Yayınlar & Eserler

Yayın Ağı
Makaleler 49
Tümü (49)
SCI-E, SSCI, AHCI (47)
SCI-E, SSCI, AHCI, ESCI (49)
Scopus (48)

1. Molecular contrastive learning with graph attention network (MoCL-GAT) for enhanced molecular representation

Dalkıran A., Rifaioglu A. S., Cetin-Atalay R., ACAR A. C., DOĞAN T., ATALAY M. V.
BMC Bioinformatics , cilt.27, sa.1, 2026 (SCI-Expanded, Scopus)

2. SELFormerMM: multimodal molecular representation learning via SELFIES, structure, text, and knowledge graph integration

Ulusoy E., Bostancı Ş., Deniz B. E., DOĞAN T.
Bioinformatics (Oxford, England) , cilt.42, sa.2, 2026 (SCI-Expanded, Scopus)

3. DTA-GNN: a toolkit for constructing target-specific drug–target affinity datasets and training graph neural networks

Özsari G., Rifaioğlu A. S., ACAR A. C., DOĞAN T., ATALAY M. V.
SoftwareX , cilt.34, 2026 (SCI-Expanded, Scopus)

4. Target-specific de novo design of drug candidate molecules with graph-transformer-based generative adversarial networks

Doğan T.
Nature Machine Intelligence , cilt.7, sa.9, ss.1-17, 2025 (SCI-Expanded, Scopus) Creative Commons License

5. Mpox: disease manifestations and therapeutic development

Wang Y., Wang X., DOĞAN T., Sam-Agudu N. A., Al-Tawfiq J. A., Pan Q.
JOURNAL OF VIROLOGY , cilt.99, 2025 (SCI-Expanded, Scopus)

6. Protein language models for predicting drug-target interactions: Novel approaches, emerging methods, and future directions

Unlu A., Ulusoy E., Yigit M. G., Darcan M., DOĞAN T.
CURRENT OPINION IN STRUCTURAL BIOLOGY , cilt.91, 2025 (SCI-Expanded, Scopus)

7. Design, synthesis, and evaluation of novel Indole-Based small molecules as sirtuin inhibitors with anticancer activities

BINARCI B., Kilic E. K., DOĞAN T., ATALAY R., KAHRAMAN D. C., BAYTAŞ S.
DRUG DEVELOPMENT RESEARCH , cilt.85, sa.7, 2024 (SCI-Expanded, Scopus)

8. Mutual annotation-based prediction of protein domain functions with Domain2GO

Ulusoy E., DOĞAN T.
PROTEIN SCIENCE , cilt.33, sa.6, 2024 (SCI-Expanded, Scopus) Sürdürülebilir Kalkınma

9. An integrative framework for clinical diagnosis and knowledge discovery from exome sequencing data

Shojaei M., Mohammadvand N., DOĞAN T., Alkan C., Çetin Atalay R., ACAR A.
Computers in Biology and Medicine , cilt.169, 2024 (SCI-Expanded, Scopus)

10. How to approach machine learning-based prediction of drug/compound–target interactions

Atas Guvenilir H., DOĞAN T.
Journal of Cheminformatics , cilt.15, sa.1, 2023 (SCI-Expanded, Scopus) Creative Commons License

11. Democratizing knowledge representation with BioCypher

Lobentanzer S., Aloy P., Baumbach J., Bohar B., Carey V. J., Charoentong P., et al.
Nature Biotechnology , cilt.41, sa.8, ss.1056-1059, 2023 (SCI-Expanded, Scopus)

12. Transfer learning for drug-target interaction prediction

DALKIRAN A., ATAKAN A., Rifaioğlu A. S., Martin M. J., Atalay R. Ç., ACAR A., et al.
Bioinformatics (Oxford, England) , cilt.39, sa.39, 2023 (Scopus) Creative Commons License

13. SELFormer: molecular representation learning via SELFIES language models

Yüksel A., Ulusoy E., Ünlü A., DOĞAN T.
Machine Learning: Science and Technology , cilt.4, sa.2, 2023 (SCI-Expanded, Scopus) Creative Commons License

14. ProFAB-open protein functional annotation benchmark

Özdilek A. S., ATAKAN A., ÖZSARI G., Acar A., ATALAY M. V., DOĞAN T., et al.
Briefings in bioinformatics , cilt.24, sa.2, 2023 (SCI-Expanded, Scopus)

15. UniProt: the Universal Protein Knowledgebase in 2023

Bateman A., Martin M., Orchard S., Magrane M., Ahmad S., Alpi E., et al.
Nucleic Acids Research , cilt.51, sa.D1, 2023 (SCI-Expanded, Scopus)

16. ASCARIS: Positional feature annotation and protein structure-based representation of single amino acid variations

Cankara F., DOĞAN T.
Computational and Structural Biotechnology Journal , cilt.21, ss.4743-4758, 2023 (SCI-Expanded, Scopus)

17. SLPred: a multi-view subcellular localization prediction tool for multi-location human proteins

ÖZSARI G., RİFAİOĞLU A. S., ATAKAN A., Tunca Dogan T., Martin M. J., ATALAY R., et al.
BIOINFORMATICS , cilt.38, sa.17, ss.4226-4229, 2022 (SCI-Expanded, Scopus)

18. Learning functional properties of proteins with language models

Unsal S., Atas H., Albayrak M., Turhan K., Acar A. C., Doğan T.
NATURE MACHINE INTELLIGENCE , cilt.4, sa.3, ss.227-245, 2022 (SCI-Expanded)

19. Machine learning-based prediction of drug approvals using molecular, physicochemical, clinical trial, and patent-related features

Ciray F., DOĞAN T.
Expert Opinion on Drug Discovery , cilt.17, sa.12, ss.1425-1441, 2022 (SCI-Expanded, Scopus) Creative Commons License Sürdürülebilir Kalkınma

20. Editorial: Machine Learning Methodologies to Study Molecular Interactions

Yakimovich A., oezguer A., DOĞAN T., Ozkirimli E.
FRONTIERS IN MOLECULAR BIOSCIENCES , cilt.8, 2021 (SCI-Expanded, Scopus) Creative Commons License

21. Data Centric Molecular Analysis and Evaluation of Hepatocellular Carcinoma Therapeutics Using Machine Intelligence-Based Tools

Cetin-Atalay R., Kahraman D. C., Nalbat E., Rifaioğlu A. S., Atakan A., Dönmez A., et al.
JOURNAL OF GASTROINTESTINAL CANCER , cilt.52, sa.4, ss.1266-1276, 2021 (Hakemli Dergi)

22. A crowdsourcing open platform for literature curation in UniProt

Wang Y., Wang Q., Huang H., Huang W., Chen Y., McGarvey P. B., et al.
PLOS BIOLOGY , cilt.19, sa.12, 2021 (SCI-Expanded, Scopus) Creative Commons License

23. Protein domain-based prediction of drug/compound-target interactions and experimental validation on LIM kinases

Doğan T., Guzelcan E., Baumann M., Koyas A., Atas H., Baxendale I., et al.
PLOS COMPUTATIONAL BIOLOGY , cilt.17, sa.11, 2021 (SCI-Expanded) Creative Commons License Sürdürülebilir Kalkınma

24. CROssBAR: comprehensive resource of biomedical relations with knowledge graph representations

Doğan T., Atas H., Joshi V., Atakan A., Rifaioğlu A. S., Nalbat E., et al.
NUCLEIC ACIDS RESEARCH , cilt.49, sa.16, 2021 (SCI-Expanded)

25. Crowdsourced mapping of unexplored target space of kinase inhibitors

Cichonska A., Ravikumar B., Allaway R. J., Wan F., Park S., Isayev O., et al.
NATURE COMMUNICATIONS , cilt.12, sa.1, 2021 (SCI-Expanded, Scopus) Creative Commons License

26. MDeePred: novel multi-channel protein featurization for deep learning-based binding affinity prediction in drug discovery

Rifaioglu A. S., Atalay R. C., KAHRAMAN D. C., DOĞAN T., Martin M., Atalay V.
BIOINFORMATICS , cilt.37, sa.5, ss.693-704, 2021 (SCI-Expanded, Scopus)

27. UniProt: the universal protein knowledgebase in 2021

Bateman A., Martin M., Orchard S., Magrane M., Agivetova R., Ahmad S., et al.
NUCLEIC ACIDS RESEARCH , cilt.49, sa.D1, 2021 (SCI-Expanded, Scopus) Creative Commons License Sürdürülebilir Kalkınma

28. iBioProVis: interactive visualization and analysis of compound bioactivity space

DÖNMEZ A., RİFAİOĞLU A. S., ACAR A. C., DOĞAN T., ATALAY R., ATALAY M. V.
BIOINFORMATICS , cilt.36, sa.14, ss.4227-4230, 2020 (SCI-Expanded, Scopus) Sürdürülebilir Kalkınma

29. DEEPScreen: high performance drug-target interaction prediction with convolutional neural networks using 2-D structural compound representations

Rifaioğlu A. S., Nalbat E., Atalay V., Martin M. J., Cetin-Atalay R., Doğan T.
CHEMICAL SCIENCE , cilt.11, sa.9, ss.2531-2557, 2020 (SCI-Expanded) Creative Commons License Sürdürülebilir Kalkınma

30. The CAFA challenge reports improved protein function prediction and new functional annotations for hundreds of genes through experimental screens

Zhou N., Jiang Y., Bergquist T. R., Lee A. J., Kacsoh B. Z., Crocker A. W., et al.
GENOME BIOLOGY , cilt.20, sa.1, 2019 (SCI-Expanded, Scopus)

31. FAIR adoption, assessment and challenges at UniProt

Garcia L., Bolleman J., Gehant S., Redaschi N., Martin M., Bateman A., et al.
SCIENTIFIC DATA , cilt.6, 2019 (SCI-Expanded, Scopus) Creative Commons License

32. Recent applications of deep learning and machine intelligence on in silico drug discovery: methods, tools and databases

Rifaioğlu A. S., Atas H., Martin M. J., Cetin-Atalay R., Atalay V., Dogan T.
BRIEFINGS IN BIOINFORMATICS , cilt.20, sa.5, ss.1878-1912, 2019 (SCI-Expanded) Creative Commons License Sürdürülebilir Kalkınma

33. DEEPred: Automated Protein Function Prediction with Multi-task Feed-forward Deep Neural Networks

Rifaioğlu A. S., Doğan T., Martin M. J., Cetin-Atalay R., Atalay V.
SCIENTIFIC REPORTS , cilt.9, 2019 (SCI-Expanded) Creative Commons License

34. UniProt: a worldwide hub of protein knowledge

Bateman A., Martin M., Orchard S., Magrane M., Alpi E., Bely B., et al.
NUCLEIC ACIDS RESEARCH , cilt.47, 2019 (SCI-Expanded, Scopus)

35. ECPred: a tool for the prediction of the enzymatic functions of protein sequences based on the EC nomenclature

Dalkiran A., Rifaioğlu A. S., Martin M. J., Cetin-Atalay R., Atalay V., Dogan T.
BMC BIOINFORMATICS , cilt.19, 2018 (SCI-Expanded)

36. HPO2GO: prediction of human phenotype ontology term associations for proteins using cross ontology annotation co-occurrences

Doğan T.
PEERJ , cilt.6, 2018 (SCI-Expanded) Sürdürülebilir Kalkınma

37. Large-scale automated function prediction of protein sequences and an experimental case study validation on PTEN transcript variants

Rifaioğlu A. S., Dogan T., Sarac O. S., Ersahin T., Saidi R., Atalay M. V., et al.
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS , cilt.86, sa.2, ss.135-151, 2018 (SCI-Expanded)

38. A Structural Perspective on the Modulation of Protein-protein Interactions with Small Molecules

Demirel H. C., Dogan T., TUNÇBAĞ N.
CURRENT TOPICS IN MEDICINAL CHEMISTRY , cilt.18, sa.8, ss.700-713, 2018 (SCI-Expanded, Scopus) Sürdürülebilir Kalkınma

39. Phylogenetic and Other Conservation-Based Approaches to Predict Protein Functional Sites

Atas H., Tunçbağ N., Doğan T.
COMPUTATIONAL DRUG DISCOVERY AND DESIGN , cilt.1762, ss.51-69, 2018 (SCI-Expanded)

40. On expert curation and scalability: UniProtKB/Swiss-Prot as a case study

Poux S., Arighi C. N., Magrane M., Bateman A., Wei C., Lu Z., et al.
BIOINFORMATICS , cilt.33, sa.21, ss.3454-3460, 2017 (SCI-Expanded, Scopus) Creative Commons License

41. From the research laboratory to the database: the Caenorhabditis elegans kinome in UniProtKB

Zaru R., Magrane M., O'Donovan C., Bateman A., Martin M. J., Alpi E., et al.
BIOCHEMICAL JOURNAL , cilt.474, ss.493-515, 2017 (SCI-Expanded, Scopus) Creative Commons License

42. UniProt: the universal protein knowledgebase

Bateman A., Martin M. J., O'Donovan C., Magrane M., Alpi E., Antunes R., et al.
NUCLEIC ACIDS RESEARCH , cilt.45, 2017 (SCI-Expanded, Scopus) Creative Commons License

43. An expanded evaluation of protein function prediction methods shows an improvement in accuracy

Jiang Y., Oron T. R., Clark W. T., Bankapur A. R., D'Andrea D., Lepore R., et al.
GENOME BIOLOGY , cilt.17, 2016 (SCI-Expanded, Scopus)

44. UniProt-DAAC: domain architecture alignment and classification, a new method for automatic functional annotation in UniProtKB

Doğan T., Macdougall A., Saidi R., Poggioli D., Bateman A., O'donovan C., et al.
BIOINFORMATICS , cilt.32, sa.15, ss.2264-2271, 2016 (SCI-Expanded) Creative Commons License

45. The UniProtKB guide to the human proteome

Breuza L., Poux S., Estreicher A., Famiglietti M. L., Magrane M., Tognolli M., et al.
DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION , 2016 (SCI-Expanded, Scopus) Creative Commons License

46. Tools and data services registry: a community effort to document bioinformatics resources

Ison J., Rapacki K., Menager H., Kalas M., Rydza E., Chmura P., et al.
NUCLEIC ACIDS RESEARCH , cilt.44, 2016 (SCI-Expanded, Scopus) Creative Commons License Sürdürülebilir Kalkınma

47. UniProt: a hub for protein information

Bateman A., Martin M. J., O'Donovan C., Magrane M., Apweiler R., Alpi E., et al.
NUCLEIC ACIDS RESEARCH , cilt.43, 2015 (SCI-Expanded, Scopus) Creative Commons License

48. Activities at the Universal Protein Resource (UniProt)

Apweiler R., Bateman A., Martin M. J., O'Donovan C., Magrane M., Alam-Faruque Y., et al.
NUCLEIC ACIDS RESEARCH , cilt.42, 2014 (SCI-Expanded, Scopus) Creative Commons License

49. Automatic Identification of Highly Conserved Family Regions and Relationships in Genome Wide Datasets Including Remote Protein Sequences

Doğan T., Karacali B.
PLOS ONE , cilt.8, sa.9, 2013 (SCI-Expanded) Creative Commons License
Hakemli Bilimsel Toplantılarda Yayımlanmış Bildiriler 4

1. In vitro validation of drug-target interactions revealed in silico by Comprehensive Resource of Biomedical Relations with Network Representations and Deep Learning (CROssBAR) in HCC

NALBAT E., Rifaioglu A. S., DOĞAN T., Martin M. J., Cetin-Atalay R., ATALAY M. V.
AACR Annual Meeting, ELECTR NETWORK, 22 - 24 Haziran 2020, cilt.80, (Özet Bildiri)

2. Unsupervised identification of redundant domain entries in InterPro database using clustering techniques

RİFAİOĞLU A. S., Doǧan T., CAN T.
6th ACM Conference on Bioinformatics, Computational Biology, and Health Informatics, BCB 2015, Georgia, Amerika Birleşik Devletleri, 9 - 12 Eylül 2015, ss.505-506, (Tam Metin Bildiri)

3. 2-D thresholding of the connectivity map following the multiple sequence alignments of diverse datasets

Doǧan T., Karaçali B.
10th IASTED International Conference on Biomedical Engineering, BioMed 2013, Innsbruck, Avusturya, 13 - 15 Şubat 2013, ss.1-8, (Tam Metin Bildiri) Creative Commons License

4. Evolutionary relationships between gene sequences via nonlinear embedding Doǧrusal olmayan gömme teknikleri altinda gen dizilerinin evrimsel i̇lişkileri

Doǧan T., Karaçcali B.
2010 15th National Biomedical Engineering Meeting, BIYOMUT2010, Antalya, Türkiye, 21 - 24 Nisan 2010, (Tam Metin Bildiri)
Metrikler

Yayın

54

Yayın (WoS)

50

Yayın (Scopus)

51

Atıf (WoS)

22030

H-İndeks (WoS)

25

Atıf (Scopus)

29270

H-İndeks (Scopus)

26

Atıf (Scholar)

41858

H-İndeks (Scholar)

28

Proje

17

Fikri Mülkiyet

1

Tez Danışmanlığı

13

Açık Erişim

37
BM Sürdürülebilir Kalkınma Amaçları
SDG 3: AMAÇ 3: SAĞLIKLI BİREYLER
SDG 9: AMAÇ 9: SANAYİ, YENİLİKÇİLİK VE ALTYAPI
SDG 15: AMAÇ 15: KARASAL YAŞAM
SDG 16: AMAÇ 16: BARIŞ VE ADALET