Publications by authors named "Elif Ozkirimli"

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Enhancing Severe Neutropenia Prediction: PKPD-Informed Labeling for Machine Learning Models Trained on Real-World Data.
Conor J O'Hanlon, Jonas Denck, Elif Ozkirimli, Stefanie Bendels, Candice Jamois

Clin Pharmacol Ther· November 2025

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Exploring data-driven chemical SMILES tokenization approaches to identify key protein-ligand binding moieties.
Asu Busra Temizer, Gökçe Uludoğan, Rıza Özçelik, Taha Koulani, Elif Ozkirimli

Mol Inform· March 2024

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A Computational Software for Training Robust Drug-Target Affinity Prediction Models: pydebiaseddta.
Melİh Barsbey, Riza ÖZçelİk, Alperen Bağ, Berk Atil, Arzucan ÖZgür, Elif Ozkirimli

J Comput Biol· November 2023

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A Framework for Improving the Generalizability of Drug-Target Affinity Prediction Models.
Riza ÖZçelİk, Alperen Bağ, Berk Atil, Melİh Barsbey, Arzucan ÖZgür, Elif Ozkirimli

J Comput Biol· November 2023

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Machine-learning-based adverse drug event prediction from observational health data: A review.
Jonas Denck, Elif Ozkirimli, Ken Wang

Drug Discov Today· September 2023

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Automatic Extraction of Medication Mentions from Tweets-Overview of the BioCreative VII Shared Task 3 Competition.
Davy Weissenbacher, Karen O'Connor, Siddharth Rawal, Yu Zhang, Richard Tzong-Han Tsai, Elif Ozkirimli

Database (Oxford)· February 2023

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Exploiting pretrained biochemical language models for targeted drug design.
Gökçe Uludoğan, Elif Ozkirimli, Kutlu O Ulgen, Nilgün Karalı, Arzucan Özgür

Bioinformatics· September 2022

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Carvacrol Enhances the Antimicrobial Potency of Berberine in Bacillus subtilis.
Basak Atas, Cemile Selin Aksoy, Fatma Gizem Avci, Nihat Alpagu Sayar, Kutlu Ulgen, Elif Ozkirimli

Curr Microbiol· March 2022

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Editorial: Machine Learning Methodologies to Study Molecular Interactions.
Artur Yakimovich, Arzucan Özgür, Tunca Doğan, Elif Ozkirimli

Front Mol Biosci· December 2021

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Labels in a haystack: Approaches beyond supervised learning in biomedical applications.
Artur Yakimovich, Anaël Beaugnon, Yi Huang, Elif Ozkirimli

Patterns (N Y)· December 2021

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ChemBoost: A Chemical Language Based Approach for Protein - Ligand Binding Affinity Prediction.
Rıza Özçelik, Hakime Öztürk, Arzucan Özgür, Elif Ozkirimli

Mol Inform· May 2021

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Exploring chemical space using natural language processing methodologies for drug discovery.
Hakime Öztürk, Arzucan Özgür, Philippe Schwaller, Teodoro Laino, Elif Ozkirimli

Drug Discov Today· April 2020

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Superior inhibition of influenza virus hemagglutinin-mediated fusion by indole-substituted spirothiazolidinones.
Gökçe Cihan-Üstündağ, Muhammet Zopun, Evelien Vanderlinden, Elif Ozkirimli, Leentje Persoons

Bioorg Med Chem· January 2020

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Synthesis and biological evaluation of indole-2-carbohydrazides and thiazolidinyl-indole-2-carboxamides as potent tubulin polymerization inhibitors.
Fusun Kazan, Z Begum Yagci, Ruoli Bai, Elif Ozkirimli, Ernest Hamel, Sumru Ozkirimli

Comput Biol Chem· June 2019

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In Silico Identification of Novel Orthosteric Inhibitors of Sphingosine Kinase 1 (SK1).
Ozge Bayraktar, Elif Ozkirimli, Kutlu O Ulgen

Curr Protein Pept Sci· March 2019

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Targeting a hidden site on class A beta-lactamases.
Fatma Gizem Avci, Fatma Ece Altinisik, Ipek Karacan, Duygu Senturk Karagoz, Serhat Ersahin, Elif Ozkirimli

J Mol Graph Model· September 2018

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DeepDTA: deep drug-target binding affinity prediction.
Hakime Öztürk, Arzucan Özgür, Elif Ozkirimli

Bioinformatics· September 2018

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Membrane Active Peptides and Their Biophysical Characterization.
Fatma Gizem Avci, Berna Sariyar Akbulut, Elif Ozkirimli

Biomolecules· August 2018

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A novel methodology on distributed representations of proteins using their interacting ligands.
Hakime Öztürk, Elif Ozkirimli, Arzucan Özgür

Bioinformatics· July 2018

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pVEC hydrophobic N-terminus is critical for antibacterial activity.
Begum Alaybeyoglu, Berna Sariyar Akbulut, Elif Ozkirimli

J Pept Sci· June 2018

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Investigation of novel pharmacological chaperones for Gaucher Disease.
Buge Yilmazer, Z Begum Yagci, Emre Bakar, Burcu Ozden, Kutlu Ulgen, Elif Ozkirimli

J Mol Graph Model· September 2017

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Sphingosine kinase 1 (SK1) allosteric inhibitors that target the dimerization site.
Ozge Bayraktar, Elif Ozkirimli, Kutlu Ulgen

Comput Biol Chem· August 2017

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Response of Escherichia coli to Prolonged Berberine Exposure.
Nilay Budeyri Gokgoz, Fatma Gizem Avci, Kubra Karaosmanoglu Yoneten, Begum Alaybeyoglu, Elif Ozkirimli

Microb Drug Resist· July 2017

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The effect of a beta-lactamase inhibitor peptide on bacterial membrane structure and integrity: a comparative study.
Begum Alaybeyoglu, Bilge Gedik Uluocak, Berna Sariyar Akbulut, Elif Ozkirimli

J Pept Sci· May 2017

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A comparative study of SMILES-based compound similarity functions for drug-target interaction prediction.
Hakime Öztürk, Elif Ozkirimli, Arzucan Özgür

BMC Bioinformatics· March 2016

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