Research Scientist @ European Molecular Biology Laboratory (EMBL)

Publications

Published Papers

  1. Integration of variant annotations using deep set networks boosts rare variant association testing.
    Brian Clarke, Eva Holtkamp, Hakime Öztürk, Marcel Mück, Magnus Wahlberg, Kayla Meyer, Felix Munzlinger, Felix Brechtmann, Florian R Hölzlwimmer, Jonas Lindner, Zhifen Chen, Julien Gagneur, Oliver Stegle.
    Nature Genetics (2024)

  2. Chemboost: A chemical language based approach for protein–ligand binding affinity prediction.
    Özcelik, Riza, Hakime Öztürk, Arzucan Özgür and Elif Ozkirimli.
    Molecular Informatics (2021)

  3. 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)

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

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

  6. 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) |

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

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

  9. 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)

Thesis

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

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