Forbidden Time Travel: Characterization of Time-Consistent Tree Reconciliation Maps. - Nikolai Nøjgaard; Manuela Geiß; Daniel Merkle; Peter F. Stadler; Nicolas Wieseke; Marc Hellmuth (WABI, 2017)

Partial Orthology, Paralogy and Xenology Relations - Satisfiability in terms of Di-Cographs. - Nikolai Nøjgaard; Nadia El-Mabrouk; Daniel Merkle; Nicolas Wieseke; Marc Hellmuth (CoRR, 2017)

Linear Time Canonicalization and Enumeration of Non-Isomorphic 1-Face Embeddings. - Marc Hellmuth; Anders S. Knudsen; Michal Kotrbcík; Daniel Merkle; Nikolai Nøjgaard (ALENEX, 2018)

Partial Homology Relations - Satisfiability in Terms of Di-Cographs. - Nikolai Nøjgaard; Nadia El-Mabrouk; Daniel Merkle; Nicolas Wieseke; Marc Hellmuth (COCOON, 2018)

Time-consistent reconciliation maps and forbidden time travel. - Nikolai Nøjgaard; Manuela Geiß; Daniel Merkle; Peter F. Stadler; Nicolas Wieseke; Marc Hellmuth (Algorithms Mol. Biol., 2018)

Atom Tracking Using Cayley Graphs. - Marc Hellmuth; Daniel Merkle; Nikolai Nøjgaard (ISBRA, 2020)

A Graph-Based Tool to Embed the π-Calculus into a Computational DPO Framework. - Jakob Lykke Andersen; Marc Hellmuth; Daniel Merkle; Nikolai Nøjgaard; Marco Peressotti (SOFSEM (Doctoral Student Research Forum), 2020)

Combining Orthology and Xenology Data in a Common Phylogenetic Tree. - Marc Hellmuth; Mira Michel; Nikolai N. Nøjgaard; David Schaller 001; Peter F. Stadler (BSB, 2021)

Graph transformation for enzymatic mechanisms. - Jakob L. Andersen; Rolf Fagerberg; Christoph Flamm; Walter Fontana; Juraj Kolcák; Christophe V. F. P. Laurent; Daniel Merkle; Nikolai Nøjgaard (Bioinform., 2021)

Cayley Graphs of Semigroups Applied to Atom Tracking in Chemistry. - Nikolai Nøjgaard; Walter Fontana; Marc Hellmuth; Daniel Merkle (J. Comput. Biol., 2021)

Efficient Modular Graph Transformation Rule Application. - Jakob L. Andersen; Rolf Fagerberg; Juraj Kolcák; Christophe V. F. P. Laurent; Daniel Merkle; Nikolai Nøjgaard (CoRR, 2022)

Characterizing Catalytic Mechanisms with Overlay Graphs. - Jakob L. Andersen; Rolf Fagerberg; Christoph Flamm; Walter Fontana; Juraj Kolcák; Christophe V. F. P. Laurent; Daniel Merkle; Nikolai Nøjgaard (CoRR, 2022)

Representing Catalytic Mechanisms with Rule Composition. - Jakob L. Andersen; Rolf Fagerberg; Christoph Flamm; Walter Fontana; Juraj Kolcák; Christophe V. F. P. Laurent; Daniel Merkle; Nikolai Nøjgaard (J. Chem. Inf. Model., 2022)

Generic Context-Aware Group Contributions. - Christoph Flamm; Marc Hellmuth; Daniel Merkle; Nikolai Nøjgaard; Peter F. Stadler (IEEE ACM Trans. Comput. Biol. Bioinform., 2022)

Automated Inference of Graph Transformation Rules. - Jakob L. Andersen; Akbar Davoodi; Rolf Fagerberg; Christoph Flamm; Walter Fontana; Juraj Kolcák; Christophe V. F. P. Laurent; Daniel Merkle; Nikolai Nøjgaard (CoRR, 2024)