| 2025 | PAKDD | Beyond Single Parsers: An Empirical Analysis of Dependency Parse Tree Aggregation. | Adithya Kulkarni, Mohna Chakraborty, Oliver Eulenstein, Qi Li |
| 2024 | FIE | Using Conceptual Blending to Teach Software Design Principles to Undergraduates. | Ashraf Gaffar, Mohamed Y. Selim, Oliver Eulenstein |
| 2022 | SDM | CPTAM: Constituency Parse Tree Aggregation Method. | Adithya Kulkarni, Nasim Sabetpour, Alexey Markin, Oliver Eulenstein, Qi Li |
| 2019 | COCOON | Feasibility Algorithms for the Duplication-Loss Cost. | Pawel Grecki, Alexey Markin, Oliver Eulenstein |
| 2019 | WABI | Consensus Clusters in Robinson-Foulds Reticulation Networks. | Alexey Markin, Oliver Eulenstein |
| 2018 | COCOON | Cophenetic Distances: A Near-Linear Time Algorithmic Framework. | Pawel Grecki, Alexey Markin, Oliver Eulenstein |
| 2018 | COCOON | Solving the Gene Duplication Feasibility Problem in Linear Time. | Alexey Markin, Venkata Sai Krishna Teja Vadali, Oliver Eulenstein |
| 2016 | COCOON | Highly Bi-Connected Subgraphs for Computational Protein Function Annotation. | Jucheol Moon, Iddo Friedberg, Oliver Eulenstein |
| 2012 | COCOON | Deep Coalescence Reconciliation with Unrooted Gene Trees: Linear Time Algorithms. | Pawel Grecki, Oliver Eulenstein |
| 2008 | ISMB | The multiple gene duplication problem revisited. | Mukul S. Bansal, Oliver Eulenstein |
| 2008 | RECOMB | Locating Multiple Gene Duplications through Reconciled Trees. | J. Gordon Burleigh, Mukul S. Bansal, Andr Wehe, Oliver Eulenstein |
| 2007 | RECOMB | Heuristics for the Gene-Duplication Problem: A | Mukul S. Bansal, J. Gordon Burleigh, Oliver Eulenstein, Andr Wehe |
| 2007 | WABI | An | Mukul S. Bansal, Oliver Eulenstein |
| 2006 | COCOON | Reconciling Gene Trees with Apparent Polytomies. | Wen-Chieh Chang, Oliver Eulenstein |
| 2002 | COCOON | Supertrees by Flipping. | Duhong Chen, Oliver Eulenstein, David Fernndez-Baca, Michael J. Sanderson |
| 2002 | PSB | Investigating Evolutionary Lines of Least Resistance Using the Inverse Protein-Folding Problem. | J. Schonfeld, Oliver Eulenstein, Kent Vander Velden, Gavin J. P. Naylor |