| 2021 | PSB | Frequent Subgraph Mining of Functional Interaction Patterns Across Multiple Cancers. | Arda Durmaz, Tim A. D. Henderson, Grkan Bebek |
| 2017 | PSB | Frequent Subgraph Mining of Personalized Signaling Pathway Networks Groups Patients with Frequently Dysregulated Disease Pathways and Predicts Prognosis. | Arda Durmaz, Tim A. D. Henderson, Douglas Brubaker, Grkan Bebek |
| 2014 | PSB | Drug Intervention Response Predictions with Paradigm (DIRPP) Identifies Drug Resistant Cancer Cell Lines and Pathway Mechanisms of Resistance. | Douglas Brubaker, Analisa Difeo, Yanwen Chen, Taylor Pearl, Kaide Zhai, Grkan Bebek, Mark R. Chance, Jill S. Barnholtz-Sloan |
| 2013 | PSB | Session introduction. | Grkan Bebek, Mehmet Koyutrk, Thomas LaFramboise, Benjamin J. Raphael, Mark R. Chance |
| 2011 | PSB | Session Introduction. | Grkan Bebek, Mehmet Koyutrk, Mark R. Chance, Nathan D. Price |
| 2011 | RECOMB | Disease Gene Prioritization Based on Topological Similarity in Protein-Protein Interaction Networks. | Sinan Erten, Grkan Bebek, Mehmet Koyutrk |
| 2005 | RECOMB | Improved Duplication Models for Proteome Network Evolution. | Grkan Bebek, Petra Berenbrink, Colin Cooper, Tom Friedetzky, Joseph H. Nadeau, Sleyman Cenk Sahinalp |