| 2015 | CaiSE | Lessons from a Hospital Business Intelligence Implementation. | Thodoros Topaloglou, Daniele Barone |
| 2015 | EUSPN | COC: An Ontology for Capturing Semantics of Circle of Care. | Xiao Dong, Reza Samavi, Thodoros Topaloglou |
| 2012 | CaiSE | Business Intelligence Modeling in Action: A Hospital Case Study. | Daniele Barone, Thodoros Topaloglou, John Mylopoulos |
| 2008 | ER | Designing Privacy-Aware Personal Health Record Systems. | Reza Samavi, Thodoros Topaloglou |
| 2007 | RE | Goal-Oriented Conceptual Database Design. | Lei Jiang, Thodoros Topaloglou, Alexander Borgida, John Mylopoulos |
| 2006 | ER | Managing Data in High Throughput Laboratories: An Experience Report from Proteomics. | Thodoros Topaloglou |
| 2006 | RE | Incorporating Goal Analysis in Database Design: A Case Study from Biological Data Management. | Lei Jiang, Thodoros Topaloglou, Alexander Borgida, John Mylopoulos |
| 2004 | VLDB | Biological Data Management: Research, Practice and Opportunities. | Thodoros Topaloglou, Susan B. Davidson, H. V. Jagadish, Victor M. Markowitz, Evan W. Steeg, Mike Tyers |
| 2001 | BIBE | Applying Data Warehousing Concepts to Gene Expression Data Management. | Victor M. Markowitz, Thodoros Topaloglou |
| 2000 | ISMB | An Evaluation of Ontology Exchange Languages for Bioinformatics. | Robin McEntire, Peter D. Karp, Neil F. Abernethy, David Benton, Gregg Helt, Matt DeJongh, Robert Kent, Anthony Kosky, Suzanna Lewis, Dan Hodnett, Eric P. Neumann, Frank Olken, Dhiraj K. Pathak, Peter Tarczy-Hornoch, Luca Toldo, Thodoros Topaloglou |
| 1999 | ISMB | Seamless Integration of Biological Applications within a Database Framework. | Thodoros Topaloglou, Anthony Kosky, Victor M. Markowitz |
| 1998 | ISMB | Advanced Query Mechanisms for Biological Databases. | I-Min A. Chen, Anthony Kosky, Victor M. Markowitz, Ernest Szeto, Thodoros Topaloglou |
| 1996 | AI | Efficient Algorithms for Qualitative Reasoning about Imprecise Space. | Thodoros Topaloglou |
| 1996 | ER | Representing Partial Spatial Information in Databases. | Thodoros Topaloglou, John Mylopoulos |
| 1995 | CIKM | Query Processing for Knowledge Bases Using Join Indices. | Adel Shrufi, Thodoros Topaloglou |
| 1993 | CIKM | Storage Management for Knowledge Bases. | Thodoros Topaloglou |
| 1992 | ICDE | Query Optimization for KBMSs: Temporal, Syntactic and Semantic Transformantions. | Thodoros Topaloglou, Arantza Illarramendi, Licia Sbattella |