Bacteria Biotope Detection, Ontology-based Normalization, and Relation Extraction using Syntactic Rules. - Ilknur Karadeniz; Arzucan Özgür (BioNLP@ACL (Shared Task), 2013)

PHISTO: pathogen-host interaction search tool. - Saliha Durmus Tekir; Tunahan Çakir; Emre Ardiç; Ali Semih Sayilirbas; Gökhan Konuk; Mithat Konuk; Hasret Sariyer; Azat Ugurlu; Ilknur Karadeniz; Arzucan Özgür; Fatih Erdogan Sevilgen; Kutlu Ö. Ülgen (Bioinform., 2013)

Detection and categorization of bacteria habitats using shallow linguistic analysis. - Ilknur Karadeniz; Arzucan Özgür (BMC Bioinform., 2015)

BOUN-ISIK Participation: An Unsupervised Approach for the Named Entity Normalization and Relation Extraction of Bacteria Biotopes. - Ilknur Karadeniz; Ömer Faruk Tuna; Arzucan Özgür (BioNLP-OST@EMNLP-IJNCLP, 2019)

Linking entities through an ontology using word embeddings and syntactic re-ranking. - Ilknur Karadeniz; Arzucan Özgür (BMC Bioinform., 2019)

Ontology-based entity tagging and normalization in the biomedical domain (Biyomedikal alanda ontoloji tabanlı varlık ismi etiketleme ve normalizasyonu) - Ilknur Karadeniz (2019)

Protein Interaction Prediction on PHI Networks Using Graph Convolution Networks. - Mehmet Burak Koca; Ilknur Karadeniz; Esmaeil Nourani; Fatih Erdogan Sevilgen (SIU, 2021)

Graph convolutional network based virus-human protein-protein interaction prediction for novel viruses. - Mehmet Burak Koca; Esmaeil Nourani; Ferda Abbasoglu; Ilknur Karadeniz; Fatih Erdogan Sevilgen (Comput. Biol. Chem., 2022)

Clustering-Based Negative Sampling Approaches for Protein-Protein Interaction Prediction. - Zehra Kesemen; Ilknur Karadeniz; Reyhan Aydogan (CIBB, 2024)