26 citations · 71 across the 21 of their papers we have counts for
5 papers · 1 filter
Assembly in Directed Hypergraphs
Christoph Flamm, Daniel Merkle, Peter F. Stadler
Assembly theory has received considerable attention in the recent past. Here we analyze the formal framework of this model and show that assembly pathways coincide with certain min…
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…
Automatic Inference of Graph Transformation Rules Using the Cyclic Nature of Chemical Reactions
Christoph Flamm, Daniel Merkle, Peter F. Stadler +1
Graph transformation systems have the potential to be realistic models of chemistry, provided a comprehensive collection of reaction rules can be extracted from the body of chemica…
Inferring Chemical Reaction Patterns Using Rule Composition in Graph Grammars
Jakob L. Andersen, Christoph Flamm, Daniel Merkle +1
Modeling molecules as undirected graphs and chemical reactions as graph rewriting operations is a natural and convenient approach tom odeling chemistry. Graph grammar rules are mos…