1 Ocak 2021 Dergi makalesi Açık Erişim

Babur, Ozgun; Luna, Augustin; Korkut, Anil; Durupinar, Funda; Siper, Metin Can; Dogrusoz, Ugur; Jacome, Alvaro Sebastian Vaca; Peckner, Ryan; Christianson, Karen E.; Jaffe, Jacob D.; Spellman, Paul T.; Aslan, Joseph E.; Sander, Chris; Demir, Emek

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  <identifier identifierType="URL">https://aperta.ulakbim.gov.tr/record/230538</identifier>
  <creators>
    <creator>
      <creatorName>Babur, Ozgun</creatorName>
      <givenName>Ozgun</givenName>
      <familyName>Babur</familyName>
      <affiliation>Univ Massachusetts, Comp Sci Dept, 100 William T Morrissey Blvd, Boston, MA 02125 USA</affiliation>
    </creator>
    <creator>
      <creatorName>Luna, Augustin</creatorName>
      <givenName>Augustin</givenName>
      <familyName>Luna</familyName>
    </creator>
    <creator>
      <creatorName>Korkut, Anil</creatorName>
      <givenName>Anil</givenName>
      <familyName>Korkut</familyName>
      <affiliation>Univ Texas MD Anderson Canc Ctr, Dept Bioinformat &amp; Computat Biol, Houston, TX 77030 USA</affiliation>
    </creator>
    <creator>
      <creatorName>Durupinar, Funda</creatorName>
      <givenName>Funda</givenName>
      <familyName>Durupinar</familyName>
      <affiliation>Univ Massachusetts, Comp Sci Dept, 100 William T Morrissey Blvd, Boston, MA 02125 USA</affiliation>
    </creator>
    <creator>
      <creatorName>Siper, Metin Can</creatorName>
      <givenName>Metin Can</givenName>
      <familyName>Siper</familyName>
      <affiliation>Oregon Hlth &amp; Sci Univ, Computat Biol Program, 3181 SW Sam Jackson Pk Rd, Portland, OR 97239 USA</affiliation>
    </creator>
    <creator>
      <creatorName>Dogrusoz, Ugur</creatorName>
      <givenName>Ugur</givenName>
      <familyName>Dogrusoz</familyName>
      <affiliation>Bilkent Univ, Comp Engn Dept, TR-06800 Ankara, Turkey</affiliation>
    </creator>
    <creator>
      <creatorName>Jacome, Alvaro Sebastian Vaca</creatorName>
      <givenName>Alvaro Sebastian Vaca</givenName>
      <familyName>Jacome</familyName>
      <affiliation>Broad Inst MIT &amp; Harvard, Cambridge, MA 02142 USA</affiliation>
    </creator>
    <creator>
      <creatorName>Peckner, Ryan</creatorName>
      <givenName>Ryan</givenName>
      <familyName>Peckner</familyName>
    </creator>
    <creator>
      <creatorName>Christianson, Karen E.</creatorName>
      <givenName>Karen E.</givenName>
      <familyName>Christianson</familyName>
      <affiliation>Broad Inst MIT &amp; Harvard, Cambridge, MA 02142 USA</affiliation>
    </creator>
    <creator>
      <creatorName>Jaffe, Jacob D.</creatorName>
      <givenName>Jacob D.</givenName>
      <familyName>Jaffe</familyName>
      <affiliation>Broad Inst MIT &amp; Harvard, Cambridge, MA 02142 USA</affiliation>
    </creator>
    <creator>
      <creatorName>Spellman, Paul T.</creatorName>
      <givenName>Paul T.</givenName>
      <familyName>Spellman</familyName>
    </creator>
    <creator>
      <creatorName>Aslan, Joseph E.</creatorName>
      <givenName>Joseph E.</givenName>
      <familyName>Aslan</familyName>
      <affiliation>Oregon Hlth &amp; Sci Univ, Knight Cardiovasc Inst, 3181 SW Sam Jackson Pk Rd, Portland, OR 97239 USA</affiliation>
    </creator>
    <creator>
      <creatorName>Sander, Chris</creatorName>
      <givenName>Chris</givenName>
      <familyName>Sander</familyName>
    </creator>
    <creator>
      <creatorName>Demir, Emek</creatorName>
      <givenName>Emek</givenName>
      <familyName>Demir</familyName>
    </creator>
  </creators>
  <titles>
    <title>Causal Interactions From Proteomic Profiles: Molecular Data Meet Pathway Knowledge</title>
  </titles>
  <publisher>Aperta</publisher>
  <publicationYear>2021</publicationYear>
  <dates>
    <date dateType="Issued">2021-01-01</date>
  </dates>
  <resourceType resourceTypeGeneral="Text">Journal article</resourceType>
  <alternateIdentifiers>
    <alternateIdentifier alternateIdentifierType="url">https://aperta.ulakbim.gov.tr/record/230538</alternateIdentifier>
  </alternateIdentifiers>
  <relatedIdentifiers>
    <relatedIdentifier relatedIdentifierType="DOI" relationType="IsIdenticalTo">10.1016/j.patter.2021.100257</relatedIdentifier>
  </relatedIdentifiers>
  <rightsList>
    <rights rightsURI="http://www.opendefinition.org/licenses/cc-by">Creative Commons Attribution</rights>
    <rights rightsURI="info:eu-repo/semantics/openAccess">Open Access</rights>
  </rightsList>
  <descriptions>
    <description descriptionType="Abstract">We present a computational method to infer causal mechanisms in cell biology by analyzing changes in high-throughput proteomic profiles on the background of prior knowledge captured in biochemical reaction knowledge bases. The method mimics a biologist's traditional approach of explaining changes in data using prior knowledge but does this at the scale of hundreds of thousands of reactions. This is a specific example of how to automate scientific reasoning processes and illustrates the power ofmapping from experimental data to prior knowledge via logic programming. The identified mechanisms can explain how experimental and physiological perturbations, propagating in a network of reactions, affect cellular responses and their phenotypic consequences. Causal pathway analysis is a powerful and flexible discovery tool for a wide range of cellular profiling data types and biological questions.</description>
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