| 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 |
| 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 | PPAM | A Parallel Algorithm for Solving the Reversal Median Problem. | Matthias Bernt, Daniel Merkle, Martin Middendorf |