- A Methodological Research on Radiogenomics: Combining Radiomics and Genomics for Classification, M KAŞIKCI, E Coşgun, E Karabulut, Journal of Biostatistics 16 (1), 2024
- Biomarker detection using corrected degree of domesticity in hybrid social network feature selection for improving classifier performance, HY Zengin, E Karabulut, BMC bioinformatics 24 (1), 407, 2023
- voomSOM: voom-based Self-Organizing Maps for Clustering RNASequencing Data, A Cephe, N Koçhan, GE Zararsız, V Eldem, E Coşgun, E Karabulut, ..., Current Bioinformatics 18 (2), 154-169, 2023
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Prof. Dr. Tunca Doğan
- Target-specific de novo design of drug candidate molecules with graph-transformer-based generative adversarial networks
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A Ünlü, E Çevrim, MG Yiğit, A Sarıgün, H Çelikbilek, O Bayram, ...
Nature Machine Intelligence, 1-17,2025
- Mpox: disease manifestations and therapeutic development
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Y Wang, X Wang, T Doğan, NA Sam-Agudu, JA Al-Tawfiq, Q Pan
Journal of Virology, e00152-25,2025
- A Benchmarking Platform for Assessing Protein Language Models on Function-related Prediction Tasks
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E Çevrim, MG Yiğit, E Ulusoy, A Yılmaz, T Doğan
Protein Function Prediction: Methods and Protocols, 241-268,2025
- ChemPile: A 250GB Diverse and Curated Dataset for Chemical Foundation Models
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A Mirza, N Alampara, M Ríos-García, M Abdelalim, J Butler, B Connolly, ...
arXiv preprint arXiv:2505.12534,2025
- ProtHGT: Heterogeneous Graph Transformers for Automated Protein Function Prediction Using Biological Knowledge Graphs and Language Models
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E Ulusoy, T Doğan
bioRxiv, 2025.04. 19.649272,2025
- Protein language models for predicting drug–target interactions: Novel approaches, emerging methods, and future directions
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A Ünlü, E Ulusoy, MG Yiğit, M Darcan, T Doğan
Current Opinion in Structural Biology 91, 103017,2025
- Molecular Contrastive Learning with Graph Attention Network (MoCL-GAT) for Enhanced Molecular Representation
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A Dalkiran, AS Rifaioglu, R Cetin-Atalay, AC Acar, T Dogan, VM Atalay
bioRxiv, 2025.09. 17.676724,2025
- OmniPath: integrated knowledgebase for multi-omics analysis
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D Turei, J Schaul, N Palacio-Escat, B Bohar, Y Bai, F Ceccarelli, E Cevrim, ...
bioRxiv, 2025.09. 11.675512
2025
- Multi-modal Representation Learning Enables Accurate Protein Function Prediction in Low-Data Setting
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S Ünsal, S Özdemir, B Kasap, ME Kalaycı, K Turhan, T Doğan, AC Acar
arXiv preprint arXiv:2412.08649,2024
- Design, synthesis, and evaluation of novel Indole‐Based small molecules as sirtuin inhibitors with anticancer activities
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B Binarci, EK Kilic, T Dogan, R Cetin Atalay, DC Kahraman, ...
Drug Development Research 85 (7), e70008,2024
- Mutual annotation‐based prediction of protein domain functions with Domain2GO, E Ulusoy, T Doğan, Protein Science 33 (6), e4988, 2024
- An integrative framework for clinical diagnosis and knowledge discovery from exome sequencing data, M Shojaei, N Mohammadvand, T Doğan, C Alkan, RÇ Atalay, AC Acar, Computers in Biology and Medicine 169, 107810, 2024
- ASCARIS: Positional feature annotation and protein structure-based representation of single amino acid variations, F Cankara, T Doğan, Computational and Structural Biotechnology Journal 21, 4743-4758, 2023
- Democratizing knowledge representation with BioCypher, S Lobentanzer, P Aloy, J Baumbach, B Bohar, VJ Carey, P Charoentong, K Danhauser, T Doğan ..., Nature Biotechnology, 1-4 21, 2023
- UniProt: the Universal Protein knowledgebase in 2023, Nucleic Acids Research 51 (D1), D523-D531, 1716,2023