5 citations · 7 across the 7 of their papers we have counts for
9 papers
Automated Inference of Graph Transformation Rules
Jakob L. Andersen, Akbar Davoodi, Rolf Fagerberg +6
The explosion of data available in life sciences is fueling an increasing demand for expressive models and computational methods. Graph transformation is a model for dynamic system…
Representing catalytic mechanisms with rule composition
Jakob L. Andersen, Rolf Fagerberg, Christoph Flamm +5
Reaction mechanisms are often presented as sequences of elementary steps, such as codified by arrow pushing. We propose an approach for representing such mechanisms using graph tra…
Efficient Modular Graph Transformation Rule Application
Jakob L. Andersen, Rolf Fagerberg, Juri Kolčák +3
Graph transformation formalisms have proven to be suitable tools for the modelling of chemical reactions. They are well established in theoretical studies and increasingly also in…
Cayley Graphs of Semigroups Applied to Atom Tracking in Chemistry
Nikolai Nøjgaard, Walter Fontana, Marc Hellmuth +1
While atom tracking with isotope-labeled compounds is an essential and sophisticated wet-lab tool in order to, e.g., illuminate reaction mechanisms, there exists only a limited amo…
Combining Orthology and Xenology Data in a Common Phylogenetic Tree
Marc Hellmuth, Mira Michel, Nikolai N. Nøjgaard +2
A rooted tree with vertex labels and set-valued edge labels defines maps and on the pairs of leaves of by setting if the last com…
Graph Transformation for Enzymatic Mechanisms
Jakob L. Andersen, Rolf Fagerberg, Christoph Flamm +5
Motivation: The design of enzymes is as challenging as it is consequential for making chemical synthesis in medical and industrial applications more efficient, cost-effective and e…
A Graph-Based Tool to Embed the π-Calculus into a Computational DPO Framework
Jakob Lykke Andersen, Marc Hellmuth, Daniel Merkle +2
Graph transformation approaches have been successfully used to analyse and design chemical and biological systems. Here we build on top of a DPO framework, in which molecules are m…
Partial Homology Relations - Satisfiability in terms of Di-Cographs
Nikolai Nøjgaard, Nadia El-Mabrouk, Daniel Merkle +2
Directed cographs (di-cographs) play a crucial role in the reconstruction of evolutionary histories of genes based on homology relations which are binary relations between genes. A…
Forbidden Time Travel: Characterization of Time-Consistent Tree Reconciliation Maps
Nikolai Nøjgaard, Manuela Geiß, Peter F. Stadler +3
In the absence of horizontal gene transfer it is possible to reconstruct the history of gene families from empirically determined orthology relations, which are equivalent to event…