Education

Bogazici University, Istanbul, Turkey
PhD in Computer Engineering    2014- 2019
M.S. in Computer Engineering    2012- 2014
Advisor: Prof. Arzucan Ozgur
Co-advisor: Prof. Elif Ozkirimli

Dokuz Eylul University, Izmir, Turkey
B.S. in Computer Engineering (with Honors)    2008- 2012
Advisor: Prof. Suleyman Sevinc


Short Bio

Hakime Öztürk received her PhD degree from the Department of Computer Engineering in Boğaziçi University in 2019. Her research interests include Bioinformatics, Information Retrieval and Machine Learning.
Hakime is a member of AILAB, TABILAB, and OzkirimliLab
She is also proud of being mentor in DjangoGirls events.


Research Summary




Published Papers

1. DeepDTA: Deep Drug-Target Binding Affinity Prediction
   Öztürk, Hakime, Arzucan Özgür and Elif Ozkirimli.
   Bioinformatics (2018), Accepted for publication |pdf | DeepDTA
   
2. A novel methodology on distributed representations of proteins using their interacting ligands
   Öztürk, Hakime, Elif Ozkirimli, and Arzucan Özgür.
   Bioinformatics (2018) | pdf | SMILESVec-based protein representation
   
3. 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) | pdf
   
4. BIOSSES: a semantic sentence similarity estimation system for the biomedical domain.
   Soğancıoğlu, Gizem, Hakime Öztürk, and Arzucan Özgür.
   Bioinformatics (2017) | pdf | BIOSSES
5. A comparative study of SMILES-based compound similarity functions for drug-target interaction prediction.
   Öztürk, Hakime, Elif Ozkirimli, and Arzucan Özgür.
   BMC bioinformatics (2016) | pdf | PLITOOL
   
6. Classification of Beta-lactamases and penicillin binding proteins using ligand-centric network models.
   Öztürk, Hakime, Elif Ozkirimli, and Arzucan Özgür.
   PloS one (2015) | pdf | web | 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 |pdf

Preprints

1. WideDTA: prediction of drug-target binding affinity
   Hakime Öztürk, Arzucan Özgür and Elif Ozkirimli.
   arXiv Preprint |pdf
2. A chemical language based approach for protein-ligand interaction prediction
   Hakime Öztürk, Arzucan Özgür and Elif Ozkirimli.
   arXiv Preprint |pdf

Oral Presentation

• DeepDTA: deep drug-target binding affinity prediction
  Hakime Öztürk, Arzucan Özgür and Elif Ozkirimli.
  17th European Conference on Computational Biology (ECCB)
  Athens, Greece, 2018
  

• A novel methodology on distributed representations of proteins using their interacting ligands
  Hakime Öztürk, Elif Ozkirimli and Arzucan Ozgur.
  26th Conference on Intelligent Systems for Molecular Biology (ISMB)
  Chicago, IL, USA, 2018
  

• A novel methodology on distributed representations of proteins using their interacting ligands: A case-study on Sphingolipid Metabolic Pathway.
  Hakime Öztürk, Mehmet Aziz Yirik, Arzucan Ozgur, Elif Ozkirimli, Kutlu O. Ulgen.
  5th International BAU Drug Design Congress, İstanbul, 2017

Poster Presentation

• DeepDTA: deep drug-target binding affinity prediction
  Hakime Öztürk, Arzucan Özgür and Elif Ozkirimli.
  17th European Conference on Computational Biology (ECCB)
  Athens, Greece, 2018 | poster
  
• A novel methodology on distributed representations of proteins using their interacting ligands
  Hakime Öztürk, Elif Ozkirimli and Arzucan Ozgur.
  26th Conference on Intelligent Systems for Molecular Biology (ISMB)
  Chicago, IL, USA, 2018 | poster
  
• A novel methodology on distributed representations of proteins using their interacting ligands: A case-study on Sphingolipid Metabolic Pathway.
  Hakime Öztürk, Mehmet Aziz Yirik, Arzucan Ozgur, Elif Ozkirimli, Kutlu O. Ulgen.
  25th Conference on Intelligent Systems for Molecular Biology and the 16th European Conference on Computational Biology (ISMB/ECCB)
  Prague, Czech Republic, 2017 | poster
  
• SMILES-based Molecular Similarity Functions for Drug-Target Interaction Prediction.
  Hakime Öztürk, Elif Ozkirimli, and Arzucan Özgür.
  International Symposium on Health Informatics and Bioinformatics (HIBIT)
  Mugla, Turkey. October, 2015 | poster
  
• Analysing β-lactamase networks created using ligand-binding information.
  Hakime Öztürk, Elif Ozkirimli, and Arzucan Özgür.
  International Symposium on Health Informatics and Bioinformatics (HIBIT).
  Ankara, Turkey. September, 2013 | poster

Master Thesis

Analysing Drug Targets using Ligand Similarity.
Hakime Öztürk
Bogazici University, 2014
Master Thesis

PhD Thesis

Text-based Machine Learning Methodologies for Modelling Drug-Target Interactions.
Hakime Öztürk
Bogazici University, 2019
PhD Thesis

Last updated 2019-04-12