Communication between the active site and the allosteric site in class A beta-lactamases. - Deniz Meneksedag; Asligul Dogan; Pinar Kanlikilicer; Elif Özkirimli Ölmez (Comput. Biol. Chem., 2013)

Targeting the Akt1 allosteric site to identify novel scaffolds through virtual screening. - Oya Gursoy Yilmaz; Elif Özkirimli Ölmez; Kutlu Ö. Ülgen (Comput. Biol. Chem., 2014)

Identification of potential Tpx inhibitors against pathogen-host interactions. - Utku Deniz; Kutlu Ö. Ülgen; Elif Özkirimli Ölmez (Comput. Biol. Chem., 2015)

A comparative study of SMILES-based compound similarity functions for drug-target interaction prediction. - Hakime Öztürk; Elif Özkirimli Ölmez; Arzucan Özgür (BMC Bioinform., 2016)

Sphingosine kinase 1 (SK1) allosteric inhibitors that target the dimerization site. - Ozge Bayraktar; Elif Özkirimli Ölmez; Kutlu Ö. Ülgen (Comput. Biol. Chem., 2017)

A novel methodology on distributed representations of proteins using their interacting ligands. - Hakime Öztürk; Elif Özkirimli Ölmez; Arzucan Özgür (Bioinform., 2018)

DeepDTA: deep drug-target binding affinity prediction. - Hakime Öztürk; Arzucan Özgür; Elif Özkirimli Ölmez (Bioinform., 2018)

A chemical language based approach for protein - ligand interaction prediction. - Hakime Öztürk; Arzucan Özgür; Elif Özkirimli Ölmez (CoRR, 2018)

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 001; Ernest Hamel; Sumru Ozkirimli (Comput. Biol. Chem., 2019)

WideDTA: prediction of drug-target binding affinity. - Hakime Öztürk; Elif Özkirimli Ölmez; Arzucan Özgür (CoRR, 2019)

BOUN-REX at CLEF-2020 ChEMU Task 2: Evaluating Pretrained Transformers for Event Extraction. - Hilal Dönmez; Abdullatif Köksal; Elif Özkirimli 001; Arzucan Özgür (CLEF (Working Notes), 2020)

An Extended Overview of the CLEF 2020 ChEMU Lab: Information Extraction of Chemical Reactions from Patents. - Jiayuan He 002; Dat Quoc Nguyen; Saber A. Akhondi; Christian Druckenbrodt; Camilo Thorne; Ralph Hoessel; Zubair Afzal; Zenan Zhai; Biaoyan Fang; Hiyori Yoshikawa; Ameer Albahem; Jingqi Wang; et al. (CLEF (Working Notes), 2020)

Vapur: A Search Engine to Find Related Protein - Compound Pairs in COVID-19 Literature. - Abdullatif Köksal; Hilal Dönmez; Riza Özçelik; Elif Ozkirimli 001; Arzucan Özgür (NLP4COVID@EMNLP, 2020)

Exploring Chemical Space using Natural Language Processing Methodologies for Drug Discovery. - Hakime Öztürk; Arzucan Özgür; Philippe Schwaller; Teodoro Laino; Elif Özkirimli Ölmez (CoRR, 2020)

PIDNA at BioASQ MESINESP: Hybrid Semantic Indexing for Biomedical Articles in Spanish. - Yi Huang; Buse Giledereli; Abdullatif Köksal; Arzucan Özgür; Elif Ozkirimli 001 (CLEF (Working Notes), 2021)

Balancing Methods for Multi-label Text Classification with Long-Tailed Class Distribution. - Yi Huang; Buse Giledereli; Abdullatif Köksal; Arzucan Özgür; Elif Ozkirimli 001 (EMNLP (1), 2021)

DebiasedDTA: Model Debiasing to Boost Drug-Target Affinity Prediction. - Riza Özçelik; Alperen Bag; Berk Atil; Arzucan Özgür; Elif Özkirimli 001 (CoRR, 2021)

Extraction of Medication Names from Twitter Using Augmentation and an Ensemble of Language Models. - Igor Kulev; Berkay Köprü; Raul Rodriguez-Esteban; Diego Saldana; Yi Huang; Alessandro La Torraca; Elif Ozkirimli 001 (CoRR, 2021)

Labels in a haystack: Approaches beyond supervised learning in biomedical applications. - Artur Yakimovich; Anaël Beaugnon; Yi Huang; Elif Ozkirimli 001 (Patterns, 2021)

Exploiting pretrained biochemical language models for targeted drug design. - Gökçe Uludogan; Elif Özkirimli 001; Kutlu Ö. Ülgen; Nilgün Karali; Arzucan Özgür (Bioinform., 2022)

A Survey on Causal Discovery: Theory and Practice. - Alessio Zanga; Elif Ozkirimli 001; Fabio Stella (Int. J. Approx. Reason., 2022)

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 202; Richard Tzong-Han Tsai; Timothy Miller 002; Dongfang Xu; Carol Anderson; Bo Liu; Qing Han; Jinfeng Zhang; Igor Kulev; et al. (Database J. Biol. Databases Curation, 2023)

A Computational Software for Training Robust Drug-Target Affinity Prediction Models: pydebiaseddta. - Melih Barsbey; Riza Özçelik; Alperen Bag; Berk Atil; Arzucan Özgür; Elif Ozkirimli 001 (J. Comput. Biol., 2023)

A Framework for Improving the Generalizability of Drug-Target Affinity Prediction Models. - Riza Özçelik; Alperen Bag; Berk Atil; Melih Barsbey; Arzucan Özgür; Elif Ozkirimli 001 (J. Comput. Biol., 2023)