Graph Transformations, Semigroups, and Isotopic Labeling

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

Research output: Chapter in Book/Report/Conference proceedingArticle in proceedingsResearchpeer-review

Abstract

The Double Pushout (DPO) 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 isotopic labeling design we convert chemical reaction networks (represented as directed hypergraphs) into transformation semigroups. Symmetries within chemical compounds 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
Title of host publicationBioinformatics Research and Applications. ISBRA 2019
EditorsZhipeng Cai, Pavel Skums, Min Li
PublisherSpringer
Publication date2019
Pages196-207
ISBN (Print)978-3-030-20241-5
ISBN (Electronic)978-3-030-20242-2
DOIs
Publication statusPublished - 2019
Event15th International Symposium on Bioinformatics Research and Applications - Barcelona, Spain
Duration: 3. Jun 20196. Jun 2019

Conference

Conference15th International Symposium on Bioinformatics Research and Applications
CountrySpain
CityBarcelona
Period03/06/201906/06/2019
SeriesLecture Notes in Computer Science
Volume11490
ISSN0302-9743

Fingerprint

Labeling
Chemical reactions
Atoms
Chemical compounds
Pyruvic Acid
Glucose
Molecules
Glycolysis

Keywords

  • Double pushout
  • Glycolysis
  • Hypergraphs
  • Isotopic labeling

Cite this

Andersen, J. L., Merkle, D., & Rasmussen, P. S. (2019). Graph Transformations, Semigroups, and Isotopic Labeling. In Z. Cai, P. Skums, & M. Li (Eds.), Bioinformatics Research and Applications. ISBRA 2019 (pp. 196-207). Springer. Lecture Notes in Computer Science, Vol.. 11490 https://doi.org/10.1007/978-3-030-20242-2_17
Andersen, Jakob L. ; Merkle, Daniel ; Rasmussen, Peter S. / Graph Transformations, Semigroups, and Isotopic Labeling. Bioinformatics Research and Applications. ISBRA 2019. editor / Zhipeng Cai ; Pavel Skums ; Min Li. Springer, 2019. pp. 196-207 (Lecture Notes in Computer Science, Vol. 11490).
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Andersen, JL, Merkle, D & Rasmussen, PS 2019, Graph Transformations, Semigroups, and Isotopic Labeling. in Z Cai, P Skums & M Li (eds), Bioinformatics Research and Applications. ISBRA 2019. Springer, Lecture Notes in Computer Science, vol. 11490, pp. 196-207, 15th International Symposium on Bioinformatics Research and Applications, Barcelona, Spain, 03/06/2019. https://doi.org/10.1007/978-3-030-20242-2_17

Graph Transformations, Semigroups, and Isotopic Labeling. / Andersen, Jakob L.; Merkle, Daniel; Rasmussen, Peter S.

Bioinformatics Research and Applications. ISBRA 2019. ed. / Zhipeng Cai; Pavel Skums; Min Li. Springer, 2019. p. 196-207 (Lecture Notes in Computer Science, Vol. 11490).

Research output: Chapter in Book/Report/Conference proceedingArticle in proceedingsResearchpeer-review

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Andersen JL, Merkle D, Rasmussen PS. Graph Transformations, Semigroups, and Isotopic Labeling. In Cai Z, Skums P, Li M, editors, Bioinformatics Research and Applications. ISBRA 2019. Springer. 2019. p. 196-207. (Lecture Notes in Computer Science, Vol. 11490). https://doi.org/10.1007/978-3-030-20242-2_17