| 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 | A Generic Framework for Engineering Graph Canonization Algorithms. | Jakob L. Andersen, Daniel Merkle |
| 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 | DNA | DNA-Templated Synthesis Optimization. | Bjarke N. Hansen, Kim S. Larsen, Daniel Merkle, Alexei Mihalchuk |
| 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 |
| 2014 | ALIFE | Towards an Optimal DNA-Templated Molecular Assembler. | Jakob L. Andersen, Christoph Flamm, Martin M. Hanczyc, Daniel Merkle |
| 2014 | ICFP | Group communication patterns for high performance computing in scala. | Felix Palludan Hargreaves, Daniel Merkle, Peter Schneider-Kamp |
| 2013 | PPAM | FooPar: A Functional Object Oriented Parallel Framework in Scala. | Felix Palludan Hargreaves, Daniel Merkle |
| 2012 | CP | Exploring Chemistry Using SMT. | Rolf Fagerberg, Christoph Flamm, Daniel Merkle, Philipp Peters |
| 2010 | ALIFE | Barrier Trees for Continuous Fitness Landscapes. | Jacob Midtgaard-Olesen, Carsten Baldauf, Daniel Merkle |
| 2009 | CPM | Finding All Sorting Tandem Duplication Random Loss Operations. | Matthias Bernt, Ming-Chiang Chen, Daniel Merkle, Hung-Lung Wang, Kun-Mao Chao, Martin Middendorf |
| 2008 | RECOMB | An Algorithm for Inferring Mitogenome Rearrangements in a Phylogenetic Tree. | Matthias Bernt, Daniel Merkle, Martin Middendorf |
| 2005 | ICCS | Modelling Ant Brood Tending Behavior with Cellular Automata. | Daniel Merkle, Martin Middendorf, Alexander Scheidler |
| 2005 | PPAM | A Parallel Algorithm for Solving the Reversal Median Problem. | Matthias Bernt, Daniel Merkle, Martin Middendorf |
| 2002 | GECCO | Studies On The Dynamics Of Ant Colony Optimization Algorithms. | Daniel Merkle, Martin Middendorf |
| 2001 | EMO | Bi-Criterion Optimization with Multi Colony Ant Algorithms. | Steffen Iredi, Daniel Merkle, Martin Middendorf |
| 2000 | GECCO | Ant Colony Optimization for Resource-Constrained Projet Scheduling. | Daniel Merkle, Martin Middendorf, Hartmut Schmeck |