26 citations · 47 across the 18 of their papers we have counts for
22 papers
Pathway Realisability in Chemical Networks
Jakob L. Andersen, Sissel Banke, Rolf Fagerberg +3
The exploration of pathways and alternative pathways that have a specific function is of interest in numerous chemical contexts. A framework for specifying and searching for pathwa…
Reconciling Inconsistent Molecular Structures from Biochemical Databases
Casper Asbjørn Eriksen, Jakob Lykke Andersen, Rolf Fagerberg +1
Information on the structure of molecules, retrieved via biochemical databases, plays a pivotal role in various disciplines, such as metabolomics, systems biology, and drug discove…
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…
Defining Autocatalysis in Chemical Reaction Networks
Jakob L. Andersen, Christoph Flamm, Daniel Merkle +1
Autocatalysis is a deceptively simple concept, referring to the situation that a chemical species catalyzes its own formation. From the perspective of chemical kinetics, autoca…
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…
Chemical Transformation Motifs - Modelling Pathways as Integer Hyperflows
Jakob L. Andersen, Christoph Flamm, Daniel Merkle +1
We present an elaborate framework for formally modelling pathways in chemical reaction networks on a mechanistic level. Networks are modelled mathematically as directed multi-hyper…
A Generic Framework for Engineering Graph Canonization Algorithms
Jakob L. Andersen, Daniel Merkle
The state-of-the-art tools for practical graph canonization are all based on the individualization-refinement paradigm, and their difference is primarily in the choice of heuristic…
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…
An Intermediate Level of Abstraction for Computational Systems Chemistry
Jakob L. Andersen, Christoph Flamm, Daniel Merkle +1
Computational techniques are required for narrowing down the vast space of possibilities to plausible prebiotic scenarios, since precise information on the molecular composition, t…
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…
A Software Package for Chemically Inspired Graph Transformation
Jakob L. Andersen, Christoph Flamm, Daniel Merkle +1
Chemical reaction networks can be automatically generated from graph grammar descriptions, where rewrite rules model reaction patterns. Because a molecule graph is connected and re…
Support for Eschenmoser's Glyoxylate Scenario
Jakob L. Andersen, Christoph Flamm, Daniel Merkle +1
A core topic of research in prebiotic chemistry is the search for plausible synthetic routes that connect the building blocks of modern life such as sugars, nucleotides, amino acid…
Group Communication Patterns for High Performance Computing in Scala
Felix P. Hargreaves, Daniel Merkle, Peter Schneider-Kamp
We developed a Functional object-oriented Parallel framework (FooPar) for high-level high-performance computing in Scala. Central to this framework are Distributed Memory Parallel…
On the Complexity of Reconstructing Chemical Reaction Networks
Rolf Fagerberg, Christoph Flamm, Daniel Merkle +2
The analysis of the structure of chemical reaction networks is crucial for a better understanding of chemical processes. Such networks are well described as hypergraphs. However, d…
FooPar: A Functional Object Oriented Parallel Framework in Scala
Felix P. Hargreaves, Daniel Merkle
We present FooPar, an extension for highly efficient Parallel Computing in the multi-paradigm programming language Scala. Scala offers concise and clean syntax and integrates funct…
Generic Strategies for Chemical Space Exploration
Jakob L. Andersen, Christoph Flamm, Daniel Merkle +1
Computational approaches to exploring "chemical universes", i.e., very large sets, potentially infinite sets of compounds that can be constructed by a prescribed collection of reac…
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…
Maximizing Output and Recognizing Autocatalysis in Chemical Reaction Networks is NP-Complete
Jakob L. Andersen, Christoph Flamm, Daniel Merkle +1
Background: A classical problem in metabolic design is to maximize the production of desired compound in a given chemical reaction network by appropriately directing the mass flow…