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ORCIDElif Özkirimli Ölmez
Person information
- affiliation: Bogazici University, Department of Chemical Engineering, Istanbul, Turkey
- affiliation: F. Hoffmann-La Roche AG, Roche Informatics, Basel, Switzerland
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Journal Articles
- 2023
[j14]Davy Weissenbacher
, Karen O'Connor, Siddharth Rawal, Yu Zhang, Richard Tzong-Han Tsai, Timothy 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 Melo Almeida, Paloma Martínez, Renzo M. Rivera Zavala, Chen-Kai Wang, Hong-Jie Dai, Luis Alberto Robles Hernandez, Graciela Gonzalez-Hernandez:
Automatic Extraction of Medication Mentions from Tweets - Overview of the BioCreative VII Shared Task 3 Competition. Database J. Biol. Databases Curation 2023 (2023)- [j13]Riza Özçelik, Alperen Bag, Berk Atil, Melih Barsbey, Arzucan Özgür, Elif Ozkirimli:
A Framework for Improving the Generalizability of Drug-Target Affinity Prediction Models. J. Comput. Biol. 30(11): 1226-1239 (2023) - [j12]Melih Barsbey, Riza Özçelik, Alperen Bag, Berk Atil, Arzucan Özgür, Elif Ozkirimli:
A Computational Software for Training Robust Drug-Target Affinity Prediction Models: pydebiaseddta. J. Comput. Biol. 30(11): 1240-1245 (2023) - 2022
- [j11]Gökçe Uludogan, Elif Özkirimli, Kutlu Ö. Ülgen, Nilgün Karali, Arzucan Özgür:
Exploiting pretrained biochemical language models for targeted drug design. Bioinform. 38(Supplement_2): ii155-ii161 (2022) - [j10]Alessio Zanga, Elif Ozkirimli, Fabio Stella:
A Survey on Causal Discovery: Theory and Practice. Int. J. Approx. Reason. 151: 101-129 (2022) - 2021
- [j9]Artur Yakimovich, Anaël Beaugnon, Yi Huang, Elif Ozkirimli:
Labels in a haystack: Approaches beyond supervised learning in biomedical applications. Patterns 2(12): 100383 (2021) - 2019
- [j8]Fusun Kazan, Z. Begum Yagci, Ruoli Bai, Elif Ozkirimli, Ernest Hamel, Sumru Ozkirimli:
Synthesis and biological evaluation of indole-2-carbohydrazides and thiazolidinyl-indole-2-carboxamides as potent tubulin polymerization inhibitors. Comput. Biol. Chem. 80: 512-523 (2019) - 2018
- [j7]Hakime Öztürk, Elif Özkirimli Ölmez, Arzucan Özgür:
A novel methodology on distributed representations of proteins using their interacting ligands. Bioinform. 34(13): i295-i303 (2018) - [j6]Hakime Öztürk, Arzucan Özgür, Elif Özkirimli Ölmez:
DeepDTA: deep drug-target binding affinity prediction. Bioinform. 34(17): i821-i829 (2018) - 2017
- [j5]Ozge Bayraktar, Elif Özkirimli Ölmez, Kutlu Ö. Ülgen:
Sphingosine kinase 1 (SK1) allosteric inhibitors that target the dimerization site. Comput. Biol. Chem. 69: 64-76 (2017) - 2016
- [j4]Hakime Öztürk, Elif Özkirimli Ölmez, Arzucan Özgür:
A comparative study of SMILES-based compound similarity functions for drug-target interaction prediction. BMC Bioinform. 17: 128 (2016) - 2015
- [j3]Utku Deniz, Kutlu Ö. Ülgen, Elif Özkirimli Ölmez:
Identification of potential Tpx inhibitors against pathogen-host interactions. Comput. Biol. Chem. 58: 126-138 (2015) - 2014
- [j2]Oya Gursoy Yilmaz, Elif Özkirimli Ölmez, Kutlu Ö. Ülgen:
Targeting the Akt1 allosteric site to identify novel scaffolds through virtual screening. Comput. Biol. Chem. 48: 1-13 (2014) - 2013
- [j1]Deniz Meneksedag, Asligul Dogan, Pinar Kanlikilicer, Elif Özkirimli Ölmez:
Communication between the active site and the allosteric site in class A beta-lactamases. Comput. Biol. Chem. 43: 1-10 (2013)
Conference and Workshop Papers
- 2021
- [c5]Yi Huang, Buse Giledereli, Abdullatif Köksal, Arzucan Özgür, Elif Ozkirimli:
PIDNA at BioASQ MESINESP: Hybrid Semantic Indexing for Biomedical Articles in Spanish. CLEF (Working Notes) 2021: 241-246 - [c4]Yi Huang, Buse Giledereli, Abdullatif Köksal, Arzucan Özgür, Elif Ozkirimli:
Balancing Methods for Multi-label Text Classification with Long-Tailed Class Distribution. EMNLP (1) 2021: 8153-8161 - 2020
- [c3]Hilal Dönmez, Abdullatif Köksal, Elif Özkirimli, Arzucan Özgür:
BOUN-REX at CLEF-2020 ChEMU Task 2: Evaluating Pretrained Transformers for Event Extraction. CLEF (Working Notes) 2020 - [c2]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:
An Extended Overview of the CLEF 2020 ChEMU Lab: Information Extraction of Chemical Reactions from Patents. CLEF (Working Notes) 2020 - [c1]Abdullatif Köksal, Hilal Dönmez, Riza Özçelik, Elif Ozkirimli, Arzucan Özgür:
Vapur: A Search Engine to Find Related Protein - Compound Pairs in COVID-19 Literature. NLP4COVID@EMNLP 2020
Informal and Other Publications
- 2022
- [i9]Gökçe Uludogan, Elif Özkirimli, Kutlu Ö. Ülgen, Nilgün Karali, Arzucan Özgür:
Exploiting Pretrained Biochemical Language Models for Targeted Drug Design. CoRR abs/2209.00981 (2022) - 2021
- [i8]Riza Özçelik, Alperen Bag, Berk Atil, Arzucan Özgür, Elif Özkirimli:
DebiasedDTA: Model Debiasing to Boost Drug-Target Affinity Prediction. CoRR abs/2107.05556 (2021) - [i7]Yi Huang, Buse Giledereli, Abdullatif Köksal, Arzucan Özgür, Elif Ozkirimli:
Balancing Methods for Multi-label Text Classification with Long-Tailed Class Distribution. CoRR abs/2109.04712 (2021) - [i6]Igor Kulev, Berkay Köprü, Raul Rodriguez-Esteban, Diego Saldana, Yi Huang, Alessandro La Torraca, Elif Ozkirimli:
Extraction of Medication Names from Twitter Using Augmentation and an Ensemble of Language Models. CoRR abs/2111.06664 (2021) - 2020
- [i5]Hakime Öztürk, Arzucan Özgür, Philippe Schwaller, Teodoro Laino, Elif Özkirimli Ölmez:
Exploring Chemical Space using Natural Language Processing Methodologies for Drug Discovery. CoRR abs/2002.06053 (2020) - [i4]Abdullatif Köksal, Hilal Dönmez, Riza Özçelik, Elif Ozkirimli, Arzucan Özgür:
Vapur: A Search Engine to Find Related Protein - Compound Pairs in COVID-19 Literature. CoRR abs/2009.02526 (2020) - 2019
- [i3]Hakime Öztürk, Elif Özkirimli Ölmez, Arzucan Özgür:
WideDTA: prediction of drug-target binding affinity. CoRR abs/1902.04166 (2019) - 2018
- [i2]Hakime Öztürk, Elif Özkirimli Ölmez, Arzucan Özgür:
DeepDTA: Deep Drug-Target Binding Affinity Prediction. CoRR abs/1801.10193 (2018) - [i1]Hakime Öztürk, Arzucan Özgür, Elif Özkirimli Ölmez:
A chemical language based approach for protein - ligand interaction prediction. CoRR abs/1811.00761 (2018)
Coauthor Index
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