- Burcak Otlu Saritas, Ph.D., 2017.
Thesis title: Tools and Techniques for Assessing Functional Relevance of Genomic Loci.
- Andac Akarsu, M.Sc., 2017.
Thesis title: A Layout Algorithm for Visualization of Graph Alignments.
- Ahmet Rasit Ozturk, Ph.D., 2016.
Thesis title: A Multiplex Primer Design Algorithm for Target Amplification of Continuous Genomic Regions.
- Umit Aslan, M.Sc., 2014.
Thesis title: Determination of the Effect of Polyadenylation SLR Values on Microarray Data Classification.
- Caglar Ata, M.Sc., 2014.
Thesis title: A Database Query Based Solution for Chemical Compound and Drug Name Recognition.
- Selin Sekmen, M.Sc., 2014.
Thesis title: Modeling of Split Step Parabolic Wave Equation Using the Graphics Processing Unit.
- Mehmet Emre Sahin, Ph.D., 2014.
Thesis title:Identification of Interaction Sites of G Protein-Coupled Receptors Using Machine Learning Techniques.
- Oyku Eren Ozsoy, Ph.D., 2014.
Thesis title: Integer Linear Programming Based Solutions for Construction of Biological Networks.
- Yigit Ilguner, M.Sc., 2013.
Thesis title: Prediction of Polyadenylation Sites By Probe Level Analysis of Microarray Data.
- Erhan Akdemir, M.Sc., 2013.
Thesis title:A Framework for Gene Coexpression Network Analysis of Lung Cancer.
- Onur Baloglu, M.Sc., 2013.
Thesis title: Analysis of 3'UTR Shortening Events in Breast Cancer
- Merter Sualp, Ph.D., 2013.
Thesis title: Machine Learning Methods for Using Network Based Information in microRNA Target Prediction
- Seyedsasan Hashemikhabir, M.S. 2012.
Thesis title: SINEC: Large Scale Signaling Network Topology Reconstruction Using
Protein-Protein Interactions and RNAI Data
- Eyup Serdar Ayaz, M.S. 2011.
Thesis title: Reconstructing Signaling Pathways from RNAi Data Using Genetic Algorithms
- Hilal Kilic, M.S. 2011.
Thesis title: Machine Learning Methods for Promoter Region Prediction
- Emrah Akkoyun, M.S. 2011.
Thesis title: Parallelization of Functional Flow to Predict Protein Functions
- Omer Nebil Yaveroglu,
Thesis title: Identification of Functionally Orthologous Protein Groups in Different Species based on Protein Network Alignment
- Anil Yigit Filiz,
Thesis title: A New Approach for Better Load Balancing of Visibility Detection and Target Acquisition Calculations
- Sertan Alkan,
Thesis title: A Graph Mining Framework based on MapReduce
- Munir Ercan,
Thesis title: A 3D Topological Tracking System For Augmented Reality
- Sevgi Yasar,
Thesis title: Multi-Resolution Visualization of Large Scale Protein Networks Enriched with Gene Ontology Annotations
- Dogacan Guney,
Thesis title: Prediction of Protein-Protein Interactions from Sequence Using Evolutionary Relations of Proteins and Species
- Furkan Kuru,
Thesis title: A Script Based Modular Game Engine Framework for Augmented Reality
- Bahar Pamuk,
Thesis title: Coevolution Based Prediction Of Protein-Protein Interactions With Reduced Training Data
- Melih Engin,
Thesis title: Text Classification In the Turkish Marketing Domain And Context-Sensitive Ad Distribution
- Mehmet Emin Turanalp,
Ph.D. 2009 (co-supervised).
Thesis title: Biological Graph Mining: Identification of Frequent Subgraphs and Use of Subgraph Patterns in Protein-Protein Interaction Prediction