Graph Transformations, Semigroups, and Isotopic Labeling

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

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Abstrakt

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.

OriginalsprogEngelsk
TitelBioinformatics Research and Applications. ISBRA 2019
RedaktørerZhipeng Cai, Pavel Skums, Min Li
ForlagSpringer
Publikationsdato2019
Sider196-207
ISBN (Trykt)978-3-030-20241-5
ISBN (Elektronisk)978-3-030-20242-2
DOI
StatusUdgivet - 2019
Begivenhed15th International Symposium on Bioinformatics Research and Applications - Barcelona, Spanien
Varighed: 3. jun. 20196. jun. 2019

Konference

Konference15th International Symposium on Bioinformatics Research and Applications
Land/OmrådeSpanien
ByBarcelona
Periode03/06/201906/06/2019
NavnLecture Notes in Computer Science
Vol/bind11490
ISSN0302-9743

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