>
          <desc>
            <address>
              <country key="FR"/>
            </address>
            <ref type="url">https://www.cnrs.fr/</ref>
          </desc>
        </org>
        <org type="institution" xml:id="struct-300016" status="VALID">
          <idno type="IdRef">026372061</idno>
          <idno type="ISNI">0000000122998025</idno>
          <idno type="ROR">https://ror.org/00jjx8s55</idno>
          <idno type="Wikidata">Q868550</idno>
          <orgName>Commissariat à l'énergie atomique et aux énergies alternatives</orgName>
          <orgName type="acronym">CEA</orgName>
          <desc>
            <address>
              <addrLine>Centre de SaclayCentre de GrenobleCentre de Cadaracheetc</addrLine>
              <country key="FR"/>
            </address>
            <ref type="url">http://www.cea.fr/</ref>
          </desc>
        </org>
        <org type="institution" xml:id="struct-419361" status="VALID">
          <idno type="IdRef">241345251</idno>
          <idno type="ROR">https://ror.org/03xjwb503</idno>
          <orgName>Université Paris-Saclay</orgName>
          <desc>
            <address>
              <addrLine>Bâtiment Bréguet, 3 Rue Joliot Curie 2e ét, 91190 Gif-sur-Yvette</addrLine>
              <country key="FR"/>
            </address>
            <ref type="url">https://www.universite-paris-saclay.fr/fr</ref>
          </desc>
        </org>
        <org type="institution" xml:id="struct-300165" status="VALID">
          <orgName>Centre Hospitalier Régional Universitaire de Besançon</orgName>
          <orgName type="acronym">CHRU Besançon</orgName>
          <desc>
            <address>
              <addrLine>3, boulevard A. Fleming - 25030 Besançon Cedex</addrLine>
              <country key="FR"/>
            </address>
            <ref type="url">http://www.chu-besancon.fr/</ref>
          </desc>
        </org>
        <org type="institution" xml:id="struct-458810" status="VALID">
          <idno type="IdRef">026403188</idno>
          <idno type="ISNI">0000000121883779</idno>
          <idno type="ROR">https://ror.org/03pcc9z86</idno>
          <orgName>Université Marie et Louis Pasteur</orgName>
          <orgName type="acronym">UMLP</orgName>
          <desc>
            <address>
              <addrLine>1 rue Goudimel25030 Besançon cedex</addrLine>
              <country key="FR"/>
            </address>
            <ref type="url">https://www.umlp.fr/</ref>
          </desc>
          <listRelation>
            <relation active="#struct-426438" type="direct"/>
          </listRelation>
        </org>
        <org type="regroupinstitution" xml:id="struct-426438" status="VALID">
          <idno type="IdRef">200716271</idno>
          <idno type="ISNI">0000 0004 4910 6615</idno>
          <idno type="ROR">https://ror.org/02dn7x778</idno>
          <orgName>Université Bourgogne Franche-Comté [COMUE]</orgName>
          <orgName type="acronym">UBFC</orgName>
          <date type="start">2015-04-01</date>
          <date type="end">2024-12-31</date>
          <desc>
            <address>
              <addrLine>32, avenue de l’observatoire25000 BESANCON</addrLine>
              <country key="FR"/>
            </address>
            <ref type="url">http://www.ubfc.fr</ref>
          </desc>
        </org>
        <org type="institution" xml:id="struct-439502" status="VALID">
          <idno type="ROR">https://ror.org/02k9vew78</idno>
          <orgName>Établissement Français du Sang Bourgogne-Franche-Comté [Besançon]</orgName>
          <orgName type="acronym">EFS BFC - Besançon</orgName>
          <desc>
            <address>
              <addrLine>1 Boulevard Fleming 25020 Besançon</addrLine>
              <country key="FR"/>
            </address>
            <ref type="url">https://www.efs.sante.fr/lefs-en-bourgogne-franche-comte</ref>
          </desc>
          <listRelation>
            <relation active="#struct-199980" type="direct"/>
          </listRelation>
        </org>
        <org type="regroupinstitution" xml:id="struct-199980" status="VALID">
          <orgName>Établissement Français du Sang [La Plaine Saint-Denis]</orgName>
          <orgName type="acronym">EFS</orgName>
          <date type="start">2000-01-01</date>
          <desc>
            <address>
              <addrLine>20 Avenue du Stade de France 93218 La Plaine Saint Denis</addrLine>
              <country key="FR"/>
            </address>
            <ref type="url">https://www.dondusang.net</ref>
          </desc>
        </org>
        <org type="institution" xml:id="struct-120930" status="VALID">
          <idno type="IdRef">256304629</idno>
          <idno type="ISNI">0000000122034461</idno>
          <idno type="ROR">https://ror.org/01x441g73</idno>
          <orgName>Centrale Lille</orgName>
          <desc>
            <address>
              <addrLine>École Centrale de Lille - Cité Scientifique - CS 20048 59651 Villeneuve d'Ascq Cedex</addrLine>
              <country key="FR"/>
            </address>
            <ref type="url">https://centralelille.fr/</ref>
          </desc>
        </org>
        <org type="regroupinstitution" xml:id="struct-374570" status="VALID">
          <idno type="IdRef">223446556</idno>
          <idno type="ISNI">0000 0001 2242 6780</idno>
          <idno type="ROR">https://ror.org/02kzqn938</idno>
          <idno type="Wikidata">Q3551621</idno>
          <orgName>Université de Lille</orgName>
          <desc>
            <address>
              <addrLine>EPE Université de Lille. -- 42 rue Paul Duez, 59000 Lille</addrLine>
              <country key="FR"/>
            </address>
            <ref type="url">https://www.univ-lille.fr/</ref>
          </desc>
        </org>
      </listOrg>
      <listOrg type="projects">
        <org type="anrProject" xml:id="projanr-48817" status="VALID">
          <idno type="anr">ANR-18-CE45-0020</idno>
          <idno type="program">APPEL À PROJETS GÉNÉRIQUE 2018</idno>
          <orgName>Transipedia</orgName>
          <desc>Signatures transcriptionnelles pour une analyse RNA-seq globale</desc>
          <date type="start">2018</date>
        </org>
        <org type="anrProject" xml:id="projanr-72323" status="VALID">
          <idno type="anr">ANR-22-CE45-0007</idno>
          <orgName>full-RNA</orgName>
          <desc>Fouille non biaisée dans les banques de données RNA-seq massives</desc>
          <date type="start">2022</date>
        </org>
        <org type="anrProject" xml:id="projanr-53312" status="VALID">
          <idno type="anr">ANR-19-CE45-0008</idno>
          <orgName>SeqDigger</orgName>
          <desc>Moteur de recherche de donne´es de se´quenc¸age en ge´nomique environnementale</desc>
          <date type="start">2019</date>
        </org>
        <org type="anrProject" xml:id="projanr-47681" status="VALID">
          <idno type="anr">ANR-16-CONV-0005</idno>
          <orgName>INCEPTION</orgName>
          <desc>Institut Convergences pour l'étude de l'Emergence des Pathologies au Travers des Individus et des populatiONs</desc>
          <date type="start">2016</date>
        </org>
        <org type="anrProject" xml:id="projanr-50388" status="VALID">
          <idno type="anr">ANR-19-P3IA-0001</idno>
          <orgName>PRAIRIE</orgName>
          <desc>PaRis Artificial Intelligence Research InstitutE</desc>
          <date type="start">2019</date>
        </org>
        <org type="anrProject" xml:id="projanr-110004" status="VALID">
          <idno type="anr">ANR-23-IAHU-0009</idno>
          <orgName>IMMUN4CURE</orgName>
          <desc>Institut des maladies auto-immunes et des immunothérapies innovantes</desc>
          <date type="start">2023</date>
        </org>
        <org type="europeanProject" xml:id="projeurop-714051" status="VALID">
          <idno type="number">872539</idno>
          <idno type="program">H2020-MSCA-RISE-2019</idno>
          <idno type="call">H2020-MSCA-RISE-2019</idno>
          <orgName>PANGAIA</orgName>
          <desc>Pan-genome Graph Algorithms and Data Integration</desc>
          <date type="start">2020-01-01</date>
          <date type="end">2025-06-30</date>
        </org>
        <org type="europeanProject" xml:id="projeurop-714357" status="VALID">
          <idno type="number">956229</idno>
          <idno type="program">H2020-MSCA-ITN-2020</idno>
          <idno type="call">H2020-MSCA-ITN-2020</idno>
          <orgName>ALPACA</orgName>
          <desc>ALgorithms for PAngenome Computational Analysis</desc>
          <date type="start">2021-01-01</date>
          <date type="end">2024-12-31</date>
        </org>
      </listOrg>
    </back>
  </text>
</TEI>