| 2014 | CIKM | High Impact Academic Paper Prediction Using Temporal and Topological Features. | Feruz Davletov, Ali Selman Aydin, Ali Cakmak |
| 2010 | SAC | Advanced querying interface for biochemical network databases. | Brendan Elliott, Stephen Mayes, Ali Cakmak, Gultekin zsoyoglu, Z. Meral zsoyoglu |
| 2008 | EDBT | Taxonomy-superimposed graph mining. | Ali Cakmak, Gultekin zsoyoglu |
| 2007 | ICDE | Evaluating Different Ranking Functions for Context-Based Literature Search. | Nattakarn Ratprasartporn, Sulieman Bani-Ahmad, Ali Cakmak, Jonathan Po, Gultekin zsoyoglu |
| 2007 | PSB | Annotating Genes Using Textual Patterns. | Ali Cakmak, Gultekin zsoyoglu |
| 2007 | SSDBM | Gene Ontology-Based Annotation Analysis and Categorization of Metabolic Pathways. | Ali Cakmak, Mustafa Kirac, Marc R. Reynolds, Z. Meral zsoyoglu, Gultekin zsoyoglu |
| 2006 | SSDBM | Task-Oriented Integrated Use of Biological Web Data Sources. | Mustafa Kirac, Ali Cakmak, Gultekin zsoyoglu |
| 2006 | SSDBM | On Data and Visualization Models for Signaling Pathways. | Nattakarn Ratprasartporn, Ali Cakmak, Gultekin zsoyoglu |