PRER: A patient representation with pairwise relative expression of proteins on biological networks. - Halil Ibrahim Kuru; Mustafa Buyukozkan; Öznur Tastan (PLoS Comput. Biol., 2021)

MatchMaker: A Deep Learning Framework for Drug Synergy Prediction. - Halil Ibrahim Kuru; Öznur Tastan; A. Ercüment Çiçek (IEEE ACM Trans. Comput. Biol. Bioinform., 2022)

DeepSide: A Deep Learning Approach for Drug Side Effect Prediction. - Onur Can Uner; Halil Ibrahim Kuru; Ramazan Gokberk Cinbis; Öznur Tastan; A. Ercüment Çiçek (IEEE ACM Trans. Comput. Biol. Bioinform., 2023)