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@ARTICLE{Mller:305453,
      author       = {J. Müller and B. Kuster$^*$ and M. The},
      title        = {{C}omputational {A}pproaches for {P}athway-{C}entric
                      {A}nalysis of {P}rotein {P}ost-{T}ranslational
                      {M}odifications.},
      journal      = {Proteomics},
      volume       = {nn},
      issn         = {1615-9853},
      address      = {Weinheim},
      publisher    = {Wiley VCH},
      reportid     = {DKFZ-2025-02171},
      pages        = {nn},
      year         = {2025},
      note         = {epub},
      abstract     = {Protein function is dynamically modulated by
                      post-translational modifications (PTMs). Many different
                      types of PTMs can nowadays be identified and quantified at a
                      large scale using mass spectrometry. It is well known that
                      many PTMs have an effect on protein function and cellular
                      processes, and they should be studied not in isolation, but
                      in the holistic context of cellular pathways. This is
                      increasingly facilitated by a wide variety of computational
                      efforts. This review aims to give a systematic overview of
                      tools for pathway-centric analysis of PTM data and
                      critically evaluate the state of play in this research
                      field. Starting from databases that make up the foundational
                      prior knowledge, we follow typical steps that an analytical
                      workflow might contain, including pathway enrichment
                      analysis, algorithms for pathway reconstruction, and the
                      integration and visualization of results. We then reflect on
                      common limitations of all existing tools and give our
                      opinion on future directions that we think are currently
                      most desirable.},
      subtyp        = {Review Article},
      keywords     = {computational biology (Other) / enrichment analysis (Other)
                      / pathways (Other) / post‐translational modifications
                      (Other)},
      cin          = {MU01},
      ddc          = {540},
      cid          = {I:(DE-He78)MU01-20160331},
      pnm          = {899 - ohne Topic (POF4-899)},
      pid          = {G:(DE-HGF)POF4-899},
      typ          = {PUB:(DE-HGF)16},
      pubmed       = {pmid:41108535},
      doi          = {10.1002/pmic.70055},
      url          = {https://inrepo02.dkfz.de/record/305453},
}