<?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-04873696</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="2026-05-21T17:51:13+02:00"/>
      </publicationStmt>
      <sourceDesc>
        <p part="N">HAL API Platform</p>
      </sourceDesc>
    </fileDesc>
  </teiHeader>
  <text>
    <body>
      <listBibl>
        <biblFull>
          <titleStmt>
            <title xml:lang="en">Metabolic modelling links Warburg effect to collagen formation, angiogenesis and inflammation in the tumoral stroma</title>
            <author role="aut">
              <persName>
                <forename type="first">Maxime</forename>
                <surname>Mahout</surname>
              </persName>
              <email type="md5">4f19d63453341bda745bfc0f3c46820b</email>
              <email type="domain">lri.fr</email>
              <idno type="idhal" notation="string">mmahout</idno>
              <idno type="idhal" notation="numeric">1307094</idno>
              <idno type="halauthorid" notation="string">2327670-1307094</idno>
              <idno type="IDREF">https://www.idref.fr/273832468</idno>
              <idno type="ORCID">https://orcid.org/0000-0002-2699-5582</idno>
              <affiliation ref="#struct-1096260"/>
              <affiliation ref="#struct-1062146"/>
              <affiliation ref="#struct-10025"/>
            </author>
            <author role="aut">
              <persName>
                <forename type="first">Laurent</forename>
                <surname>Schwartz</surname>
              </persName>
              <idno type="halauthorid">443894-0</idno>
              <affiliation ref="#struct-300068"/>
            </author>
            <author role="aut">
              <persName>
                <forename type="first">Romain</forename>
                <surname>Attal</surname>
              </persName>
              <idno type="halauthorid">114903-0</idno>
              <affiliation ref="#struct-300020"/>
            </author>
            <author role="aut">
              <persName>
                <forename type="first">Ashraf</forename>
                <surname>Bakkar</surname>
              </persName>
              <idno type="halauthorid">1054768-0</idno>
              <affiliation ref="#struct-540493"/>
            </author>
            <author role="aut">
              <persName>
                <forename type="first">Sabine</forename>
                <surname>Peres</surname>
              </persName>
              <email type="md5">971a6259790e099e459fb4f9f7278563</email>
              <email type="domain">univ-lyon1.fr</email>
              <idno type="idhal" notation="string">sabine-peres</idno>
              <idno type="idhal" notation="numeric">17757</idno>
              <idno type="halauthorid" notation="string">2196230-17757</idno>
              <idno type="ORCID">https://orcid.org/0000-0002-4467-9989</idno>
              <idno type="IDREF">https://www.idref.fr/108927245</idno>
              <affiliation ref="#struct-1096260"/>
              <affiliation ref="#struct-10025"/>
            </author>
            <editor role="depositor">
              <persName>
                <forename>Sabine</forename>
                <surname>Peres</surname>
              </persName>
              <email type="md5">971a6259790e099e459fb4f9f7278563</email>
              <email type="domain">univ-lyon1.fr</email>
            </editor>
          </titleStmt>
          <editionStmt>
            <edition n="v1" type="current">
              <date type="whenSubmitted">2025-01-08 13:36:59</date>
              <date type="whenModified">2026-03-11 11:04:02</date>
              <date type="whenReleased">2025-01-08 13:54:07</date>
              <date type="whenProduced">2024</date>
              <date type="whenEndEmbargoed">2025-01-08</date>
              <ref type="file" target="https://hal.science/hal-04873696v1/document">
                <date notBefore="2025-01-08"/>
              </ref>
              <ref type="file" subtype="greenPublisher" n="1" target="https://hal.science/hal-04873696v1/file/2024_PLOS.pdf" id="file-4873696-4237657">
                <date notBefore="2025-01-08"/>
              </ref>
            </edition>
            <respStmt>
              <resp>contributor</resp>
              <name key="166853">
                <persName>
                  <forename>Sabine</forename>
                  <surname>Peres</surname>
                </persName>
                <email type="md5">971a6259790e099e459fb4f9f7278563</email>
                <email type="domain">univ-lyon1.fr</email>
              </name>
            </respStmt>
          </editionStmt>
          <publicationStmt>
            <distributor>CCSD</distributor>
            <idno type="halId">hal-04873696</idno>
            <idno type="halUri">https://hal.science/hal-04873696</idno>
            <idno type="halBibtex">mahout:hal-04873696</idno>
            <idno type="halRefHtml">&lt;i&gt;PLoS ONE&lt;/i&gt;, 2024, 19 (12), pp.e0313962. &lt;a target="_blank" href="https://dx.doi.org/10.1371/journal.pone.0313962"&gt;&amp;#x27E8;10.1371/journal.pone.0313962&amp;#x27E9;&lt;/a&gt;</idno>
            <idno type="halRef">PLoS ONE, 2024, 19 (12), pp.e0313962. &amp;#x27E8;10.1371/journal.pone.0313962&amp;#x27E9;</idno>
            <availability status="restricted">
              <licence target="https://creativecommons.org/licenses/by/4.0/">CC BY 4.0 - Attribution<ref corresp="#file-4873696-4237657"/></licence>
            </availability>
          </publicationStmt>
          <seriesStmt>
            <idno type="stamp" n="CNRS">CNRS - Centre national de la recherche scientifique</idno>
            <idno type="stamp" n="INRIA">INRIA - Institut National de Recherche en Informatique et en Automatique</idno>
            <idno type="stamp" n="UNIV-LYON1">Université Claude Bernard - Lyon I</idno>
            <idno type="stamp" n="CSI">Cité des Sciences et de l'Industrie</idno>
            <idno type="stamp" n="APHP" corresp="INSERM">AP-HP</idno>
            <idno type="stamp" n="CENTRALESUPELEC">Ecole CentraleSupélec</idno>
            <idno type="stamp" n="INRIA2">INRIA 2</idno>
            <idno type="stamp" n="UNIV-PARIS-SACLAY">Université Paris-Saclay</idno>
            <idno type="stamp" n="LBBE" corresp="UNIV-LYON1">Laboratoire de biométrie et biologie évolutive </idno>
            <idno type="stamp" n="UDL">UDL</idno>
            <idno type="stamp" n="UNIV-LYON">Université de Lyon</idno>
            <idno type="stamp" n="UNIVERSITE-PARIS-SACLAY" corresp="UNIV-PARIS-SACLAY">Université Paris-Saclay</idno>
            <idno type="stamp" n="LISN">Laboratoire Interdisciplinaire des Sciences du Numérique</idno>
            <idno type="stamp" n="GS-COMPUTER-SCIENCE">Graduate School Computer Science</idno>
            <idno type="stamp" n="LISN-BIOINFO" corresp="LISN">BioInformatique </idno>
            <idno type="stamp" n="INRIA-LYS">INRIA-LYON</idno>
            <idno type="stamp" n="INEE-CNRS">Institut écologie et environnement du CNRS</idno>
            <idno type="stamp" n="PSACLAY-TEST">Université Paris-Saclay - Collection pour tests</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">Metabolic modelling links Warburg effect to collagen formation, angiogenesis and inflammation in the tumoral stroma</title>
                <author role="aut">
                  <persName>
                    <forename type="first">Maxime</forename>
                    <surname>Mahout</surname>
                  </persName>
                  <email type="md5">4f19d63453341bda745bfc0f3c46820b</email>
                  <email type="domain">lri.fr</email>
                  <idno type="idhal" notation="string">mmahout</idno>
                  <idno type="idhal" notation="numeric">1307094</idno>
                  <idno type="halauthorid" notation="string">2327670-1307094</idno>
                  <idno type="IDREF">https://www.idref.fr/273832468</idno>
                  <idno type="ORCID">https://orcid.org/0000-0002-2699-5582</idno>
                  <affiliation ref="#struct-1096260"/>
                  <affiliation ref="#struct-1062146"/>
                  <affiliation ref="#struct-10025"/>
                </author>
                <author role="aut">
                  <persName>
                    <forename type="first">Laurent</forename>
                    <surname>Schwartz</surname>
                  </persName>
                  <idno type="halauthorid">443894-0</idno>
                  <affiliation ref="#struct-300068"/>
                </author>
                <author role="aut">
                  <persName>
                    <forename type="first">Romain</forename>
                    <surname>Attal</surname>
                  </persName>
                  <idno type="halauthorid">114903-0</idno>
                  <affiliation ref="#struct-300020"/>
                </author>
                <author role="aut">
                  <persName>
                    <forename type="first">Ashraf</forename>
                    <surname>Bakkar</surname>
                  </persName>
                  <idno type="halauthorid">1054768-0</idno>
                  <affiliation ref="#struct-540493"/>
                </author>
                <author role="aut">
                  <persName>
                    <forename type="first">Sabine</forename>
                    <surname>Peres</surname>
                  </persName>
                  <email type="md5">971a6259790e099e459fb4f9f7278563</email>
                  <email type="domain">univ-lyon1.fr</email>
                  <idno type="idhal" notation="string">sabine-peres</idno>
                  <idno type="idhal" notation="numeric">17757</idno>
                  <idno type="halauthorid" notation="string">2196230-17757</idno>
                  <idno type="ORCID">https://orcid.org/0000-0002-4467-9989</idno>
                  <idno type="IDREF">https://www.idref.fr/108927245</idno>
                  <affiliation ref="#struct-1096260"/>
                  <affiliation ref="#struct-10025"/>
                </author>
              </analytic>
              <monogr>
                <idno type="halJournalId" status="VALID">28700</idno>
                <idno type="issn">1932-6203</idno>
                <idno type="eissn">1932-6203</idno>
                <title level="j">PLoS ONE</title>
                <imprint>
                  <publisher>Public Library of Science</publisher>
                  <biblScope unit="volume">19</biblScope>
                  <biblScope unit="issue">12</biblScope>
                  <biblScope unit="pp">e0313962</biblScope>
                  <date type="datePub">2024</date>
                  <date type="dateEpub">2024-12-03</date>
                </imprint>
              </monogr>
              <idno type="doi">10.1371/journal.pone.0313962</idno>
            </biblStruct>
          </sourceDesc>
          <profileDesc>
            <langUsage>
              <language ident="en">English</language>
            </langUsage>
            <textClass>
              <classCode scheme="halDomain" n="info.info-bi">Computer Science [cs]/Bioinformatics [q-bio.QM]</classCode>
              <classCode scheme="halDomain" n="sdv.can">Life Sciences [q-bio]/Cancer</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>Cancer cells are known to express the Warburg effect-increased glycolysis and formation of lactic acid even in the presence of oxygen-as well as high glutamine uptake. In tumors, cancer cells are surrounded by collagen, immune cells, and neoangiogenesis. Whether collagen formation, neoangiogenesis, and inflammation in cancer are associated with the Warburg effect needs to be established. Metabolic modelling has proven to be a tool of choice to understand biological reality better and make in silico predictions. Elementary Flux Modes (EFMs) are essential for conducting an unbiased decomposition of a metabolic model into its minimal functional units. EFMs can be investigated using our tool, aspefm, an innovative approach based on logic programming where biological constraints can be incorporated. These constraints allow networks to be characterized regardless of their size. Using a metabolic model of the human cell containing collagen, neoangiogenesis, and inflammation markers, we derived a subset of EFMs of biological relevance to the Warburg effect. Within this model, EFMs analysis provided more adequate results than parsimonious flux balance analysis and flux sampling. Upon further inspection, the EFM with the best linear regression fit to cancer cell lines exometabolomics data was selected. The minimal pathway, presenting the Warburg effect, collagen synthesis, angiogenesis, and release of inflammation markers, showed that collagen production was possible directly de novo from glutamine uptake and without extracellular import of glycine and proline, collagen's main constituents.</p>
            </abstract>
          </profileDesc>
        </biblFull>
      </listBibl>
    </body>
    <back>
      <listOrg type="structures">
        <org type="researchteam" xml:id="struct-1096260" status="VALID">
          <idno type="RNSR">201521243E</idno>
          <idno type="ROR">https://ror.org/02gqj2v09</idno>
          <orgName>Equipe de recherche européenne en algorithmique et biologie formelle et expérimentale</orgName>
          <orgName type="acronym">ERABLE</orgName>
          <date type="start">2022-01-01</date>
          <date type="end">2027-06-30</date>
          <desc>
            <address>
              <addrLine>Université Claude Bernard (Lyon 1), Campus DOUA 43, Boulevard du 11 Novembre 1918 69622 Villeurbanne cedex</addrLine>
              <country key="FR"/>
            </address>
            <ref type="url">http://www.inria.fr/equipes/erable</ref>
          </desc>
          <listRelation>
            <relation active="#struct-10025" type="direct"/>
            <relation active="#struct-194495" type="indirect"/>
            <relation active="#struct-301088" type="indirect"/>
            <relation active="#struct-301767" type="indirect"/>
            <relation name="UMR5558" active="#struct-441569" type="indirect"/>
            <relation active="#struct-1096051" type="direct"/>
            <relation active="#struct-300009" type="indirect"/>
          </listRelation>
        </org>
        <org type="researchteam" xml:id="struct-1062146" status="VALID">
          <orgName>BioInformatique - LISN</orgName>
          <orgName type="acronym">BioInfo</orgName>
          <date type="start">2021-01-01</date>
          <desc>
            <address>
              <addrLine>Université Paris-Saclay, Bâtiment 650, 91190 Gif-sur-Yvette</addrLine>
              <country key="FR"/>
            </address>
          </desc>
          <listRelation>
            <relation active="#struct-1061259" type="direct"/>
            <relation active="#struct-300009" type="indirect"/>
            <relation active="#struct-411575" type="indirect"/>
            <relation active="#struct-419361" type="indirect"/>
            <relation name="UMR9015" active="#struct-441569" type="indirect"/>
            <relation active="#struct-1065371" type="direct"/>
          </listRelation>
        </org>
        <org type="laboratory" xml:id="struct-10025" status="VALID">
          <idno type="IdRef">15069671X</idno>
          <idno type="ISNI">0000000403863493</idno>
          <idno type="RNSR">199411998X</idno>
          <idno type="ROR">https://ror.org/03skt0t88</idno>
          <orgName>Laboratoire de Biométrie et Biologie Evolutive - UMR 5558</orgName>
          <orgName type="acronym">LBBE</orgName>
          <date type="start">1995-01-01</date>
          <desc>
            <address>
              <addrLine>43 Bld du 11 Novembre 1918 69622 VILLEURBANNE CEDEX</addrLine>
              <country key="FR"/>
            </address>
            <ref type="url">http://lbbe.univ-lyon1.fr/</ref>
          </desc>
          <listRelation>
            <relation active="#struct-194495" type="direct"/>
            <relation active="#struct-301088" type="indirect"/>
            <relation active="#struct-301767" type="direct"/>
            <relation name="UMR5558" active="#struct-441569" type="direct"/>
          </listRelation>
        </org>
        <org type="regroupinstitution" xml:id="struct-300068" status="VALID">
          <idno type="ROR">https://ror.org/00pg5jh14</idno>
          <orgName>Assistance publique - Hôpitaux de Paris (AP-HP)</orgName>
          <orgName type="acronym">AP-HP</orgName>
          <desc>
            <address>
              <country key="FR"/>
            </address>
          </desc>
        </org>
        <org type="institution" xml:id="struct-300020" status="VALID">
          <idno type="IdRef">027977617</idno>
          <orgName>Cité des Sciences et de l'Industrie</orgName>
          <orgName type="acronym">CSI</orgName>
          <date type="start">1985-01-01</date>
          <desc>
            <address>
              <addrLine>30 avenue Corentin-Cariou 75930 Paris Cedex 19</addrLine>
              <country key="FR"/>
            </address>
            <ref type="url">https://www.cite-sciences.fr/</ref>
          </desc>
          <listRelation>
            <relation active="#struct-1716002" type="direct"/>
          </listRelation>
        </org>
        <org type="institution" xml:id="struct-540493" status="INCOMING">
          <orgName>October University for Modern Sciences and Arts (MSA)</orgName>
          <desc>
            <address>
              <country key="EG"/>
            </address>
          </desc>
        </org>
        <org type="institution" xml:id="struct-194495" status="VALID">
          <idno type="IdRef">026402823</idno>
          <idno type="ISNI">0000000121686185</idno>
          <idno type="ROR">https://ror.org/029brtt94</idno>
          <orgName>Université Claude Bernard Lyon 1</orgName>
          <orgName type="acronym">UCBL</orgName>
          <desc>
            <address>
              <addrLine>43, boulevard du 11 novembre 1918, 69622 Villeurbanne cedex</addrLine>
              <country key="FR"/>
            </address>
            <ref type="url">http://www.univ-lyon1.fr/</ref>
          </desc>
          <listRelation>
            <relation active="#struct-301088" type="direct"/>
          </listRelation>
        </org>
        <org type="regroupinstitution" xml:id="struct-301088" status="VALID">
          <idno type="ROR">https://ror.org/01rk35k63</idno>
          <orgName>Université de Lyon</orgName>
          <desc>
            <address>
              <addrLine>92 rue Pasteur - CS 30122, 69361 Lyon Cedex 07</addrLine>
              <country key="FR"/>
            </address>
            <ref type="url">https://www.universite-lyon.fr/</ref>
          </desc>
        </org>
        <org type="institution" xml:id="struct-301767" status="VALID">
          <idno type="ROR">https://ror.org/01c7wz417</idno>
          <orgName>VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement</orgName>
          <orgName type="acronym">VAS</orgName>
          <date type="start">2010-01-01</date>
          <desc>
            <address>
              <addrLine>Université de Lyon, VetAgro Sup, 69280 Marcy l'Etoile (campus vétérinaire); Université de Clermont, VetAgro Sup, 63370 Lempdes (campus agronomique)</addrLine>
              <country key="FR"/>
            </address>
            <ref type="url">http://www.vetagro-sup.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="laboratory" xml:id="struct-1096051" status="VALID">
          <idno type="RNSR">202224236C</idno>
          <idno type="ROR">https://ror.org/022gakr41</idno>
          <orgName>Centre Inria de Lyon</orgName>
          <desc>
            <address>
              <addrLine>Inria de Lyon / Bâtiment CEI-2 / Campus La Doua - Villeurbanne / 56, Boulevard Niels Bohr / CS 52132 / 69 603 Villeurbanne</addrLine>
              <country key="FR"/>
            </address>
            <ref type="url">https://www.inria.fr/fr/centre-inria-de-lyon</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="laboratory" xml:id="struct-1061259" status="VALID">
          <idno type="IdRef">253160316</idno>
          <idno type="RNSR">202123711L</idno>
          <idno type="ROR">https://ror.org/00rd81916</idno>
          <idno type="Wikidata">Q109620676</idno>
          <orgName>Laboratoire Interdisciplinaire des Sciences du Numérique</orgName>
          <orgName type="acronym">LISN</orgName>
          <date type="start">2021-01-01</date>
          <desc>
            <address>
              <addrLine>Campus Universitaire bât 507Rue du Belvédère91405 Orsay cedexet Campus Universitaire bât 6401 rue Raimond Castaing91190 Gif-sur-Yvette</addrLine>
              <country key="FR"/>
            </address>
            <ref type="url">https://www.lisn.upsaclay.fr/</ref>
          </desc>
          <listRelation>
            <relation active="#struct-300009" type="direct"/>
            <relation active="#struct-411575" type="direct"/>
            <relation active="#struct-419361" type="direct"/>
            <relation name="UMR9015" active="#struct-441569" type="direct"/>
          </listRelation>
        </org>
        <org type="institution" xml:id="struct-411575" status="VALID">
          <idno type="IdRef">184443237</idno>
          <idno type="ROR">https://ror.org/019tcpt25</idno>
          <orgName>CentraleSupélec</orgName>
          <desc>
            <address>
              <addrLine>3, rue Joliot Curie,Plateau de Moulon,91192 GIF-SUR-YVETTE Cedex</addrLine>
              <country key="FR"/>
            </address>
            <ref type="url">http://www.centralesupelec.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="department" xml:id="struct-1065371" status="VALID">
          <orgName>Science des Données</orgName>
          <orgName type="acronym">SDD</orgName>
          <date type="start">2021-01-01</date>
          <desc>
            <address>
              <country key="FR"/>
            </address>
          </desc>
          <listRelation>
            <relation active="#struct-1061259" type="direct"/>
            <relation active="#struct-300009" type="indirect"/>
            <relation active="#struct-411575" type="indirect"/>
            <relation active="#struct-419361" type="indirect"/>
            <relation name="UMR9015" active="#struct-441569" type="indirect"/>
          </listRelation>
        </org>
        <org type="regroupinstitution" xml:id="struct-1716002" status="VALID">
          <idno type="IdRef">152700838</idno>
          <orgName>Universcience</orgName>
          <date type="start">2007-01-01</date>
          <desc>
            <address>
              <addrLine>Cité des sciences et de l'industrie, 30 avenue Corentin-Cariou, 75930 Paris Cedex 19</addrLine>
              <country key="FR"/>
            </address>
            <ref type="url">https://www.universcience.fr/fr/accueil</ref>
          </desc>
        </org>
      </listOrg>
    </back>
  </text>
</TEI>