| 2024 | NeSy | Large-Scale Knowledge Integration for Enhanced Molecular Property Prediction. | Yasir Ghunaim, Robert Hoehndorf |
| 2024 | NeSy | Enhancing Geometric Ontology Embeddings for | Olga Mashkova, Fernando Zhapa-Camacho, Robert Hoehndorf |
| 2024 | NeSy | Lattice-Preserving | Fernando Zhapa-Camacho, Robert Hoehndorf |
| 2023 | NeSy | From Axioms over Graphs to Vectors, and Back Again: Evaluating the Properties of Graph-based Ontology Embeddings. | Fernando Zhapa-Camacho, Robert Hoehndorf |
| 2022 | IJCAI | Positive-Unlabeled Learning with Adversarial Data Augmentation for Knowledge Graph Completion. | Zhenwei Tang, Shichao Pei, Zhao Zhang, Yongchun Zhu, Fuzhen Zhuang, Robert Hoehndorf, Xiangliang Zhang |
| 2019 | IJCAI | EL Embeddings: Geometric Construction of Models for the Description Logic EL++. | Maxat Kulmanov, Wang Liu-Wei, Yuan Yan, Robert Hoehndorf |
| 2019 | WWW | Semi-Supervised Entity Alignment via Knowledge Graph Embedding with Awareness of Degree Difference. | Shichao Pei, Lu Yu, Robert Hoehndorf, Xiangliang Zhang |
| 2016 | FOIS | Large-Scale Reasoning over Functions in Biomedical Ontologies. | Robert Hoehndorf, Liam Mencel, Georgios V. Gkoutos, Paul N. Schofield |
| 2012 | PSB | Linking PharmGKB to Phenotype Studies and Animal Models of Disease for Drug Repurposing. | Robert Hoehndorf, Anika Oellrich, Dietrich Rebholz-Schuhmann, Paul N. Schofield, Georgios V. Gkoutos |
| 2010 | FOIS | Realism for scientific ontologies. | Michel Dumontier, Robert Hoehndorf |
| 2009 | SoMeT | Developing Consistent and Modular Software Models with Ontologies. | Robert Hoehndorf, Axel-Cyrille Ngonga Ngomo, Heinrich Herre |
| 2007 | WWW | BOWiki - a Collaborative Annotation and Ontology Curation Framework. | Michael Backhaus, Janet Kelso, Joshua Bacher, Heinrich Herre, Robert Hoehndorf, Frank Loebe, Johann Visagie |
| 2006 | ISMB | A top-level ontology of functions and its application in the Open Biomedical Ontologies. | Patryk Burek, Robert Hoehndorf, Frank Loebe, Johann Visagie, Heinrich Herre, Janet Kelso |