Elif Özkirimli Ölmez

According to our database, Elif Özkirimli Ölmez authored at least 24 papers between 2013 and 2023.

Collaborative distances:

• Dijkstra number of five.
• Erdős number of four.

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

J. Comput. Biol., November, 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

J. Comput. Biol., November, 2023

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, Timothy A. Miller, Dongfang Xu, Carol Anderson, Bo Liu, Qing Han, Jinfeng Zhang, Igor Kulev, Berkay Köprü, Raul Rodriguez-Esteban, Elif Ozkirimli, Ammer Ayach, Roland Roller, Stephen R. Piccolo, Peijin Han, V. G. Vinod Vydiswaran, Ramya Tekumalla, Juan M. Banda, Parsa Bagherzadeh, Sabine Bergler, João Figueira Silva, Tiago Almeida, Paloma Martínez, Renzo M. Rivera Zavala, Chen-Kai Wang, Hong-Jie Dai, Luis Alberto Robles Hernandez, Graciela Gonzalez-Hernandez

Database J. Biol. Databases Curation, February, 2023

2022

A Survey on Causal Discovery: Theory and Practice.

Alessio Zanga, Elif Ozkirimli, Fabio Stella

Int. J. Approx. Reason., 2022

Exploiting Pretrained Biochemical Language Models for Targeted Drug Design.

Gökçe Uludogan, Elif Özkirimli, Kutlu Ö. Ülgen, Nilgün Karali, Arzucan Özgür

CoRR, 2022

2021

Labels in a haystack: Approaches beyond supervised learning in biomedical applications.

Artur Yakimovich, Anaël Beaugnon, Yi Huang, Elif Ozkirimli

Patterns, 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

CoRR, 2021

DebiasedDTA: Model Debiasing to Boost Drug-Target Affinity Prediction.

Riza Özçelik, Alperen Bag, Berk Atil, Arzucan Özgür, Elif Özkirimli

CoRR, 2021

Balancing Methods for Multi-label Text Classification with Long-Tailed Class Distribution.

Yi Huang, Buse Giledereli, Abdullatif Köksal, Arzucan Özgür, Elif Ozkirimli

Proceedings of the 2021 Conference on Empirical Methods in Natural Language Processing, 2021

PIDNA at BioASQ MESINESP: Hybrid Semantic Indexing for Biomedical Articles in Spanish.

Yi Huang, Buse Giledereli, Abdullatif Köksal, Arzucan Özgür, Elif Ozkirimli

Proceedings of the Working Notes of CLEF 2021 - Conference and Labs of the Evaluation Forum, Bucharest, Romania, September 21st - to, 2021

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

Vapur: A Search Engine to Find Related Protein - Compound Pairs in COVID-19 Literature.

Abdullatif Köksal, Hilal Dönmez, Riza Özçelik, Elif Ozkirimli, Arzucan Özgür

Proceedings of the 1st Workshop on NLP for COVID-19@ EMNLP 2020, Online, December 2020, 2020

An Extended Overview of the CLEF 2020 ChEMU Lab: Information Extraction of Chemical Reactions from Patents.

Jiayuan He, Dat Quoc Nguyen, Saber A. Akhondi, Christian Druckenbrodt, Camilo Thorne, Ralph Hoessel, Zubair Afzal, Zenan Zhai, Biaoyan Fang, Hiyori Yoshikawa, Ameer Albahem, Jingqi Wang, Yuankai Ren, Zhi Zhang, Yaoyun Zhang, Mai Hoang Dao, Pedro Ruas, Andre Lamurias, Francisco M. Couto, Jenny Copara, Nona Naderi, Julien Knafou, Patrick Ruch, Douglas Teodoro, Daniel M. Lowe, John Mayfield, Abdullatif Köksal, Hilal Dönmez, Elif Özkirimli, Arzucan Özgür, Darshini Mahendran, Gabrielle Gurdin, Nastassja Lewinski, Christina Tang, Bridget T. McInnes, C. S. Malarkodi, Pattabhi Rk Rao, Sobha Lalitha Devi, Lawrence Cavedon, Trevor Cohn, Timothy Baldwin, Karin Verspoor

Proceedings of the Working Notes of CLEF 2020, 2020

BOUN-REX at CLEF-2020 ChEMU Task 2: Evaluating Pretrained Transformers for Event Extraction.

Hilal Dönmez, Abdullatif Köksal, Elif Özkirimli, Arzucan Özgür

Proceedings of the Working Notes of CLEF 2020, 2020

2019

WideDTA: prediction of drug-target binding affinity.

Hakime Öztürk, Elif Özkirimli Ölmez, Arzucan Özgür

CoRR, 2019

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., 2019

2018

A chemical language based approach for protein - ligand interaction prediction.

Hakime Öztürk, Arzucan Özgür, Elif Özkirimli Ölmez

CoRR, 2018

DeepDTA: deep drug-target binding affinity prediction.

Hakime Öztürk, Arzucan Özgür, Elif Özkirimli Ölmez

Bioinform., 2018

A novel methodology on distributed representations of proteins using their interacting ligands.

Hakime Öztürk, Elif Özkirimli Ölmez, Arzucan Özgür

Bioinform., 2018

2017

Sphingosine kinase 1 (SK1) allosteric inhibitors that target the dimerization site.

Ozge Bayraktar, Elif Özkirimli Ölmez, Kutlu Ö. Ülgen

Comput. Biol. Chem., 2017

2016

A comparative study of SMILES-based compound similarity functions for drug-target interaction prediction.

Hakime Öztürk, Elif Özkirimli Ölmez, Arzucan Özgür

BMC Bioinform., 2016

2015

Identification of potential Tpx inhibitors against pathogen-host interactions.

Utku Deniz, Kutlu Ö. Ülgen, Elif Özkirimli Ölmez

Comput. Biol. Chem., 2015

2014

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

2013

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