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A. Rifaioglu · SciRah

Researcher profile · Semantic Scholar

A. Rifaioglu

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A. Rifaioglu — researcher profile on SciRah

h-index: 10
Works: 37
Citations: 1,631

Most-cited papers

Recent applications of deep learning and machine intelligence on in silico drug discovery: methods, tools and databases
A. Rifaioglu, Heval Atas, M. Martin, R. Cetin-Atalay +2 more
2018Briefings Bioinform.461 citations Open access
Semantic Scholar
The CAFA challenge reports improved protein function prediction and new functional annotations for hundreds of genes through experimental screens
Nai-Hui Zhou, Yuxiang Jiang, T. Bergquist, Alexandra J. Lee +163 more
2019Genome Biology451 citations Open access
Semantic Scholar
DEEPScreen: high performance drug–target interaction prediction with convolutional neural networks using 2-D structural compound representations
A. Rifaioglu, Esra Nalbat, V. Atalay, M. Martin +2 more
2018bioRxiv196 citations Open access
Semantic Scholar
ECPred: a tool for the prediction of the enzymatic functions of protein sequences based on the EC nomenclature
Alperen Dalkıran, A. Rifaioglu, M. Martin, Rengul Cetin Atalay +2 more
2018BMC Bioinformatics165 citations Open access
Semantic Scholar
MDeePred: novel multi-channel protein featurization for deep learning-based binding affinity prediction in drug discovery
A. Rifaioglu, R. Cetin-Atalay, D. Kahraman, Tunca Dogan +2 more
2020Bioinform.90 citations Open access
Semantic Scholar
Crowdsourced mapping of unexplored target space of kinase inhibitors
A. Cichońska, Balaguru Ravikumar, Robert J. Allaway, Fangping Wan +83 more
2020Nature Communications75 citations Open access
Semantic Scholar
Transfer learning for drug–target interaction prediction
Alperen Dalkıran, Ahmet Atakan, A. Rifaioglu, M. Martin +4 more
2023Bioinform.60 citations Open access
Semantic Scholar
CROssBAR: comprehensive resource of biomedical relations with knowledge graph representations
Tunca Dogan, Heval Atas, Vishal Joshi, Ahmet Atakan +9 more
2021Nucleic Acids Research40 citations Open access
Semantic Scholar
Compartments in medulloblastoma with extensive nodularity are connected through differentiation along the granular precursor lineage
David R. Ghasemi, K. Okonechnikov, A. Rademacher, Stephan M. Tirier +22 more
2022bioRxiv18 citations Open access
Semantic Scholar
Large‐scale automated function prediction of protein sequences and an experimental case study validation on PTEN transcript variants
A. Rifaioglu, Tunca Dogan, O. S. Sarac, Tulin Ersahin +4 more
2018Proteins: Structure, Function, and Bioinformatics13 citations Open access
Semantic Scholar
Target Specific De Novo Design of Drug Candidate Molecules with Graph Transformer-based Generative Adversarial Networks
Atabey Ünlü, Elif Çevrim, Ahmet Sarigun, Hayriye Çelikbilek +6 more
2023arXiv.org9 citations Open access
Semantic Scholar
A spatiotemporal cancer cell trajectory underlies glioblastoma heterogeneity
G. de Jong, F. Memi, Tannia Gracia, O. Lazareva +43 more
2025bioRxiv8 citations Open access
Semantic Scholar
Target-specific de novo design of drug candidate molecules with graph-transformer-based generative adversarial networks
Atabey Ünlü, Elif Çevrim, M. Yiğit, Ahmet Sarigun +7 more
2025Nature Machine Intelligence8 citations Open access
Semantic Scholar
iBioProVis: interactive visualization and analysis of compound bioactivity space
A. Donmez, A. Rifaioglu, A. Acar, Tunca Dogan +2 more
2020Bioinform.8 citations Open access
Semantic Scholar
SLPred: a multi-view subcellular localization prediction tool for multi-location human proteins
Gökhan Özsari, A. Rifaioglu, Ahmet Atakan, Tunca Dogan +3 more
2022Bioinform.6 citations Open access
Semantic Scholar
Predicting the Specificity- Determining Positions of Receptor Tyrosine Kinase Axl
Tülay Karakulak, A. Rifaioglu, J. Rodrigues, E. Karaca
2021Frontiers in Molecular Biosciences6 citations Open access
Semantic Scholar
Multi-task Deep Neural Networks in Automated Protein Function Prediction
A. Rifaioglu, Tunca Dogan, M. Martin, R. Cetin-Atalay +1 more
20176 citations
Semantic Scholar
Drug Repurposing Approach to Identify Candidate Drug Molecules for Hepatocellular Carcinoma
T. Başer, A. Rifaioglu, M. Atalay, R. Atalay
2024International Journal of Molecular Sciences4 citations Open access
Semantic Scholar
CROssBARv2: A Unified Computational Framework for Heterogeneous Biomedical Data Representation and LLM-Driven Exploration
Bunyamin Sen, Erva Ulusoy, Melih Darcan, Mert Ergün +5 more
2026bioRxiv2 citations Open access
Semantic Scholar
ProFAB - open protein functional annotation benchmark
A. Özdilek, Ahmet Atakan, Gökhan Özsari, A. Acar +3 more
2023Briefings Bioinform.2 citations Open access
Semantic Scholar
Data Centric Molecular Analysis and Evaluation of Hepatocellular Carcinoma Therapeutics Using Machine Intelligence-Based Tools
R. Cetin-Atalay, D. Kahraman, Esra Nalbat, A. Rifaioglu +6 more
2021Journal of Gastrointestinal Cancer2 citations Open access
Semantic Scholar
CROssBAR: Comprehensive Resource of Biomedical Relations with Deep Learning Applications and Knowledge Graph Representations
Tunca Dogan, Heval Atas, Vishal Joshi, Ahmet Atakan +9 more
2020bioRxiv2 citations Open access
Semantic Scholar
challenge reports improved protein function prediction and new functional annotations for hundreds of genes through experimental screens
Naihui Zhou, Yuxiang Jiang, T. Bergquist, Alex J. Lee +162 more
2 citations
Semantic Scholar
On the state of protein function prediction: a report on the fourth CAFA challenge
R. Ramola, M. C. De Paolis Kaluza, D. Piovesan, Yi-Su Peng +149 more
2026bioRxiv1 citations Open access
Semantic Scholar
SpaCEy links spatial tissue patterns to clinical outcomes using explainable graph neural networks
A. Rifaioglu, Egle-Helene Ervin, Ahmet Sarigun, Deniz Germen +3 more
2026Nature Communications1 citations Open access
Semantic Scholar
Molecular contrastive learning with graph attention network (MoCL-GAT) for enhanced molecular representation
Alperen Dalkıran, A. Rifaioglu, R. Cetin-Atalay, A. Acar +2 more
2025bioRxiv1 citations Open access
Semantic Scholar
SpaCEy: Discovery of Functional Spatial Tissue Patterns by Association with Clinical Features Using Explainable Graph Neural Networks
A. Rifaioglu, Egle-Helene Ervin, Ahmet Sarigun, Deniz Germen +3 more
2026bioRxiv0 citations Open access
Semantic Scholar
DTA-GNN: a toolkit for constructing target-specific drug-target affinity datasets and training graph neural networks
Gökhan Özsari, A. Rifaioglu, A. Acar, Tunca Dogan +1 more
2026SoftwareX0 citations Open access
Semantic Scholar
Author Correction: Compartments in medulloblastoma with extensive nodularity are connected through differentiation along the granular precursor lineage
David R. Ghasemi, K. Okonechnikov, A. Rademacher, Stephan M. Tirier +22 more
2024Nature Communications0 citations Open access
Semantic Scholar
Predicting the Specificity-Determining Positions of Paralogous Complexes
Tülay Karakulak, A. Rifaioglu, J. Rodrigues, E. Karaca
2021bioRxiv0 citations Open access
Semantic Scholar
Deep learning for prediction of drug-target interaction space and protein functions (İlaç-hedef protein etkileşim uzayı ve protein fonksiyonlarının tahmini için derin öğrenme)
A. Rifaioglu
20200 citations
Semantic Scholar
Abstract 5235:In vitrovalidation of drug-target interactions revealedin silicoby Comprehensive Resource of Biomedical Relations with Network Representations and Deep Learning (CROssBAR) in HCC
Esra Nalbat, A. Rifaioglu, Tunca Dogan, M. Martin +2 more
2020Experimental and Molecular Therapeutics0 citations Open access
Semantic Scholar
Towards networking biomedical data using the CROssBAR API
Vishal Joshi, Hermann Zellner, R. Saidi, Tunca Dogan +7 more
20200 citations Open access
Semantic Scholar
Large-Scale Benchmarking of Protein Descriptors for Protein Ligand Prediction in Target-Based Modelling and Proteochemometrics
Heval Ata, A. Rifaioglu, R. Atalay, V. Atalay
20190 citations
Semantic Scholar
Investigation of multi-task deep neural networks for protein function prediction
A. Rifaioglu, Tunca Dogan, M. Martin, R. Cetin-Atalay +1 more
20170 citations Open access
Semantic Scholar
Multi-task Deep Neural Networks in Protein Function Prediction
A. Rifaioglu, Tunca Dogan, M. Martin, R. Atalay +1 more
20170 citations
Semantic Scholar
Unsupervised identification of redundant domain entries in InterPro database using clustering techniques
A. Rifaioglu, Tunca Dogan, Tolga Can
2015ACM International Conference on Bioinformatics, Computational Biology and Biomedicine0 citations Open access
Semantic Scholar

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V. Atalay×15
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