Publications

Chaves JBJA, Ucer Yediel Y, Löbe M, Kirsten T, Karim MdR, Decker S, Beyan O. Making Data Analytics FAIR:  A Metadata Driven Approach for Sharing Phenotyping Algorithms. Methods of Information in Medicine. Special Issue: Application of FAIR principles in Health Research. ME19-02-0011. (Submitted)

Karim MdR, Rahman MdA, Jares JB, Decker S, Beyan O. A Snapshot Neural Ensemble Method for Cancer Type Prediction Based on Copy Number Variations. Neural Computing and Applications. NCAA-D-19-00120-R1. (Under Review, Minor Revision)

Gleim LC, Karim MdR, Zimmermann L, Kohlbacher O, Stenzhorn H, Decker S, Beyan O. Enabling Ad-hoc Reuse of Private Data Repositories through Schema Extraction. Journal of Biomedical Semantics. JBSM-D-18-00058. (Accepted)

Beyan O, Choudhury A, van Soest J, Kohlbacher O, Zimmermann L, Stenzhorn H, Karim MdR, Dumontier M, Decker S, Bonino da Silva Santos LO, Dekker A. Distributed Analytics on Sensitive Medical Data: The Personal Health Train. Data Intelligence 2 (2020), 96–107. doi: 10.1162/dint_a_00032

Karim MdR, Wicaksono G, Costa IG, Decker S, Beyan O. Prognostically Relevant Subtypes and Survival Prediction for Breast Cancer Based on Multimodal Genomics Data. IEEE Access. Vol. 7, pp. 133850 – 133864 (2019). doi: 10.1109/access.2019.2941796.

Winter A, Stäubert S, Ammon D, Aiche S, Beyan O, Bischoff V, Daumke P. et al. Smart medical information technology for healthcare (SMITH). Methods of Information in Medicine. 57, no. S 01 (2018): e92-e105.

Karim MdR, Cochez M, Beyan OD, Ahmed CF, Decker S. Mining maximal frequent patterns in transactional databases and dynamic data streams: a spark-based approach. Information Sciences. 432 (2018): 278-300.

Porter E, La Gioia A, Salahuddin S, Decker S, Shahzad A, Elahi MA, O’Halloran M, Beyan OMinimum information for dielectric measurements of biological tissues (MINDER): A framework for repeatable and reusable data. International Journal of RF and Microwave Computer‐Aided Engineering. 28, no. 3 (2018): e21201.

Debruyne C, Beyan OD, Grant R, Collins S, Decker S, Harrower N. A semantic architecture for preserving and interpreting the information contained in Irish historical vital records. International Journal on Digital Libraries. 17, no. 3 (2016): 159-174.

Felzmann H, Beyan T, Ryan M, Beyan OImplementing an ethical approach to big data analytics in assistive robotics for elderly with dementia. ACM SIGCAS Computers and Society. 45, no. 3 (2016): 280-286.

Beyan OD, Baykal N. A knowledge based search tool for performance measures in health care systems. Journal of Medical Systems. February 2012; 36(1):201-21. Epub 2010 Apr 14.

Koçgil OD, Baykal N. An integrated approach to breast diseases and breast cancer registry and research: BDRS as a web-based multi-institutional model. Computers in Biology and Medicine. November 2007; 37(10):1414-25.

Karaduman OD, Erkmen AM, Baykal N. Integrated Treatment Planning Using an Intelligent Learning for Clinical Decision Support by Reinforcement Feedback. WSEAS Transactions on Computers. July 2006; 5(7), 1541-8.

Saka O, Gülkesen KH, Gülden B, Koçgil OD. Evaluation of two search methods in PubMed; the Regular Search and Search by MeSH Terms. Acta Informatica Medica. Volume 13, No. 4, Pages 180-1832, December 2005.

Karim MdR, Cochez M, Beyan O, Decker S, Lange C. OncoNetExplainer: Explainable Predictions of Cancer Types Based on Gene Expression Data. The 9th IEEE International Conference on Bioinformatics and Bioengineering (IEEE BIBE 2019). Athens, Greece, October 28-30, 2019. (Accepted)

Karim MdR, Cochez M, Jares JB, Uddin M, Beyan O, Decker S. Drug-Drug Interaction Prediction Based on Knowledge Graph Embeddings and Convolutional-LSTM Network. The 10th ACM Conference on Bioinformatics, Computational Biology, and Health Informatics (ACM BCB 2019). Niagara Falls, New York, September 7-10, 2019.

Nguyen BP, Reese T, Decker S, Malone DC, Boyce RD, Beyan O. Clinical Decision Support Services to Detect Potential Drug-Drug Interaction using Clinical Quality Language. Medinfo 2019, Health and Wellbeing E-Networks for all. The 17th World Congress of Medical and Health Informatics. Lyon, France August 25-30, 2019.

Löbe M, Beyan O, Stäubert S, Meineke F, Ammon D, Winter A, Decker S, Löffler M, Kirsten T. Design of the SMITH Metadata Services. Medinfo 2019, Health and Wellbeing E-Networks for all. The 17th World Congress of Medical and Health Informatics. Lyon, France August 25-30, 2019.

Mietchen D, Schwaiger V, Beyan OFAIR Ethics: Making Ethical Review Processes more Machine Actionable. Ethics and Social Aspects of Data, RDA 12th Plenary. Gaborone, Botswana, 7 November 2018.

Karim MdR, Rahman MdA, Decker S, Beyan O. Cancer Risk and Type Prediction Based on Copy Number Variations with LSTM and Deep Belief Networks. Artificial Intelligence International Conference (A2IC2018). Barcelona, Spain, 21-23 November 2018.

Karim MdR, Nguyen BP, Zimmermann L, Kirsten T, Lobe M, Meineke F, Stenzhorn H, Kohlbacher O, Decker S, Beyan O. A Distributed Analytics Platform to Execute FHIR-based Phenotyping Algorithms. 11th International Semantic Web Applications and Tools for Healthcare and Life Sciences (SWAT4HCLS 2018). Antwerp, Belgium, 3-6 December 2018.

Eibl E, Sakik S, Schneider N, Beyan O, Lukas N. Identification of SHACL Constraints from a Knowledge Graph. 11th International Semantic Web Applications and Tools for Healthcare and Life Sciences (SWAT4HCLS 2018). Antwerp, Belgium, 3-6 December 2018.

Beyan O, Wuchner A, Eisengräber-Pabst D, Quix C, Zaschke C, Schumacher O. Research Data in the Fraunhofer Digital Project: Creating a FAIR Research Data Infrastructure and Culture. Workshop on Research Objects (RO 2018). 29 October 2018, Amsterdam, Netherlands.

Gleim LC, Karim MdR, Zimmermann L, Kohlbacher O, Stenzhorn H, Decker S, Beyan O. Schema Extraction for Privacy Preserving Processing of Sensitive Data. 15th European Semantic Web Conference (ESWC 2018), SeWeBMeDA 2018. Heraklion, Crete, Greece, 3-7 June 2018. In: Joint Proceedings of MEPDaW, SeWeBMeDA and SWeTI 2018, Volume 2112, Issue 1, Pages 36-47.

Beyan O, Juehne A, LeMay K, Durst L, Uhlmansiek M, Wolski M, Hudson Vitale C, Morley-Fletcher E, McIntosh. Reproducible Health Data Service Workflows Adoption and Training Guide for Biomedical Service Centers. Göttingen-CODATA RDM Symposium 2018. 18-20 March 2018, Göttingen, Germany.

Könning JW, Velasco CA, Yehya M , Decker S, Beyan ORepresenting medication guidelines for use in production rule systems in the context of POLYCARE project. International Academy, Research, and Industry Association -IARIA-: FUTURE COMPUTING 2018, The Tenth International Conference on Future Computational Technologies and Applications. Barcelona, Spain, 18-22 February 2018. IARIA, 2018. ISBN: 978-1-61208-608-8: S.15-23, p. 15-23. (Best Paper Award)

Karim MdR, Heinrichs M, Gleim LC, Cochez M, Porter E, La Gioia A, Salahuddin S, Decker S, O’Halloran M, Beyan ODTowards a FAIR Sharing of Scientific Experiments: Improving Discoverability and Reusability of Dielectric Measurements of Biological Tissues. 10th International Semantic Web Applications and Tools for Healthcare and Life Sciences (SWAT4HCLS) Conference. Rome, Italy, 4-7 December 2017.

Beyan OD, Handschuh S, Koumpis A, Fragidis G, Decker S. A Framework for Applying Data Integration and Curation Pipelines to Support Integration of Migrants and Refugees in Europe. 17th Working Conference on Virtual Enterprises (PRO-VE). October 2016, Porto, Portugal. IFIP Advances in Information and Communication Technology, AICT-480, pp.588-596, 2016, Collaboration in a Hyperconnected World.

Beyan OD, Decker S. An RDF Based Semantic Approach to Model Temporal Relations in Health Records. 9th International Conference Semantic Web Applications and Tools for Life Sciences (SWAT4LS). Amsterdam, Netherland, 5-8 December 2016.

Felzmann H, Beyan T, Ryan M, Beyan O. Implementing an ethical approach to big data analytics in assistive robotics for elderly with dementia. ETHICOMP2015. De Montfort University, Leicester, UK. 7–9 September 2015.

Beyan O, Mealy PJ, Grant D, Grant R, Harrower N, Breathnach C, Collins S, Decker S. Historical Data Preservation and Interpretation Pipeline for Irish Civil Registration Records. On the Move (OTM) Confederated International Conferences “On the Move to Meaningful Internet Systems”. Rhodes, Greece, October 2015.  In: Ciuciu I. et al. (eds) On the Move to Meaningful Internet Systems: OTM 2015 Workshops. Lecture Notes in Computer Science, vol 9416. Springer, Cham

Debruyne C, Beyan OD, Grant R, Collins S, Decker S. On a linked data platform for irish historical vital records. International Conference on Theory and Practice of Digital Libraries (TPDL). Poznań, Poland, 14-18 September 2015. In: Kapidakis S., Mazurek C., Werla M. (eds) Research and Advanced Technology for Digital Libraries. TPDL 2015. Lecture Notes in Computer Science, vol 9316. Springer, Cham.

Felzmann H, Murphy K, Casey D, Beyan ORobot-assisted care for elderly with dementia: is there a potential for genuine end-user empowerment? The Emerging Policy and Ethics of Human Robot Interaction. 2 March 2015, Portland, OR, USA.

Kazemzadeh L, Kamdar MR, Beyan OD, Decker S, Barry F. LinkedPPI: Enabling Intuitive, Integrative Protein-Protein Interaction Discovery. 13th International Semantic Web Conference (ISWC)-4th Workshop on Linked Science 2014— Making Sense Out of Data (LISC2014). Riva del Garda, Italy, 19 October 2014.

Debruyne C, Beyan OD, Decker S, Collins S. Using Semantic Technologies to Create Virtual Families from Historical Vital Records. European Data Infrastructure, 1st European Ontology Network (EUON) Workshop. De Meervaart Conference Centre, Amsterdam, The Netherlands, 25 September 2014.

Beyan OD, Breathnach C, Collins S, Debruyne C, Decker S, Grant D, Grant R, Gurrin B. Towards Linked Vital Registration Data for Reconstituting Families and Creating Longitudinal Health Histories. Vienna Summer of Logic (VSL) 2014, Knowledge Representation for Health Care (KR4HC). Vienna, Austria, July 2014.

Rakhmawati NA, Hasnain A, Beyan O, Iqbal A, Decker S. The Cost And Benefit of Exploiting Links in Federated SPARQL Query. 10th International Conference on Web Information Systems and Technologies (WEBIST 2014). Barcelona, Spain, April 2014.

Beyan OD, Iqbal A, Khan Y, Antoniades A, Keane J, Hasapis P, Georgousopoulos C, Ioannidi M, Decker S, Sahay R. Querying Phenotype-Genotype Associations across Multiple Knowledge Bases using Semantic Web Technologies. 13th IEEE International Conference on BioInformatics and BioEngineering (BIBE). Chania-Greece; November 2013.

Sahay R, Ntalaperas D, Kamateri E, Hasapis P, Beyan OD, Strippoli MPF, Demetriou CA, Gklarou-Stavropoulou T, Brochhausen M, Tarabanis K, Bouras T, Tian D, Aristodimou A, Antoniades A, Georgousopoulos C, Hauswirth M, Decker S. An Ontology for Clinical Trial Data Integration. IEEE International Conference on Systems, Man, and Cybernetics (SMC). Manchester, UK, October 2013.

Perakis K, Bouras T, Ntalaperas D, Hasapis P, Georgousopoulos C, Sahay R, Beyan OD, Potlog C, Usurelu D. Advancing Patient Record Safety and EHR Semantic Interoperability. IEEE International Conference on Systems, Man, and Cybernetics (SMC). Manchester, UK, October 2013.

Hacaloğlu T, Beyan OD. Measuring Innovative Characteristics of Students in Higher Education. 2nd International Engineering Education Conference (IEEC2012). Antalya, Turkey, October-November 2012.

Beyan OD, Tercan B. Sağlık Bakımında Bilgi Yönetimi (Knowledge Management in Health Care). VIII. Ulusal Tıp Bilişimi Kongresi (TURKMIA’11). Antalya, Turkey, November 2011.

Beyan T, Beyan OD. Kaliteli Tıbbi Bakım İçin Sağlık Malzemeleri Tedarik Zincirinde Bilişim Teknolojilerine Dayalı Dönüşüm: Genel Bir Çerçeve Önerisi (Transformation of Health Materials Supply Chain Based on Information Technologies For Qualified Healthcare). VIII. Ulusal Tıp Bilişimi Kongresi (TURKMIA’11). Antalya, Turkey, November 2011.

Beyan OD, Beyan T, Baykal N. Sağlık Bakımı Performans Ölçümü Ontolojisi ve Bilgi Tabanı (An Ontology and Knowledge Base For Healthcare Perfomance Measurements).VII. Ulusal Tıp Bilişimi Kongresi (TURKMIA’10). Northern Cyprus, October 2010.

Koçgil OD, Beyan T, Baykal N. Sağlık Bakımı Performans Ölçümü İçin Bir Karşılaştırma Aracı Önerisi (A Framework Proposal for Health Care Performance Measurement and its Application to National Health Care System). The Ministry of Health of Turkey, the International Congress on Quality and Performance in Healthcare. Antalya, Turkey, March 2009.

Koçgil OD, Baykal N, Beyan T. Sağlık ve Sağlık Bakım Sistemlerinde Performans İzleme ve Değerlendirme (Performance Measurement and Assessment in Health Care Systems). The Ministry of Health of Turkey, the Second e-Health Congress.Antalya, Turkey, October 2007.

Beyan T, Baykal N, Koçgil OD. Kompleks Adaptif Sistem Olarak Sağlık Sistemleri ve Performans (Health Systems as Complex Adaptive Systems and Performance). The Ministry of Health of Turkey, the Second e-Health Congress. Antalya, Turkey, October 2007.

Karaduman OD, Erkmen AM, Baykal N. Intelligent “Health Restoration System”: Reinforcement Learning Feedback to Diagnosis and Treatment Planning. 5th World Scientific and Engineering Academy and Society (WSEAS) International Conference on Telecommunications and Informatics.İstanbul, Turkey, 27-29 May 2006.

Akman E, Beyan T, Koçgil OD, Mizani M. Yeni Bir Sağlık Standardı: Bakım Kaydının Sürekliliği (A New Health Standard, Continuity of Care Records). II. Ulusal Tıp Bilişimi Kongresi (Medical Informatics ’05). Antalya, Turkey, November 2005.

Saka O, Gülkesen KH, Gülden B, Koçgil OD. Evaluation of two search methods in PubMed; the Regular Search and Search by MeSH Terms. European Medical Informatics Conference (MIE) 2005. Geneva, Switzerland, 2005. In: Connecting Medical Informatics and Bio-Informatics, European Notes in Medical Informatics (ENMI) 2005, Pages 1293-1298.

Koçgil OD. ODTÜ İnternet Üzerinden Bilişim Yüksek Lisans Programı Deneyimi (Internet Based Distance Education Experience of METU). ÖYP-YUUP Uzaktan Eğitim Çalıştayı. Mersin, Turkey, 2004.

Koçgil OD, Baykal N, Baykal A. Cancer Informatics (Poster). 10th Biomedical Science and Technology Symposium (BIOMED 2003). Northern Cyprus, October 2003.

Koçgil OD, Baykal N, Baykal A. Integrated breast diseases research and cancer registry in Turkey. American Medical Informatics Association (AMIA) Annual Symposium. 8-12 November 2003, Washington, DC, US. In: AMIA Annual Symposium Proceeding, 2003: 897.

Koçgil OD, Baykal N. Campus Wide Asynchronous Distance Learning: METU Experience. 5th Multi-Conference on Systemics, Cybernetics and Informatics (SCI 2001). Orlando, Florida, US, July 2001. Proceeding Book, Volume 8, Pages 170-4.

Nguyen BP, Reese T, Decker S, Malone D, Boyce RD, Beyan O. Implementation of Clinical Decision Support Services to Detect Potential Drug-Drug Interaction Using Clinical Quality Language. Stud Health Technol Inform. 2019 Aug 21;264:724-728. doi: 10.3233/SHTI190318. PubMed PMID: 31438019.

Löbe M, Beyan O, Stäubert S, Meineke F, Ammon D, Winter A, Decker S, Löffler M, Kirsten T. Design of Metadata Services for Clinical Data Interoperability in Germany. Stud Health Technol Inform. 2019 Aug 21;264:1528-1529. doi:10.3233/SHTI190518. PubMed PMID: 31438215.

Beyan T, Felzmann H, Ryan M, Lang N, Beyan O. D1.2 Ethics Framework. MARIO: Managing active and healthy aging with use of caring service robots. H2020. 2015.

Cortis K, Koumpis A, Casey D, Murphy K, Beyan O, Beyan T, Ricciardi F, Sancarlo D, Giuliani F, Raciti M, Reforgiato D, Trochidis I, Mongiovì M, Bleaden A, Ghrissi M, Pegman G. D10.5 Data Management Plan. MARIO: Managing active and healthy aging with use of caring service robots. H2020. 2015.

Jones M, Freitas A, Asooja K, Beyan O, Sahay R. D5.1 SIFEM Conceptual Model. SIFEM: Semantic Infostructure interlinking an open source Finite Element tool and libraries with a model repository for the multi-scale Modelling and 3d visualization of the inner-ear. FP7. 2014.

Beyan OD. Doctor of Philosophy Degree in Medical Informatics. A New Ontology and Knowledge Base System for Performance Measurement in Health Care. Middle East Technical University, Informatics Institute, Department of Health Informatics. 2010.

Beyan OD. Master of Science Degree in Sociology. Questioning Effects Of Patient Empowerment Antecedent By Information And Communication Technologies In Breast Cancer Patients: A Case Study From Turkey. Middle East Technical University, Faculty of Arts and Sciences, Department of Sociology. 2010.

Koçgil OD. Master of Science Degree in Information Systems. Proposal for an Integrated Breast Diseases Research and National Cancer Registry System Design and Implementation. Middle East Technical University, Informatics Institute, Department of Information Systems. 2003.