Combining Graph Transformations and Semigroups for Isotopic Labeling Design

Jakob L. Andersen, Daniel Merkle*, Peter S. Rasmussen

*Corresponding author for this work

Research output: Contribution to journalJournal articleResearchpeer-review


The double pushout approach for graph transformation naturally allows an abstraction level of biochemical systems in which individual atoms of molecules can be traced automatically within chemical reaction networks. Aiming at a mathematical rigorous approach for isotope labeling design, we convert chemical reaction networks (represented as directed hypergraphs) into transformation semigroups. Symmetries within molecules correspond to permutations, whereas (not necessarily invertible) chemical reactions define the transformations of the semigroup. An approach for the automatic inference of informative labeling of atoms is presented, which allows to distinguish the activity of different pathway alternatives within reaction networks. To illustrate our approaches, we apply them to the reaction network of glycolysis, which is an important and well-understood process that allows for different alternatives to convert glucose into pyruvate.

Original languageEnglish
JournalJournal of Computational Biology
Issue number2
Pages (from-to)269-287
Number of pages19
Publication statusPublished - Feb 2020


  • algorithmic cheminformatics
  • chemical reaction networks
  • computational biology
  • double pushout
  • graph transformations

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