Publications

Published Papers

1. Exploring chemical space using natural language processing methodologies for drug discovery.
   Öztürk, Hakime, Arzucan Özgür, Philippe Schwaller, Teodoro Laino and Elif Ozkirimli.
   Drug Discovery Today (2020)

2. DeepDTA: Deep Drug-Target Binding Affinity Prediction.
   Öztürk, Hakime, Elif Ozkirimli and Arzucan Özgür .
   Bioinformatics (2018) | www

3. A novel methodology on distributed representations of proteins using their interacting ligands.
   Öztürk, Hakime, Elif Ozkirimli, and Arzucan Özgür.
   Bioinformatics (2018) |www

4. Construction of miRNA-miRNA networks revealing the complexity of miRNA-mediated mechanisms in trastuzumab treated breast cancer cell lines.
   Cilek, Emine Ezel, Hakime Ozturk, and Bala Gur Dedeoglu
   PloS one (2017) |
   

5. BIOSSES: a semantic sentence similarity estimation system for the biomedical domain.
   Soğancıoğlu, Gizem, Hakime Öztürk, and Arzucan Özgür.
   Bioinformatics (2017) | www

6. A comparative study of SMILES-based compound similarity functions for drug-target interaction prediction.
   Öztürk, Hakime, Elif Ozkirimli, and Arzucan Özgür.
   BMC bioinformatics (2016) |

7. Classification of Beta-lactamases and penicillin binding proteins using ligand-centric network models.
   Öztürk, Hakime, Elif Ozkirimli, and Arzucan Özgür.
   PloS one (2015) | PLITOOL

Workshop Papers

1. CNN-based Chemical-Protein Interactions Classification
   Yüksel, Atakan, Hakime Öztürk, Arzucan Özgür and Elif Ozkirimli.
   Proceedings of the BioCreative VI Workshop, Bethesda, MD
   

Preprints

1. WideDTA: prediction of drug-target binding affinity
   Hakime Öztürk, Arzucan Özgür and Elif Ozkirimli.
   arXiv Preprint (2019)

2. A chemical language based approach for protein-ligand interaction prediction
   Hakime Öztürk, Arzucan Özgür and Elif Ozkirimli.
   arXiv Preprint (2018)

Thesis

Text-based Machine Learning Methodologies for Modelling Drug-Target Interactions.
PhD Thesis - 2019

Analysing Drug Targets using Ligand Similarity.
MSc Thesis - 2014 .