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  1. CROssBARv2: A Unified Computational Framework for Heterogeneous Biomedical Data Representation and LLM-Driven Exploration

    Article • April 2026, openRxiv

    Dr Tunca Dogan

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

    Article • March 2026, openRxiv

    Dr Tunca Dogan

  3. ECLIPSE: Exploration of Complex Ligand-Protein Interactions through Learning from Systems-level Heterogeneous Biomedical Knowledge Graphs

    Article • November 2025, Cold Spring Harbor Laboratory Press

    Dr Tunca Dogan

  4. Mpox: disease manifestations and therapeutic development

    Article • Journal of Virology, September 2025, ASM Journals

    Dr Tunca Dogan

  5. Molecular Contrastive Learning with Graph Attention Network (MoCL-GAT) for Enhanced Molecular Representation

    Article • September 2025, Cold Spring Harbor Laboratory Press

    Dr Tunca Dogan

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

    Article • Nature Machine Intelligence, September 2025, Springer Science + Business Media

    Dr Tunca Dogan

  7. ProtHGT: Heterogeneous Graph Transformers for Automated Protein Function Prediction Using Biological Knowledge Graphs and Language Models

    Article • April 2025, Cold Spring Harbor Laboratory Press

    Dr Tunca Dogan

  8. A Benchmarking Platform for Assessing Protein Language Models on Function-related Prediction Tasks

    Article • April 2025, Cold Spring Harbor Laboratory Press

    Dr Tunca Dogan

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

    Article • Current Opinion in Structural Biology, April 2025, Elsevier

    Dr Tunca Dogan

  10. A Benchmarking Platform for Assessing Protein Language Models on Function-Related Prediction Tasks

    Article • January 2025, Springer Science + Business Media

    Dr Tunca Dogan

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

    Article • Drug Development Research, October 2024, Wiley

    Dr Tunca Dogan

  12. Mutual annotation‐based prediction of protein domain functions with Domain2GO

    Article • Protein Science, May 2024, Wiley

    Dr Tunca Dogan

  13. Democratizing knowledge representation with BioCypher

    Article • Nature Biotechnology, June 2023, Springer Science + Business Media

    Dr Tunca Dogan

  14. SELFormer: molecular representation learning via SELFIES language models

    Article • Machine Learning Science and Technology, June 2023, Institute of Physics Publishing

    Dr Tunca Dogan

  15. Transfer learning for drug–target interaction prediction

    Article • Bioinformatics, June 2023, Oxford University Press (OUP)

    Dr Tunca Dogan

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

    Article • Journal of Cheminformatics, February 2023, Springer Science + Business Media

    Dr Tunca Dogan

  17. ProFAB—open protein functional annotation benchmark

    Article • Briefings in Bioinformatics, February 2023, Oxford University Press (OUP)

    Dr Tunca Dogan

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

    Article • Computational and Structural Biotechnology Journal, January 2023, Elsevier

    Dr Tunca Dogan

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

    Article • Expert Opinion on Drug Discovery, December 2022, Taylor & Francis

    Dr Tunca Dogan

  20. UniProt: the Universal Protein Knowledgebase in 2023

    Article • Nucleic Acids Research, November 2022, Oxford University Press (OUP)

    Dr Tunca Dogan

  21. ASCARIS: Positional Feature Annotation and Protein Structure-Based Representation of Single Amino Acid Variations

    Article • November 2022, Cold Spring Harbor Laboratory Press

    Dr Tunca Dogan

  22. Mutual Annotation-Based Prediction of Protein Domain Functions with Domain2GO

    Article • November 2022, Cold Spring Harbor Laboratory Press

    Dr Tunca Dogan

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

    Article • Bioinformatics, July 2022, Oxford University Press (OUP)

    Dr Tunca Dogan

  24. How to Best Represent Proteins in Machine Learning-based Prediction of Drug/Compound-Target Interactions

    Article • May 2022, Cold Spring Harbor Laboratory Press

    Dr Tunca Dogan

  25. Learning functional properties of proteins with language models

    Article • Nature Machine Intelligence, March 2022, Springer Science + Business Media

    Dr Tunca Dogan

  26. A crowdsourcing open platform for literature curation in UniProt

    Article • PLoS Biology, December 2021, PLOS

    Dr Tunca Dogan

  27. Editorial: Machine Learning Methodologies to Study Molecular Interactions

    Article • Frontiers in Molecular Biosciences, December 2021, Frontiers

    Dr Tunca Dogan

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

    Article • Journal of Gastrointestinal Cancer, December 2021, Springer Science + Business Media

    Dr Tunca Dogan

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

    Article • PLoS Computational Biology, November 2021, PLOS

    Dr Tunca Dogan

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

    Article • Nucleic Acids Research, June 2021, Oxford University Press (OUP)

    Dr Tunca Dogan

  31. Protein Domain-Based Prediction of Compound–Target Interactions and Experimental Validation on LIM Kinases

    Article • June 2021, Cold Spring Harbor Laboratory Press

    Dr Tunca Dogan

  32. Crowdsourced mapping of unexplored target space of kinase inhibitors

    Article • Nature Communications, June 2021, Springer Science + Business Media

    Dr Olexandr Isayev, Dr Tunca Dogan

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

    Article • Bioinformatics, December 2020, Oxford University Press (OUP)

    Dr Tunca Dogan

  34. UniProt: the universal protein knowledgebase in 2021

    Article • Nucleic Acids Research, November 2020, Oxford University Press (OUP)

    Dr Tunca Dogan

  35. Evaluation of Methods for Protein Representation Learning: A Quantitative Analysis

    Article • October 2020, Cold Spring Harbor Laboratory Press

    Dr Tunca Dogan

  36. CROssBAR: Comprehensive Resource of Biomedical Relations with Deep Learning Applications and Knowledge Graph Representations

    Article • September 2020, Cold Spring Harbor Laboratory Press

    Dr Tunca Dogan

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

    Article • Bioinformatics, May 2020, Oxford University Press (OUP)

    Dr Tunca Dogan

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

    Article • Chemical Science, January 2020, Royal Society of Chemistry

    Dr Tunca Dogan

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

    Article • November 2019, Springer Science + Business Media

    Dr Tunca Dogan, Professor Casey Greene, Dr Christophe Dessimoz

  40. FAIR adoption, assessment and challenges at UniProt

    Article • Scientific Data, September 2019, Springer Science + Business Media

    Dr Tunca Dogan

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

    Article • May 2019, Cold Spring Harbor Laboratory Press

    Dr Tunca Dogan, Dr Christophe Dessimoz, Professor Casey Greene

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

    Article • Scientific Reports, May 2019, Springer Science + Business Media

    Dr Tunca Dogan

  43. DEEPScreen: High Performance Drug-Target Interaction Prediction with Convolutional Neural Networks Using 2-D Structural Compound Representations

    Article • December 2018, Cold Spring Harbor Laboratory Press

    Dr Tunca Dogan

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

    Article • BMC Bioinformatics, September 2018, Springer Science + Business Media

    Dr Tunca Dogan

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

    Article • PeerJ, August 2018, PeerJ

    Dr Tunca Dogan

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

    Article • Briefings in Bioinformatics, July 2018, Oxford University Press (OUP)

    Dr Tunca Dogan

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

    Article • July 2018, PeerJ

    Dr Tunca Dogan

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

    Article • Current Topics in Medicinal Chemistry, July 2018, Bentham Science Publishers

    Dr Tunca Dogan

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

    Article • March 2018, PeerJ

    Dr Tunca Dogan

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

    Article • March 2018, PeerJ

    Dr Tunca Dogan

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

    Article • January 2018, Springer Science + Business Media

    Dr Tunca Dogan

  52. Large-scale automated protein function prediction and an experimental validation

    Article • Proteins Structure Function and Bioinformatics, November 2017, Wiley

    Tunca Dogan, Ahmet Sureyya Rifaioglu, Dr Tunca Dogan

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

    Article • Biochemical Journal, February 2017, Portland Press Ltd.

    Dr Tunca Dogan

  54. UniProt: the universal protein knowledgebase

    Article • Nucleic Acids Research, November 2016, Oxford University Press (OUP)

    Dr Tunca Dogan

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

    Article • September 2016, Springer Science + Business Media

    Professor Casey Greene, Dr Christophe Dessimoz, Dr Tunca Dogan, Professor Giorgio Valentini

  56. UniProt Tools

    Article • March 2016, Wiley

    Dr Tunca Dogan

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

    Article • Bioinformatics, March 2016, Oxford University Press (OUP)

    Dr Tunca Dogan

  58. The UniProtKB guide to the human proteome

    Article • Database, January 2016, Oxford University Press (OUP)

    Dr Tunca Dogan

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

    Article • Nucleic Acids Research, November 2015, Oxford University Press (OUP)

    Mr Rafael C Jimenez, Björn Grüning, Dr Tunca Dogan, Matúš Kalaš

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

    Article • September 2015, ACM (Association for Computing Machinery)

    Ahmet Sureyya Rifaioglu, Dr Tunca Dogan

  61. UniProt: a hub for protein information

    Article • Nucleic Acids Research, October 2014, Oxford University Press (OUP)

    Dr Tunca Dogan

  62. Activities at the Universal Protein Resource (UniProt)

    Article • Nucleic Acids Research, November 2013, Oxford University Press (OUP)

    Dr Tunca Dogan

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

    Article • PLOS One, September 2013, PLOS

    Dr Tunca Dogan

  64. 2-D Thresholding of the Connectivity Map Following the Multiple Sequence Alignments of Diverse Datasets

    Article • January 2013, ACTA Press

    Dr Tunca Dogan

  65. Evolutionary relationships between gene sequences via nonlinear embedding

    Article • April 2010, Institute of Electrical & Electronics Engineers (IEEE)

    Dr Tunca Dogan