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Oya Beyan

Oya Deniz Beyan

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affiliation: University of Cologne, Faculty of Medicine, Cologne, Germany
affiliation: Fraunhofer Institute for Applied Information Technology (FIT), Sankt Augustin, Germany
affiliation: RWTH Aachen University, Germany
affiliation: National University of Ireland Galway, INSIGHT Centre for Data Analytics, Ireland
affiliation (PhD 2010): Middle East Technical University, Department of Health Informatics, Ankara, Turkey

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2020 – today

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2024
[j19]
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Cara Dannenberg, Johannes Heimann, Adamantios Koumpis, Oya Beyan:
Identification of Medical Ecosystems in the Field of Mental Health and Cardiovascular Diseases at the Cologne Site. Int. J. Online Biomed. Eng. 20(5): 66-77 (2024)
[j18]
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Feifei Li, Yuanbin Wang, Oya Beyan, Mirjam Schöneck, Liliana Lourenco Caldeira:
Voxel-Wise Medical Image Generalization for Eliminating Distribution Shift. ACM Trans. Knowl. Discov. Data 18(7): 167 (2024)
[c37]
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Alina Troglio, Masoud Abedi, Martin Golebiewski, Frank A. Meineke, Toralf Kirsten, Barbara Namer, Oya Beyan, Ekaterina Kutafina:
Semi-Automatic Export of Electrophysiological Metadata to NFDI4Health Local Data Hubs: Use Case of Microneurography odML-Tables - A Technical Case Report. GMDS 2024: 40-48
[c36]
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Julia Gehrmann, Oya Beyan:
Early Multimodal Data Integration for Data-Driven Medical Research - A Scoping Review. GMDS 2024: 49-58
[c35]
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Julia Gehrmann, Oya Beyan:
Data Quality in Medical Real-World Data - An Oncological Use Case. MIE 2024: 9-13
[c34]
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Md. Mostafa Kamal, Ekaterina Kutafina, Oya Beyan:
Real-Time Visualization and Analysis Architecture for Data Integration Processes at Cologne University Hospital's Medical Data Integration Center. MIE 2024: 48-52
[c33]
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Muhammad Adnan, Ekaterina Kutafina, Oya Beyan:
Cybersecurity Frameworks in Healthcare Data: Short Literature Review. MIE 2024: 301-302
[c32]
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Barbara Namer, Alina Troglio, Toralf Kirsten, Oya Beyan, Ekaterina Kutafina:
Harmonizing Microneurography Metadata with Local Data Hubs: A Concept. MIE 2024: 358-359
[c31]
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Feifei Li, Ekaterina Kutafina, Mirjam Schöneck, Liliana Lourenco Caldeira, Oya Beyan:
How Data Infrastructure Deals with Bias Problems in Medical Imaging. MIE 2024: 726-730
[c30]
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Filip Rehburg, Miriam Hübner, Sylvia Thun, Oya Beyan:
Review of Key Elements in Developing a Common Data Model for Rare Diseases: Identifying Common Success Factors. MIE 2024: 1396-1400
[i15]
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  - journals/corr/abs-2402-03812
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Oussama Zoubia, Zeyd Boukhers, Nagaraj Bahubali Asundi, Sezin Dogan, Adamantios Koumpis, Christoph Lange, Oya Beyan:
FDO Manager: Minimum Viable FAIR Digital Object Implementation. CoRR abs/2402.03812 (2024)
2023
[j17]
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Md. Rezaul Karim, Tanhim Islam, Md Shajalal, Oya Beyan, Christoph Lange, Michael Cochez, Dietrich Rebholz-Schuhmann, Stefan Decker:
Explainable AI for Bioinformatics: Methods, Tools and Applications. Briefings Bioinform. 24(5) (2023)
[j16]
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  - journals/cmpb/AltiniRTPPPBSGDBPRELKBBVMNCEGBB23
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Nicola Altini, Michele Rossini, Sándor Turkevi-Nagy, Francesco Pesce, Paola Pontrelli, Berardino Prencipe, Francesco Berloco, Surya Seshan, Jean-Baptiste Gibier, Aníbal Pedraza Dorado, Gloria Bueno, Licia Peruzzi, Mattia Rossi, Albino Eccher, Feifei Li, Adamantios Koumpis, Oya Beyan, Jonathan Barratt, Huy Quoc Vo, Chandra Mohan, Hien Van Nguyen, Pietro Antonio Cicalese, Angela Ernst, Loreto Gesualdo, Vitoantonio Bevilacqua, Jan Ulrich Becker:
Performance and limitations of a supervised deep learning approach for the histopathological Oxford Classification of glomeruli with IgA nephropathy. Comput. Methods Programs Biomed. 242: 107814 (2023)
[j15]
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Stanislav Kirichenko, Adamantios Koumpis, Oya Beyan:
Stakeholders of Cardiovascular Innovation Ecosystems in Germany: A First Level Analysis and an Example. Int. J. Online Biomed. Eng. 19(18): 4-17 (2023)
[j14]
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Lars Quakulinski, Adamantios Koumpis, Oya Deniz Beyan:
Transparency in Medical Artificial Intelligence Systems. Int. J. Semantic Comput. 17(4): 495-510 (2023)
[c29]
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Yongli Mou, Feifei Li, Sven Weber, Sabith Haneef, Hans Meine, Liliana Caldeira, Mehrshad Jaberansary, Sascha Welten, Yeliz Ucer Yediel, Guido P. M. Prause, Stefan Decker, Oya Beyan, Toralf Kirsten:
Distributed Privacy-Preserving Data Analysis in NFDI4Health With the Personal Health Train. CoRDI 2023
[c28]
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  - conf/globecom/MouGLLBRDD23
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Yongli Mou, Fengyang Guo, Wei Lu, Yongzhao Li, Oya Beyan, Thomas Rose, Schahram Dustdar, Stefan Decker:
Towards FAIR Data in Distributed Machine Learning Systems. GLOBECOM 2023: 6450-6455
[c27]
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Zeyd Boukhers, Arnim Bleier, Yeliz Ucer Yediel, Mio Hienstorfer-Heitmann, Mehrshad Jaberansary, Sascha Welten, Adamantios Koumpis, Oya Beyan:
PADME-SoSci: A Platform for Analytics and Distributed Machine Learning for the Social Sciences. JCDL 2023: 251-252
[c26]
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Lars Quakulinski, Adamantios Koumpis, Oya Deniz Beyan:
The Library of Babel as a Digital Library of Human Mistakes. JCDL 2023: 288-290
[c25]
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  - conf/mie/AlkarkouklyKB23
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Samer Alkarkoukly, Md. Mostafa Kamal, Oya Beyan:
Breaking Barriers for Interoperability: A Reference Implementation of CSV-FHIR Transformation Using Open-Source Tools. MIE 2023: 43-47
[c24]
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Julia Gehrmann, Oya Beyan:
Integrating Cross-Departmental Data. MIE 2023: 125-126
[c23]
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  - conf/mie/LiSBC23
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Feifei Li, Mirjam Schöneck, Oya Beyan, Liliana Lourenco Caldeira:
Voxel-Wise Medical Imaging Transformation and Adaption Based on CycleGAN and Score-Based Diffusion. MIE 2023: 1027-1028
[c22]
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Yongli Mou, Jiahui Geng, Feng Zhou, Oya Beyan, Chunming Rong, Stefan Decker:
pFedV: Mitigating Feature Distribution Skewness via Personalized Federated Learning with Variational Distribution Constraints. PAKDD (2) 2023: 283-294
[c21]
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  - conf/www/Boukhers0B23
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Zeyd Boukhers, Christoph Lange, Oya Beyan:
Enhancing Data Space Semantic Interoperability through Machine Learning: a Visionary Perspective. WWW (Companion Volume) 2023: 1462-1467
[c20]
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Mehrshad Jaberansary, Macedo Maia, Yeliz Ucer Yediel, Oya Beyan, Toralf Kirsten:
Analyzing Distributed Medical Data in FAIR Data Spaces. WWW (Companion Volume) 2023: 1480-1484
[i14]
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  - journals/corr/abs-2302-04737
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Md. Rezaul Karim, Lina Molinas Comet, Oya Beyan, Dietrich Rebholz-Schuhmann, Stefan Decker:
A Biomedical Knowledge Graph for Biomarker Discovery in Cancer. CoRR abs/2302.04737 (2023)
[i13]
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  - journals/corr/abs-2303-08932
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Zeyd Boukhers, Christoph Lange, Oya Beyan:
Enhancing Data Space Semantic Interoperability through Machine Learning: a Visionary Perspective. CoRR abs/2303.08932 (2023)
[i12]
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  - journals/corr/abs-2303-18200
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Zeyd Boukhers, Arnim Bleier, Yeliz Ucer Yediel, Mio Hienstorfer-Heitmann, Mehrshad Jaberansary, Adamantios Koumpis, Oya Beyan:
PADME-SoSci: A Platform for Analytics and Distributed Machine Learning for the Social Sciences. CoRR abs/2303.18200 (2023)
[i11]
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  - journals/corr/abs-2309-06171
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Maximilian Jugl, Sascha Welten, Yongli Mou, Yeliz Ucer Yediel, Oya Deniz Beyan, Ulrich Sax, Toralf Kirsten:
Privacy-Preserving Linkage of Distributed Datasets using the Personal Health Train. CoRR abs/2309.06171 (2023)
[i10]
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  - journals/corr/abs-2310-08365
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Md. Rezaul Karim, Lina Molinas Comet, Md Shajalal, Oya Beyan, Dietrich Rebholz-Schuhmann, Stefan Decker:
From Large Language Models to Knowledge Graphs for Biomarker Discovery in Cancer. CoRR abs/2310.08365 (2023)
2022
[j13]
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  - journals/tcbb/KarimCZSRBD22
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Md. Rezaul Karim, Michael Cochez, Achille Zappa, Ratnesh Sahay, Dietrich Rebholz-Schuhmann, Oya Beyan, Stefan Decker:
Convolutional Embedded Networks for Population Scale Clustering and Bio-Ancestry Inferencing. IEEE ACM Trans. Comput. Biol. Bioinform. 19(1): 369-382 (2022)
[c19]
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Lars Quakulinski, Adamantios Koumpis, Oya Deniz Beyan:
Establishing Transparency in Artificial Intelligence Systems. TransAI 2022: 116-121
[i9]
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  - journals/corr/abs-2212-13261
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Md. Rezaul Karim, Tanhim Islam, Oya Beyan, Christoph Lange, Michael Cochez, Dietrich Rebholz-Schuhmann, Stefan Decker:
Explainable AI for Bioinformatics: Methods, Tools, and Applications. CoRR abs/2212.13261 (2022)
2021
[j12]
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  - journals/access/KarimJDCBRD21
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Md. Rezaul Karim, Jiao Jiao, Till Döhmen, Michael Cochez, Oya Beyan, Dietrich Rebholz-Schuhmann, Stefan Decker:
DeepKneeExplainer: Explainable Knee Osteoarthritis Diagnosis From Radiographs and Magnetic Resonance Imaging. IEEE Access 9: 39757-39780 (2021)
[j11]
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Md. Rezaul Karim, Oya Beyan, Achille Zappa, Ivan G. Costa, Dietrich Rebholz-Schuhmann, Michael Cochez, Stefan Decker:
Deep learning-based clustering approaches for bioinformatics. Briefings Bioinform. 22(1): 393-415 (2021)
[j10]
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  - journals/dint/WeltenNYSDB21
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Sascha Welten, Laurenz Neumann, Yeliz Ucer Yediel, Luiz Olavo Bonino da Silva Santos, Stefan Decker, Oya Beyan:
DAMS: A Distributed Analytics Metadata Schema. Data Intell. 3(4): 528-547 (2021)
[c18]
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  - conf/medinfo/Martinez-Garcia21
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Alicia Martinez-García, Giorgio Cangioli, Catherine E. Chronaki, Matthias Löbe, Oya Beyan, Anthony Juehne, Carlos Luis Parra Calderón:
FAIRness for FHIR: Towards Making Health Datasets FAIR Using HL7 FHIR. MedInfo 2021: 22-26
[c17]
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Yongli Mou, Sascha Welten, Mehrshad Jaberansary, Yeliz Ucer Yediel, Toralf Kirsten, Stefan Decker, Oya Beyan:
Distributed Skin Lesion Analysis Across Decentralised Data Sources. MIE 2021: 352-356
[c16]
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  - conf/pkdd/MouGWRDB21
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Yongli Mou, Jiahui Geng, Sascha Welten, Chunming Rong, Stefan Decker, Oya Beyan:
Optimized Federated Learning on Class-Biased Distributed Data Sources. PKDD/ECML Workshops (1) 2021: 146-158
[i8]
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  - journals/corr/abs-2103-13226
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Yongli Mou, Sascha Welten, Yeliz Ucer Yediel, Toralf Kirsten, Oya Deniz Beyan:
Distributed Learning for Melanoma Classification using Personal Health Train. CoRR abs/2103.13226 (2021)
[i7]
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  - journals/corr/abs-2110-09074
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Jiahui Geng, Yongli Mou, Feifei Li, Qing Li, Oya Beyan, Stefan Decker, Chunming Rong:
Towards General Deep Leakage in Federated Learning. CoRR abs/2110.09074 (2021)
2020
[j9]
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  - journals/biomedsem/GleimKZKSDB20
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Lars Christoph Gleim, Md. Rezaul Karim, Lukas Zimmermann, Oliver Kohlbacher, Holger Stenzhorn, Stefan Decker, Oya Beyan:
Enabling ad-hoc reuse of private data repositories through schema extraction. J. Biomed. Semant. 11(1): 6 (2020)
[j8]
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Oya Beyan, Ananya Choudhury, Johan van Soest, Oliver Kohlbacher, Lukas Zimmermann, Holger Stenzhorn, Md. Rezaul Karim, Michel Dumontier, Stefan Decker, Luiz Olavo Bonino da Silva Santos, Andre Dekker:
Distributed Analytics on Sensitive Medical Data: The Personal Health Train. Data Intell. 2(1-2): 96-107 (2020)
[j7]
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  - journals/dint/McQuiltonBBGCIL20
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Peter McQuilton, Dominique Batista, Oya Beyan, Ramón Granell, Simon J. Coles, Massimiliano Izzo, Allyson L. Lister, Robert Pergl, Philippe Rocca-Serra, Ben Schaap, Hugh P. Shanahan, Milo Thurston, Susanna-Assunta Sansone:
Helping the Consumers and Producers of Standards, Repositories and Policies to Enable FAIR Data. Data Intell. 2(1-2): 151-157 (2020)
[j6]
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  - journals/nca/KarimRJDB20
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Md. Rezaul Karim, Ashiqur Rahman, Joao Bosco Jares, Stefan Decker, Oya Beyan:
A snapshot neural ensemble method for cancer-type prediction based on copy number variations. Neural Comput. Appl. 32(19): 15281-15299 (2020)
[c15]
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  - conf/bibm/0001DCBRD20
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Md. Rezaul Karim, Till Döhmen, Michael Cochez, Oya Beyan, Dietrich Rebholz-Schuhmann, Stefan Decker:
DeepCOVIDExplainer: Explainable COVID-19 Diagnosis from Chest X-ray Images. BIBM 2020: 1034-1037
[i6]
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  - journals/corr/abs-2004-04582
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Md. Rezaul Karim, Till Döhmen, Dietrich Rebholz-Schuhmann, Stefan Decker, Michael Cochez, Oya Beyan:
DeepCOVIDExplainer: Explainable COVID-19 Predictions Based on Chest X-ray Images. CoRR abs/2004.04582 (2020)
[i5]
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  - journals/corr/abs-2009-09795
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Dinh-An Ho, Oya Beyan:
Biases in Data Science Lifecycle. CoRR abs/2009.09795 (2020)

2010 – 2019

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2019
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Md. Rezaul Karim, Galih Wicaksono, Ivan G. Costa, Stefan Decker, Oya Beyan:
Prognostically Relevant Subtypes and Survival Prediction for Breast Cancer Based on Multimodal Genomics Data. IEEE Access 7: 133850-133864 (2019)
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Md. Rezaul Karim, Michael Cochez, Joao Bosco Jares, Mamtaz Uddin, Oya Beyan, Stefan Decker:
Drug-Drug Interaction Prediction Based on Knowledge Graph Embeddings and Convolutional-LSTM Network. BCB 2019: 113-123
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  - conf/bibe/0001CBD019
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Md. Rezaul Karim, Michael Cochez, Oya Beyan, Stefan Decker, Christoph Lange:
OncoNetExplainer: Explainable Predictions of Cancer Types Based on Gene Expression Data. BIBE 2019: 415-422
[c12]
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  - conf/medinfo/NguyenRDMBB19
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Binh-Phi Nguyen, Thomas J. Reese, Stefan Decker, Daniel C. Malone, Richard D. Boyce, Oya Beyan:
Implementation of Clinical Decision Support Services to Detect Potential Drug-Drug Interaction Using Clinical Quality Language. MedInfo 2019: 724-728
[c11]
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Matthias Löbe, Oya Beyan, Sebastian Stäubert, Frank A. Meineke, Danny Ammon, Alfred Winter, Stefan Decker, Markus Löffler, Toralf Kirsten:
Design of Metadata Services for Clinical Data Interoperability in Germany. MedInfo 2019: 1528-1529
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  - journals/corr/abs-1908-01288
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Md. Rezaul Karim, Michael Cochez, Joao Bosco Jares, Mamtaz Uddin, Oya Beyan, Stefan Decker:
Drug-Drug Interaction Prediction Based on Knowledge Graph Embeddings and Convolutional-LSTM Network. CoRR abs/1908.01288 (2019)
[i3]
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  - journals/corr/abs-1909-04169
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Md. Rezaul Karim, Michael Cochez, Oya Beyan, Stefan Decker, Christoph Lange:
OncoNetExplainer: Explainable Predictions of Cancer Types Based on Gene Expression Data. CoRR abs/1909.04169 (2019)
2018
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Md. Rezaul Karim, Michael Cochez, Oya Deniz Beyan, Chowdhury Farhan Ahmed, Stefan Decker:
Mining maximal frequent patterns in transactional databases and dynamic data streams: A spark-based approach. Inf. Sci. 432: 278-300 (2018)
[c10]
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Md. Rezaul Karim, Binh-Phi Nguyen, Lukas Zimmermann, Toralf Kirsten, Matthias Löbe, Frank A. Meineke, Holger Stenzhorn, Oliver Kohlbacher, Stefan Decker, Oya Beyan:
A distributed analytics platform to execute FHIR based phenotyping algorithms. SWAT4LS 2018
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Andra Waagmeester, Christopher J. O. Baker, Andrea Splendiani, Oya Deniz Beyan, M. Scott Marshall:
Proceedings of the 11th International Conference Semantic Web Applications and Tools for Life Sciences, SWAT4LS 2018, Antwerp, Belgium, December 3-6, 2018. CEUR Workshop Proceedings 2275, CEUR-WS.org 2018 [contents]
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Oya Beyan, Andrea Wuchner, Dirk Eisengräber-Pabst, Christoph Quix, Christian Zaschke, Oliver Schumacher:
Research Data in the Fraunhofer Digital Project: Creating a FAIR Research Data Infrastructure and Culture. RO 2018
[i1]
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  - journals/corr/abs-1805-12218
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Md. Rezaul Karim, Michael Cochez, Oya Beyan, Achille Zappa, Ratnesh Sahay, Stefan Decker, Dietrich Rebholz-Schuhmann:
Recurrent Deep Embedding Networks for Genotype Clustering and Ethnicity Prediction. CoRR abs/1805.12218 (2018)
2017
[c9]
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Md. Rezaul Karim, Matthias Heinrichs, Lars Christoph Gleim, Michael Cochez, Emily Porter, Alessandra La Gioia, Saqib Salahuddin, Stefan Decker, Martin O'Halloran, Oya Beyan:
Towards a FAIR Sharing of Scientific Experiments: Improving Discoverability and Reusability of Dielectric Measurements of Biological Tissues. SWAT4LS 2017
2016
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Christophe Debruyne, Oya Deniz Beyan, Rebecca Grant, Sandra Collins, Stefan Decker, Natalie Harrower:
A semantic architecture for preserving and interpreting the information contained in Irish historical vital records. Int. J. Digit. Libr. 17(3): 159-174 (2016)
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Oya Deniz Beyan, Siegfried Handschuh, Adamantios Koumpis, Garyfallos Fragidis, Stefan Decker:
A Framework for Applying Data Integration and Curation Pipelines to Support Integration of Migrants and Refugees in Europe. PRO-VE 2016: 588-596
[c7]
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Oya Beyan, Stefan Decker:
An RDF Based Semantic Approach to Model Temporal Relations in Health Records. SWAT4LS 2016
2015
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Heike Felzmann, Timur Beyan, Mark Ryan, Oya Beyan:
Implementing an ethical approach to big data analytics in assistive robotics for elderly with dementia. SIGCAS Comput. Soc. 45(3): 280-286 (2015)
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Christophe Debruyne, Oya Deniz Beyan, Rebecca Grant, Sandra Collins, Stefan Decker:
On a Linked Data Platform for Irish Historical Vital Records. TPDL 2015: 99-110
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Oya Beyan, P. J. Mealy, Dolores Grant, Rebecca Grant, Natalie Harrower, Ciara Breathnach, Sandra Collins, Stefan Decker:
Historical Data Preservation and Interpretation Pipeline for Irish Civil Registration Records. OTM Workshops 2015: 466-475
2014
[c4]
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  - conf/semweb/KazemzadehKBDB14
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Laleh Kazemzadeh, Maulik R. Kamdar, Oya Deniz Beyan, Stefan Decker, Frank Barry:
LinkedPPI: Enabling Intuitive, Integrative Protein-Protein Interaction Discovery. LISC@ISWC 2014: 48-59
2013
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Oya Deniz Beyan, Aftab Iqbal, Yasar Khan, Athos Antoniades, John A. Keane, Panagiotis Hasapis, Christos Georgousopoulos, Myrto Ioannidi, Stefan Decker, Ratnesh Sahay:
Querying phenotype-genotype associations across multiple knowledge bases using Semantic Web technologies. BIBE 2013: 1-5
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Ratnesh Sahay, Dimitrios Ntalaperas, Eleni Kamateri, Panagiotis Hasapis, Oya Deniz Beyan, Marie-Pierre F. Strippoli, Christiana Demetriou, Thomai Gklarou-Stavropoulou, Mathias Brochhausen, Konstantinos A. Tarabanis, Thanassis Bouras, David Tian, Aristos Aristodimou, Athos Antoniades, Christos Georgousopoulos, Manfred Hauswirth, Stefan Decker:
An Ontology for Clinical Trial Data Integration. SMC 2013: 3244-3250
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Konstantinos Perakis, Thanassis Bouras, Dimitrios Ntalaperas, Panagiotis Hasapis, Christos Georgousopoulos, Ratnesh Sahay, Oya Deniz Beyan, Cristi Potlog, Daniela Usurelu:
Advancing Patient Record Safety and EHR Semantic Interoperability. SMC 2013: 3251-3257
2012
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  - journals/jms/BeyanB12
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Oya Deniz Beyan, Nazife Baykal:
A Knowledge Based Search Tool for Performance Measures in Health Care Systems. J. Medical Syst. 36(1): 201-221 (2012)
2010
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Oya Deniz Beyan:
A new ontology and knowledge base system for performance measurement in health care ; Sağlık bakımında performans ölçümü için yeni bir ontoloji ve bilgi tabanı sistemi. Middle East Technical University, Çankaya, Ankara, Turkey, 2010

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