These are the recent publications. For the full list, please click here.

Journal Articles

  1. R. Tatton, E. Ayday, Y. Yoo, and A. Halimi, “ShareTrace: Contact Tracing with Asynchronous, Parallel Message Passing on a Temporal Graph,” arXiv [cs.DC], Mar. 23, 2022. [Online]. Available: Description: Provides a design and implementation of an efficient form of the ShareTrace algorithm for infection risk propagation by using asynchronous message passing on a temporal graph. Research was partly supported by the Cisco Research University Funding grant number 2800379.

  2. X. Zhu, E. Ayday, R. Vitenberg, and N.R. Veeraragavan. “Privacy-Preserving Search for a Similar Genomic Makeup in the Cloud”, IEEE Transactions on Dependable and Secure Computing 2021
  3. A. C. Oksuz, E. Ayday, and U. Gudukbay “Privacy-Preserving and Robust Watermarking on Sequential Genome Data using Belief Propagation and Local Differential Privacy”, Bioinformatics, 2021.
  4. M. B. Sariyildiz, R. G. Cinbis, and E. Ayday. “Key Protected Classification for GAN Attack Resilient Collaborative Learning,” Pattern Recognition, 2020.
  5. N. Almadhoun, E. Ayday, and O. Ulusoy “Differential privacy under dependent tuples—the case of genomic privacy”, Bioinformatics, 2020.
  6. H.I. Ozercan, A.M. Ileri, E. Ayday, C. Alkan, “Realizing the potential of blockchain technologies in genomics”, Genome Research, 28 (9), 2019
  7. N. Thenen, E. Ayday, and E. Cicek. “Re-Identification of Individuals in Genomic Data-Sharing Beacons via allele inference”, Bioinformatics, 2018.
  8. X. Zhu, E. Ayday, and R. Vitenberg. “A privacy-preserving framework for outsourcing location-based services to the cloud”, IEEE Transactions on Dependable and Secure Computing, 2019



  1. chil22-poster: Poster for the CHIL 2022 Conference. Github. Accessed: May 03, 2022. [Online]. Available: Presented at the 2022 Conference on Health, Inference, and Learning (CHIL). Research was partly supported by the Cisco Research University Funding grant number 2800379.

Referred Conference Papers

  1. A. Halimi and E. Ayday. ” Real-Time Privacy Risk Quantification in Online Social Networks”, Proceedings of the IEEE/ACM International Conference on Advances in Social Networks Analysis and Mining (ASONAM), 2021 (acceptance rate ~ 20%).
  2. T. Ji, E. Yilmaz, E. Ayday, and P.Li, “The Curse of Correlations for Robust Fingerprinting of Relational Databases", Proceedings of International Symposium on Research in Attacks, Intrusions and Defenses (RAID), 2021 (acceptance rate ~ 20%).
  3. E. Ayday, Y. Yoo, and A. Halimi, “ShareTrace: An Iterative Message Passing Algorithm for Efficient and Effective Disease Risk Assessment on an Interaction Graph”, ACM Conference on Bioinformatics, Computational Biology, and Health Informatics (ACM BCB), 2021 (acceptance rate ~ 25%).
  4. K. Ayoz, E. Ayday, and A. E. Cicek, “Genome Reconstruction Attacks Against Genomic Data-Sharing Beacons", Proceedings of Privacy Enhancing Technologies Symposium (PETS), 2021 (acceptance rate ~ 19%).
  5. T. Ji, P. Li, E. Yilmaz, E. Ayday, Y. Ye, J. Sun, “Differentially Private Binary- and Matrix-Valued Data Query: An XOR Mechanism", 47th International Conference on Very Large Data Bases (VLDB’21), Copenhagen, Denmark, August 16-20, 2021 (acceptance rate ~ 20%).
  6. P. Fang, P. Gao, C. Liu, E. Ayday, K. Jee, T. Wang, Y. Ye, Z. Liu, and X. Xiao, “Back-Propagating System Dependency Impact for Attack Investigation”,  Proceedings of Usenix Security Symposium, 2022 (acceptance rate ~ 16%).
  7. B. Durmaz and E. Ayday, “Entering Watch Dogs: Evaluating Privacy Risks Against Large-Scale Facial Search and Data”, Proceedings of BigSecurity: International Workshop on Security and Privacy in Big Data (IEEE INFOCOM workshop), 2021.
  8. E. Yilmaz, E. Ayday, * T. Ji, and P. Li, “Preserving Genomic Privacy via Selective Sharing”, Proceedings of ACM Workshop on Privacy in the Electronic Society (WPES), 2020 (acceptance rate ~ 44%).
  9. D. Demirag and E. Ayday, “Tracking the Invisible: Privacy-Preserving Contact Tracing to Control the Spread of a Virus”, In Proceedings of Data Privacy Management (DPM) International Workshop (in conjunction with ESORICS), 2020.
  10. A. Halimi and E. Ayday. ”Efficient Quantification of Profile Matching Risk in Social Networks”, Proceedings of the 25th European Symposium on Research in Computer Security (ESORICS), UK, 2020 (acceptance rate ~ 19%).
  11. A. Halimi and E. Ayday. ”Profile Matching Across Online  Social  Networks”, Proceedings of International Conference on Information and Communications Security (ICICS), Denmark, 2020 (acceptance rate ~ 23%).
  12. K. Ayoz, M. Aysen, E. Ayday, and A. E. Cicek, “The Effect of Kinship in Re-identification Attacks Against Genomic Data Sharing Beacons", Proceedings of European Conference of Computational Biology (ECCB), 2020 (acceptance rate ~ 19%).
  13. N. Almadhoun, E. Ayday, and O. Ulusoy “Inference attacks against differentially private query results from genomic datasets including dependent tuples”, Proceedings of Intelligent Systems for Molecular Biology (ISMB), 2020, also in Bioinformatics, 2020 (acceptance rate ~ 19%).
  14. E. Ayday, E. Yilmaz, and A. Yilmaz, “Robust optimization-based watermarking scheme for sequential data”, Proceedings of International Symposium on Research in Attacks, Intrusions and Defenses (RAID), 2019 (acceptance rate ~ 20%).
  15. M. Namazi, C. Eryonucu, E. Ayday, F. Pérez-González, “Dynamic attribute-based privacy-preserving genomic susceptibility testing”, Proceedings of the 34th ACM/SIGAPP Symposium on Applied Computing, 2019 (acceptance rate ~ 25%).
  16. C. Eryonucu, E. Ayday, E. Zeydan, “A Demonstration of Privacy-Preserving Aggregate Queries for Optimal Location Selection”, IEEE 19th International Symposium on "A World of Wireless, Mobile and Multimedia Networks", 2018.
  17. J. Choi, V. Zhao, D. Demirag, J. Clark, M. Mannan, E. Ayday, and K. Butler. “One Time Programming Made Practical", Proceedings of Financial Cryptography, 2019.

Book Chapter

  1. E. Ayday, “Genome Privacy”, Encyclopedia of Cryptography, Security and Privacy, 2021. 
  2. E. Ayday, “Responsible Genomic Data Sharing”, Elsevier 2019. 
  3. E. Ayday and J.-P. Hubaux. “Threats and Solutions for Genomic Data Privacy” in Medical Data Privacy Handbook, Editors: Gkoulalas-Divanis, Aris, Loukides, Grigorios, Springer, 2015

Technical Reports

  1. N.A. Alser, G. Kale, O. Mutlu, O. Tastan, and E. Ayday, “Near-Optimal Privacy-Utility Tradeoff in Genomic Studies Using Selective SNP Hiding”, arXiv preprint arXiv:2106.05211, 2021.
  2. E. Yilmaz, T.Ji, E. Ayday, and P.Li, “Genomic Data Sharing under Dependent Local Differential Privacy”, arXiv preprint arXiv:2102.07357, 2021.
  3. A. Halimi, L. Dervishi, E. Ayday, A. Pyrgelis, J.R. Troncoso-Pastoriza, J-P. Hubaux, X. Jiang, and J Vaidya, “Privacy-Preserving and Efficient Verification of the Outcome in Genome-Wide Association Studies”, arXiv preprint arXiv:2101.08879, 2021.