| 2007 | ER | An Extendable System for Conceptual Modeling and Simulation of Signal Transduction Pathways. | Silke Eckstein, Claudia Tubner |
| 2007 | ICDM | Discovering Gene Expression Data from the Tables of Full Text Publications. | Brigitte Mathiak, Andreas Kupfer, Carolina Rio Bartulos, Tatjana Scope, Johann Weiland, Silke Eckstein |
| 2007 | ICDM | Modeling and Management of Signal Transduction Pathways with Live Sequence Charts. | Claudia Tubner, Brigitte Mathiak, Silke Eckstein |
| 2006 | CBMS | A Coevolution Approach for Database Schemas and Related Ontologies. | Andreas Kupfer, Silke Eckstein, Karl Neumann, Brigitte Mathiak |
| 2006 | ER | Handling Changes of Database Schemas and Corresponding Ontologies. | Andreas Kupfer, Silke Eckstein, Karl Neumann, Brigitte Mathiak |
| 2006 | ICDM | Using image classification for biomedical literature retrieval. | Brigitte Mathiak, Andreas Kupfer, Tatjana Scope, Britta Strmann, Silke Eckstein |
| 2006 | PAKDD | Improving Literature Preselection by Searching for Images. | Brigitte Mathiak, Andreas Kupfer, Richard Mnch, Claudia Tubner, Silke Eckstein |
| 2003 | CaiSE | Conceptual Modelling of Mobile Object Systems: Some Language Constructs. | Peter Ahlbrecht, Silke Eckstein, Karl Neumann |
| 2003 | COMPSAC | Conceptual Modelling of Mobile Object Systems: Language Constructs for Distinguishing Between Mobile and Stationary Subsystems. | Peter Ahlbrecht, Silke Eckstein, Karl Neumann |
| 2001 | CaiSE | Increasing Reusability in Information Systems Development by Applying Generic Methods. | Silke Eckstein, Peter Ahlbrecht, Karl Neumann |
| 1998 | ER | The TROLL Approach to Conceptual Modeling: Syntax, Semantics and Tools. | Antonio Grau, Juliana Kster Filipe, Mojgan Kowsari, Silke Eckstein, Ralf Pinger, Hans-Dieter Ehrich |