| 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 |
| 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 |
| 2019 | KES | A pattern-based approach to a cell tracking ontology. | Patryk Burek, Nico Scherf, Heinrich Herre |
| 2017 | HealthCom | Outline of the construction and application of a GFO-based TCM diagnoses ontology for syndrome differentiation of psoriasis vulgaris. | Hai Long, Yan Zhu, Lirong Jia, Junhui Wang, Heinrich Herre |
| 2016 | FOIS | Towards an Ontology of Space for GFO. | Ringo Baumann, Frank Loebe, 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 |
| 2012 | FOIS | Ontology of Time in GFO. | Ringo Baumann, Frank Loebe, Heinrich Herre |
| 2009 | SoMeT | Ontological Analysis of Functional Decomposition. | Patryk Burek, Heinrich Herre, Frank Loebe |
| 2009 | SoMeT | Developing Consistent and Modular Software Models with Ontologies. | Robert Hoehndorf, Axel-Cyrille Ngonga Ngomo, Heinrich Herre |
| 2008 | FOIS | Formal Semantics and Ontologies - Towards an Ontological Account of Formal Semantics. | Frank Loebe, Heinrich Herre |
| 2008 | IDC | A Platform for Collaborative Management of Semantic Grid Metadata. | Michael Hartung, Frank Loebe, Heinrich Herre, Erhard Rahm |
| 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 |
| 2005 | AIME | Ontology of Time and Situoids in Medical Conceptual Modeling. | Heinrich Herre, Barbara Heller |
| 2004 | EKAW | On the Foundations of UML as an Ontology Representation Language. | Giancarlo Guizzardi, Gerd Wagner, Heinrich Herre |
| 2004 | EKAW | The Theory of Top-Level Ontological Mappings and Its Application to Clinical Trial Protocols. | Barbara Heller, Heinrich Herre, Kristin Lippoldt |
| 2002 | CoopIS | Towards Ontological Foundations for UML Conceptual Models. | Giancarlo Guizzardi, Heinrich Herre, Gerd Wagner |
| 2002 | ER | On the General Ontological Foundations of Conceptual Modeling. | Giancarlo Guizzardi, Heinrich Herre, Gerd Wagner |
| 2001 | FOIS | GOL: toward an axiomatized upper-level ontology. | Wolfgang Degen, Barbara Heller, Heinrich Herre, Barry Smith |
| 1995 | ECSQARU | Nonmonotonic Belief State Frames and Reasoning Frames (extended abstract). | Joeri Engelfriet, Heinrich Herre, Jan Treur |
| 1994 | JELIA | Compactness Properties of Nonmonotonic Inference Operations. | Heinrich Herre |
| 1992 | JELIA | Disjunctive Logic Programming, Constructivity and Strong Negation. | Heinrich Herre, David Pearce |
| 1991 | KI | Non-Monotonic Reasoning For Clause Logic Programming In A General Setting. | Heinrich Herre |