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09/19/2023
On the Realisability of Chemical Pathways
The exploration of pathways and alternative pathways that have a specifi...
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08/24/2023
Reconciling Inconsistent Molecular Structures from Biochemical Databases
Information on the structure of molecules, retrieved via biochemical dat...
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01/12/2022
Representing catalytic mechanisms with rule composition
Reaction mechanisms are often presented as sequences of elementary steps...
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01/12/2022
Efficient Modular Graph Transformation Rule Application
Graph transformation formalisms have proven to be suitable tools for the...
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08/09/2021
Cayley Graphs of Semigroups Applied to Atom Tracking in Chemistry
While atom tracking with isotope-labeled compounds is an essential and s...
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07/07/2021
Defining Autocatalysis in Chemical Reaction Networks
Autocatalysis is a deceptively simple concept, referring to the situatio...
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06/04/2021
Rewriting Theory for the Life Sciences: A Unifying Theory of CTMC Semantics (Long version)
The Kappa biochemistry and the MØD organic chemistry frameworks are amon...
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02/05/2021
Graph Transformation for Enzymatic Mechanisms
Motivation: The design of enzymes is as challenging as it is consequenti...
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10/29/2019
A Graph-Based Tool to Embed the π-Calculus into a Computational DPO Framework
Graph transformation approaches have been successfully used to analyse a...
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12/07/2017
Chemical Transformation Motifs - Modelling Pathways as Integer Hyperflows
We present an elaborate framework for formally modelling pathways in che...
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11/22/2017
A Generic Framework for Engineering Graph Canonization Algorithms
The state-of-the-art tools for practical graph canonization are all base...
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11/01/2017