| 2020 | GECCO | A weighted population update rule for PACO applied to the single machine total weighted tardiness problem. | Daniel Abitz, Tom Hartmann, Martin Middendorf |
| 2015 | GECCO | Evolutionary Inheritance Mechanisms for Multi-criteriaDecision Making in Multi-agent Systems. | Ruby L. V. Moritz, Martin Middendorf |
| 2015 | GECCO | A Visual Method for Analysis and Comparison of Search Landscapes. | Sebastian Volke, Dirk Zeckzer, Gerik Scheuermann, Martin Middendorf |
| 2013 | GECCO | Refined ranking relations for multi objective optimization andapplication to P-ACO. | Ruby L. V. Moritz, Enrico Reich, Maik Schwarz, Matthias Bernt, Martin Middendorf |
| 2013 | WABI | Unifying Parsimonious Tree Reconciliation. | Nicolas Wieseke, Matthias Bernt, Martin Middendorf |
| 2012 | BIBE | Annotation guided local similarity search in multiple sequences and its application to mitochondrial genomes. | Ruby L. V. Moritz, Matthias Bernt, Martin Middendorf |
| 2012 | WABI | Preserving Inversion Phylogeny Reconstruction. | Matthias Bernt, Kun-Mao Chao, Jyun-Wei Kao, Martin Middendorf, Eric Tannier |
| 2011 | GECCO | Bonding as a swarm: applying bee nest-site selection behaviour to protein docking. | Konrad Diwold, Daniel Himmelbach, Ren Meier, Carsten Baldauf, Martin Middendorf |
| 2010 | ALIFE | Bee Nest Site Selection as an Optimization Process. | Konrad Diwold, Madeleine Beekman, Martin Middendorf |
| 2010 | ICCCI | Sensor Placement in Water Networks Using a Population-Based Ant Colony Optimization Algorithm. | Konrad Diwold, Thomas Ruhnke, Martin Middendorf |
| 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 |
| 2009 | GECCO | Evolved cooperation and emergent communication structures in learning classifier based organic computing systems. | Alexander Scheidler, Martin Middendorf |
| 2008 | FPL | Hyperreconfigurable architectures. | Sebastian Lange, Martin Middendorf |
| 2008 | RECOMB | An Algorithm for Inferring Mitogenome Rearrangements in a Phylogenetic Tree. | Matthias Bernt, Daniel Merkle, Martin Middendorf |
| 2007 | CEC | An ant colony optimizer for melody creation with baroque harmony. | Michael Geis, 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 |
| 2004 | FCCM | Hyperreconfigurable Architectures for Fast Run Time Reconfiguration. | Sebastian Lange, Martin Middendorf |
| 2004 | FPL | The Partition into Hypercontexts Problem for Hyperreconfigurable Architectures. | Sebastian Lange, Martin Middendorf |
| 2003 | CEC | A hierarchical particle swarm optimizer. | Stefan Janson, Martin Middendorf |
| 2003 | EMO | Solving Multi-criteria Optimization Problems with Population-Based ACO. | Michael Guntsch, 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 | FPL | Task Rearrangement on Partially Reconfigurable FPGAs with Restricted Buffer. | Hossam A. ElGindy, Martin Middendorf, Hartmut Schmeck, Bernd Schmidt |
| 2000 | GECCO | Ant Colony Optimization for Resource-Constrained Projet Scheduling. | Daniel Merkle, Martin Middendorf, Hartmut Schmeck |
| 1998 | EuroPar | On Optimal k-linear Scheduling of Tree-Like Graphs for LogP-Machines. | Wolf Zimmermann, Martin Middendorf, Welf Lwe |
| 1998 | PPSN | An Island Model Based Ant System with Lookahead for the Shortest Supersequence Problem. | Ren Michel, Martin Middendorf |
| 1994 | ISAAC | On the Approximation of Finding Various Minimal, Maximal, and Consistent Sequences. | Martin Middendorf |