Elif Ozkirimli

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Arzucan OzgurDepartment of Computer Engineering, Bogazici UniversityVerified email at boun.edu.tr
Hakime ÖztürkGerman Cancer Research Center (DKFZ)Verified email at dkfz-heidelberg.de
Berna Sariyar AkbulutMarmara UniversityVerified email at marmara.edu.tr
Kutlu O. UlgenProfessor of Chemical Engineering, Bogazici UniversityVerified email at boun.edu.tr
Fatma Gizem AvcıÜsküdar ÜniversitesiVerified email at uskudar.edu.tr
Begum AlaybeyogluMassachusetts Institute of TechnologyVerified email at mit.edu
Rıza ÖzçelikPh.D. Candidate, Biomedical Engineering, Eindhoven University of TechnologyVerified email at tue.nl
Abdullatif KöksalCIS - Ludwig Maximillian University of MunichVerified email at lmu.de
Burak AlakentAssociate Professor of Chemical Engineering, Bogazici UniversityVerified email at boun.edu.tr
Pinar KanlikilicerMD Anderson Cancer CenterVerified email at mdanderson.org
Nihat Alpagu SayarAssociate Professor of Bioengineering, Marmara UniversityVerified email at marmara.edu.tr
Philippe SchwallerAssistant Professor, Laboratory of Artificial Chemical Intelligence - EPFLVerified email at epfl.ch
Teodoro LainoIBM Research ZurichVerified email at zurich.ibm.com
Fatma Ece Altınışık KayaMarmara ÜniversitesiVerified email at marmara.edu.tr
Hilal DönmezMSc. Student @ Computer Engineering, Boğaziçi UniversityVerified email at boun.edu.tr
Robert GeahlenDistinguished Professor of Medicinal Chemistry, Purdue UniversityVerified email at purdue.edu
Kavita ShahPurdueVerified email at purdue.edu
Didem Vardar-UluVerified email at wellesley.edu
Naze Gul AvciAshvattha TherapeuticsVerified email at avttx.com
Atakan YukselBoğaziçi UniversityVerified email at boun.edu.tr

Elif Ozkirimli

Head of Data Science and Advanced Analytics, Roche

Verified email at boun.edu.tr

Bioinformatics Computational Biology Structural Biology Natural Language Processing


Title Sort by citations Sort by year Sort by title	Cited by Cited by	Year
DeepDTA: deep drug–target binding affinity prediction H Öztürk, A Özgür, E Ozkirimli Bioinformatics 34 (17), i821-i829, 2018	816	2018
Membrane active peptides and their biophysical characterization FG Avci, B Sariyar Akbulut, E Ozkirimli Biomolecules 8 (3), 77, 2018	160	2018
WideDTA: prediction of drug-target binding affinity H Öztürk, E Ozkirimli, A Özgür arXiv preprint arXiv:1902.04166, 2019	153	2019
A comparative study of SMILES-based compound similarity functions for drug-target interaction prediction H Öztürk, E Ozkirimli, A Özgür BMC bioinformatics 17 (1), 1-11, 2016	121	2016
Exploring chemical space using natural language processing methodologies for drug discovery H Öztürk, A Özgür, P Schwaller, T Laino, E Ozkirimli Drug Discovery Today 25 (4), 689-705, 2020	93	2020
Classification of beta-lactamases and penicillin binding proteins using ligand-centric network models H Öztürk, E Ozkirimli, A Özgür PloS one 10 (2), e0117874, 2015	92	2015
Src kinase activation: A switched electrostatic network E Ozkirimli, CB Post Protein Science 15 (5), 1051-1062, 2006	90	2006
An electrostatic network and long‐range regulation of Src kinases E Ozkirimli, SS Yadav, WT Miller, CB Post Protein Science 17 (11), 1871-1880, 2008	73	2008
Comparison of three perturbation molecular dynamics methods for modeling conformational transitions H Huang, E Ozkirimli, CB Post Journal of Chemical Theory and Computation 5 (5), 1304-1314, 2009	63	2009
Balancing methods for multi-label text classification with long-tailed class distribution Y Huang, B Giledereli, A Köksal, A Özgür, E Ozkirimli arXiv preprint arXiv:2109.04712, 2021	43	2021
A novel methodology on distributed representations of proteins using their interacting ligands H Öztürk, E Ozkirimli, A Özgür Bioinformatics 34 (13), i295-i303, 2018	38	2018
Generation of an analog-sensitive Syk tyrosine kinase for the study of signaling dynamics from the B cell antigen receptor H Oh, E Ozkirimli, K Shah, ML Harrison, RL Geahlen Journal of Biological Chemistry 282 (46), 33760-33768, 2007	36	2007
Alpha7 helix plays an important role in the conformational stability of PTP1B E Ozkirimli Olmez, B Alakent Journal of Biomolecular Structure and Dynamics 28 (5), 675-693, 2011	35	2011
The uptake mechanism of the cell penetrating pVEC peptide IO Akdag, E Ozkirimli	25	2013
A systematic methodology for large scale compound screening: A case study on the discovery of novel S1PL inhibitors U Deniz, E Ozkirimli, KO Ulgen Journal of Molecular Graphics and Modelling 63, 110-124, 2016	24	2016
ChemBoost: A Chemical Language Based Approach for Protein–Ligand Binding Affinity Prediction R Özçelik, H Öztürk, A Özgür, E Ozkirimli Molecular Informatics, 2021	22*	2021
An evolutionarily conserved allosteric site modulates beta-lactamase activity FG Avci, FE Altinisik, D Vardar Ulu, E Ozkirimli Olmez, B Sariyar Akbulut Journal of enzyme inhibition and medicinal chemistry 31 (sup3), 33-40, 2016	21	2016
Superior inhibition of influenza virus hemagglutinin-mediated fusion by indole-substituted spirothiazolidinones G Cihan-Üstündağ, M Zopun, E Vanderlinden, E Ozkirimli, L Persoons, ... Bioorganic & medicinal chemistry 28 (1), 115130, 2020	20	2020
Labels in a haystack: Approaches beyond supervised learning in biomedical applications A Yakimovich, A Beaugnon, Y Huang, E Ozkirimli Patterns 2 (12), 2021	19	2021
Protein-peptide interactions revolutionize drug development E Ozkirimli Olmez, B Sariyar Akbulut Binding Protein, 49, 2012	18*	2012

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