Asst. Prof. ZEYNEP İLKNUR KARADENİZ EROL

Publication Network

Articles 6

1. BioTriplex: a full-text annotated corpus for fine-tuning language models in gene-disease relation extraction tasks

Collins C., Fytas P., Karadeniz İ., Zheng H., Baker S., Stenius U., et al.

Bioinformatics , vol.42, no.2, 2026 (SCI-Expanded, Scopus)

2. Graph convolutional network based virus-human protein-protein interaction prediction for novel viruses

Koca M. B., Nourani E., Abbasoğlu F., Karadeniz İ., Sevilgen F. E.

Computational Biology and Chemistry , vol.101, 2022 (SCI-Expanded, Scopus)

3. Linking entities through an ontology using word embeddings and syntactic re-ranking

Karadeniz I., ÖZGÜR TÜRKMEN A.

BMC Bioinformatics , vol.20, no.1, 2019 (SCI-Expanded, Scopus)

4. Detection and categorization of bacteria habitats using shallow linguistic analysis

Karadeniz I., ÖZGÜR TÜRKMEN A.

BMC Bioinformatics , vol.16, no.10, 2015 (SCI-Expanded, Scopus)

5. Literature mining and ontology based analysis of host-Brucella gene-gene interaction network

Karadeniz I., Hur J., He Y., ÖZGÜR TÜRKMEN A.

Frontiers in Microbiology , vol.6, no.DEC, 2015 (SCI-Expanded, Scopus)

6. PHISTO: Pathogen-host interaction search tool

Durmuş Tekir S., Çakir T., Ardiç E., Sayilirbaş A. S., Konuk G., Konuk M., et al.

Bioinformatics , vol.29, no.10, pp.1357-1358, 2013 (SCI-Expanded, Scopus)

Papers Presented at Peer-Reviewed Scientific Conferences 8

1. MetninOzU at BioLaySumm2025: Text Summarization with Reverse Data Augmentation and Injecting Salient Sentences

Çelik Evgin E., KARADENİZ EROL Z. İ., YILDIZ O. T.

ACL 2025 - Proceedings of the 24th Workshop on Biomedical Language Processing (Shared Tasks), Viyana, Austria, 27 July 2025, (Full Text)

2. Clustering-Based Negative Sampling Approaches for Protein-Protein Interaction Prediction

Kesemen Z., Karadeniz İ., Aydoğan R.

19th International Meeting on Computational Intelligence Methods for Bioinformatics and Biostatistics, CIBB 2024, Benevento, Italy, 4 - 06 September 2024, vol.15276 LNBI, pp.3-14, (Full Text)

3. ISIKSumm at BioLaySumm Task 1: BART-based Summarization System Enhanced with Bio-Entity Labels

Çolak Ç., Karadeniz I.

22nd Workshop on Biomedical Natural Language Processing and BioNLP Shared Tasks, BioNLP 2023, Toronto, Canada, 13 July 2023, pp.636-640, (Full Text)

4. Protein interaction prediction on PHI networks using graph convolution networks Çizge evrişim aǧi kullanarak patojen-konak aǧlarinda protein etkileşim tahmini

Koca M. B., Karadeniz I., Nourani E., Sevilgen F. E.

29th IEEE Conference on Signal Processing and Communications Applications, SIU 2021, Virtual, Istanbul, Turkey, 9 - 11 June 2021, (Full Text)

5. ISIKUN at the FinCausal 2020: Linguistically informed Machine-learning Approach for Causality Identification in Financial Documents

Özenir H. G., Karadeniz I.

1st Joint Workshop on Financial Narrative Processing and MultiLing Financial Summarisation, FNP-FNS 2020, Virtual, Barcelona, Spain, 12 December 2020, pp.85-89, (Full Text)

6. BOUN-ISIK Participation: An Unsupervised Approach for the Named Entity Normalization and Relation Extraction of Bacteria Biotopes

Karadeniz I., Tuna Ö. F., Özgu A.

5th Workshop on BioNLP Open Shared Tasks, BioNLP-OST@EMNLP-IJNCLP 2019, Hong Kong, China, 04 November 2019, pp.150-157, (Full Text)

7. PHISTO: A new web platform for pathogen-human interactions

Tekir S. D., Çakir T., Ardiç E., Karadeniz I., ÖZGÜR TÜRKMEN A., Sevilgen F. E., et al.

11th International Conference on Computational Methods in Systems Biology, CMSB 2013, Klosterneuburg, Austria, 22 - 24 September 2013, vol.8130 LNBI, pp.268-269, (Full Text)

8. Bacteria Biotope Detection, Ontology-based Normalization, and Relation Extraction using Syntactic Rules

Karadeniz İ., ÖZGÜR TÜRKMEN A.

2013 Workshop on Biomedical Natural Language, BioNLP 2013, Sofija, Bulgaria, 09 October 2013, vol.2013-October, pp.170-177, (Full Text)

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