| 2023 | COCOON | Linear Time Algorithms for NP-Hard Problems Restricted to GaTEx Graphs. | Marc Hellmuth, Guillaume E. Scholz |
| 2023 | COCOON | Fitch Graph Completion. | Marc Hellmuth, Peter F. Stadler, Sandhya Thekkumpadan Puthiyaveedu |
| 2020 | SOFSEM | A Graph-Based Tool to Embed the π-Calculus into a Computational DPO Framework. | Jakob Lykke Andersen, Marc Hellmuth, Daniel Merkle, Nikolai Njgaard, Marco Peressotti |
| 2018 | ALENEX | Linear Time Canonicalization and Enumeration of Non-Isomorphic 1-Face Embeddings. | Marc Hellmuth, Anders S. Knudsen, Michal Kotrbck, Daniel Merkle, Nikolai Njgaard |
| 2018 | COCOON | Partial Homology Relations - Satisfiability in Terms of Di-Cographs. | Nikolai Njgaard, Nadia El-Mabrouk, Daniel Merkle, Nicolas Wieseke, Marc Hellmuth |
| 2017 | WABI | Forbidden Time Travel: Characterization of Time-Consistent Tree Reconciliation Maps. | Nikolai Njgaard, Manuela Gei, Daniel Merkle, Peter F. Stadler, Nicolas Wieseke, Marc Hellmuth |
| 2015 | COCOON | On Symbolic Ultrametrics, Cotree Representations, and Cograph Edge Decompositions and Partitions. | Marc Hellmuth, Nicolas Wieseke |