| 2023 | ER | Ontology patterns for function modeling with GFO (short paper). | Patryk Burek, Frank Loebe, Heinrich Herre |
| 2021 | KES | Overview of GFO 2.0 Functions: An ontology module for representing teleological knowledge. | Patryk Burek, Frank Loebe, Heinrich Herre |
| 2021 | KES | Cybersecurity Ontology for Dynamic Analysis of IT Systems. | Jakub Pastuszuk, Patryk Burek, Bogdan Ksiezopolski |
| 2020 | EKAW | On the Formal Representation and Annotation of Cellular Genealogies. | Patryk Burek, Nico Scherf, Heinrich Herre |
| 2020 | FOIS | Towards GFO 2.0: Architecture, Modules and Applications. | Patryk Burek, Frank Loebe, Heinrich Herre |
| 2020 | KES | A Lightweight Approach to the Multi-perspective Modeling of Processes and Objects. | Patryk Burek, Heinrich Herre |
| 2020 | KES | Towards a Modern Ontology Development Environment. | Adrian Stadnicki, Filip Filip Pietron, Patryk Burek |
| 2019 | KES | A pattern-based approach to a cell tracking ontology. | Patryk Burek, Nico Scherf, Heinrich Herre |
| 2014 | GI | Search Ontology, a new approach towards Semantic Search. | Alexandr Uciteli, Christoph Goller, Patryk Burek, Sebastian Siemoleit, Breno Faria, Halyna Galanzina, Timo Weiland, Doreen Drechsler-Hake, Wolfram Bartussek, Heinrich Herre |
| 2013 | GI | Representation, Realization, and Ascription of Functions for Material Entities. | Patryk Burek, Heinrich Herre |
| 2009 | SoMeT | Ontological Analysis of Functional Decomposition. | Patryk Burek, Heinrich Herre, Frank Loebe |
| 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 |
| 2005 | KES | Essentialized Conceptual Structures in Ontology Modeling. | Patryk Burek |
| 2004 | AIMSA | Adoption of the Classical Theory of Definition to Ontology Modeling. | Patryk Burek |