| 2026 | ACL | Topic-Based Watermarks for Large Language Models. | Alexander Nemecek, Yuzhou Jiang, Erman Ayday |
| 2026 | ICISSP | VESPA: Vulnerability-Enhanced Selective Privacy Preservation Adaptation against Nucleotide Inference for Genomic Embeddings in Large Language Models. | Reem Al-Saidi, Erman Ayday, Ziad Kobti |
| 2025 | AAAI | Little Is Enough: Boosting Privacy by Sharing Only Hard Labels in Federated Semi-Supervised Learning. | Amr Abourayya, Jens Kleesiek, Kanishka Rao, Erman Ayday, Bharat Rao, Geoffrey I. Webb, Michael Kamp |
| 2025 | ESORICS | A User-Centric, Privacy-Preserving, and Verifiable Ecosystem for Personal Data Management and Utilization. | Osama Zafar, Mina Namazi, Yuqiao Xu, Youngjin Yoo, Erman Ayday |
| 2025 | IJCNLP | The Feasibility of Topic-Based Watermarking on Academic Peer Reviews. | Alexander Nemecek, Yuzhou Jiang, Erman Ayday |
| 2025 | TrustCom | Comparing Reconstruction Attacks on Pretrained Versus Full Fine-tuned Large Language Model Embeddings on Homo Sapiens Splice Sites Genomic Data. | Reem Al-Saidi, Erman Ayday, Ziad Kobti |
| 2024 | CCS | WPES '24: 23rd Workshop on Privacy in the Electronic Society (WPES). | Erman Ayday, Jaideep Vaidya |
| 2024 | ESORICS | Privacy-Preserving Optimal Parameter Selection for Collaborative Clustering. | Maryam Ghasemian, Erman Ayday |
| 2023 | DBSEC | Probabilistic Fingerprinting Scheme for Correlated Data. | Emre Yilmaz, Erman Ayday |
| 2023 | NDSS | Privacy-Preserving Database Fingerprinting. | Tianxi Ji, Erman Ayday, Emre Yilmaz, Ming Li, Pan Li |
| 2022 | AMIA | Facilitating Federated Genomic Data Analysis by Identifying Record Correlations while Ensuring Privacy. | Leonard Dervishi, Xinyue Wang, Wentao Li, Anisa Halimi, Jaideep Vaidya, Xiaoqian Jiang, Erman Ayday |
| 2022 | AMIA | How to Achieve Privacy in Large Diverse Health Systems. | Gamze Grsoy, Bradley A. Malin, Erman Ayday, Ellen Wright Clayton |
| 2022 | ESORICS | Privacy-Preserving Link Prediction. | Didem Demirag, Mina Namazi, Erman Ayday, Jeremy Clark |
| 2022 | HealthCom | ShareTrace: Contact Tracing with the Actor Model. | Ryan Tatton, Erman Ayday, Youngjin Yoo, Anisa Halimi |
| 2021 | INFOCOM | Entering Watch Dogs | Bahadir Durmaz, Erman Ayday |
| 2021 | RAID | The Curse of Correlations for Robust Fingerprinting of Relational Databases. | Tianxi Ji, Emre Yilmaz, Erman Ayday, Pan Li |
| 2020 | ESORICS | Tracking the Invisible: Privacy-Preserving Contact Tracing to Control the Spread of a Virus. | Didem Demirag, Erman Ayday |
| 2020 | ESORICS | Efficient Quantification of Profile Matching Risk in Social Networks Using Belief Propagation. | Anisa Halimi, Erman Ayday |
| 2020 | ICICS | Profile Matching Across Online Social Networks. | Anisa Halimi, Erman Ayday |
| 2019 | FC | One-Time Programs Made Practical. | Lianying Zhao, Joseph I. Choi, Didem Demirag, Kevin R. B. Butler, Mohammad Mannan, Erman Ayday, Jeremy Clark |
| 2019 | PSB | Session Introduction. | Gamze Grsoy, Arif Ozgun Harmanci, Haixu Tang, Erman Ayday, Steven E. Brenner |
| 2019 | RAID | Robust Optimization-Based Watermarking Scheme for Sequential Data. | Erman Ayday, Emre Yilmaz, Arif Yilmaz |
| 2019 | SAC | Dynamic attribute-based privacy-preserving genomic susceptibility testing. | Mina Namazi, Cihan Eryonucu, Erman Ayday, Fernando Prez-Gonzlez |
| 2018 | WoWMoM | A Demonstration of Privacy-Preserving Aggregate Queries for Optimal Location Selection. | Cihan Eryonucu, Erman Ayday, Engin Zeydan |
| 2016 | CCS | Privacy and Security in the Genomic Era. | Erman Ayday, Jean-Pierre Hubaux |
| 2016 | FC | Cryptographic Solutions for Genomic Privacy. | Erman Ayday |
| 2016 | ICMLA | A Privacy-Preserving Solution for the Bipartite Ranking Problem. | Noushin Salek Faramarzi, Erman Ayday, H. Altay Gvenir |
| 2015 | CCS | Differential Privacy with Bounded Priors: Reconciling Utility and Privacy in Genome-Wide Association Studies. | Florian Tramr, Zhicong Huang, Jean-Pierre Hubaux, Erman Ayday |
| 2015 | ESORICS | Can you Really Anonymize the Donors of Genomic Data in Today's Digital World? | Mohammed Alser, Nour Almadhoun, Azita Nouri, Can Alkan, Erman Ayday |
| 2015 | FC | On Non-cooperative Genomic Privacy. | Mathias Humbert, Erman Ayday, Jean-Pierre Hubaux, Amalio Telenti |
| 2015 | SP | Privacy Threats and Practical Solutions for Genetic Risk Tests. | Ludovic Barman, Mohammed Taha Elgraini, Jean Louis Raisaro, Jean-Pierre Hubaux, Erman Ayday |
| 2015 | SP | GenoGuard: Protecting Genomic Data against Brute-Force Attacks. | Zhicong Huang, Erman Ayday, Jacques Fellay, Jean-Pierre Hubaux, Ari Juels |
| 2015 | SP | Quantifying Genomic Privacy via Inference Attack with High-Order SNV Correlations. | Sahel Shariati Samani, Zhicong Huang, Erman Ayday, Mark J. Elliot, Jacques Fellay, Jean-Pierre Hubaux, Zoltn Kutalik |
| 2014 | CCS | Controlled Functional Encryption. | Muhammad Naveed, Shashank Agrawal, Manoj Prabhakaran, XiaoFeng Wang, Erman Ayday, Jean-Pierre Hubaux, Carl A. Gunter |
| 2013 | CCS | Addressing the concerns of the lacks family: quantification of kin genomic privacy. | Mathias Humbert, Erman Ayday, Jean-Pierre Hubaux, Amalio Telenti |
| 2013 | ESORICS | Privacy-Preserving Processing of Raw Genomic Data. | Erman Ayday, Jean Louis Raisaro, Urs Hengartner, Adam Molyneaux, Jean-Pierre Hubaux |
| 2013 | GLOBECOM | Personal use of the genomic data: Privacy vs. storage cost. | Erman Ayday, Jean Louis Raisaro, Jean-Pierre Hubaux |
| 2013 | ITW | Iterative similarity inference via message passing in factor graphs for Collaborative Filtering. | Jun Zou, Arash Einolghozati, Erman Ayday, Faramarz Fekri |
| 2013 | NDSS | Privacy-Enhancing Technologies for Medical Tests Using Genomic Data. | Erman Ayday, Jean Louis Raisaro, Jean-Pierre Hubaux |
| 2012 | ISIT | BPRS: Belief Propagation based iterative recommender system. | Erman Ayday, Arash Einolghozati, Faramarz Fekri |
| 2012 | SECON | BP-P2P: Belief propagation-based trust and reputation management for P2P networks. | Erman Ayday, Faramarz Fekri |
| 2011 | GLOBECOM | Robust Reputation Management Using Probabilistic Message Passing. | Erman Ayday, Faramarz Fekri |
| 2011 | ISIT | Application of belief propagation to trust and reputation management. | Erman Ayday, Faramarz Fekri |
| 2010 | RecSys | A belief propagation based recommender system for online services. | Erman Ayday, Faramarz Fekri |
| 2009 | ISIT | An iterative algorithm for trust and reputation management. | Erman Ayday, Hanseung Lee, Faramarz Fekri |
| 2008 | MASS | Using node accountability in credential based routing for mobile ad-hoc networks. | Erman Ayday, Faramarz Fekri |
| 2008 | SECON | AuCRB: An Efficient Mechanism to Provide Availability, Reliability and Authentication for Multihop Broadcasting in Wireless Networks. | Erman Ayday, Farshid Delgosha, Faramarz Fekri |
| 2007 | INFOCOM | Location-Aware Security Services for Wireless Sensor Networks Using Network Coding. | Erman Ayday, Farshid Delgosha, Faramarz Fekri |
| 2007 | IWCMC | MKPS: a multivariate polynomial scheme for symmetric key-establishment in distributed sensor networks. | Farshid Delgosha, Erman Ayday, Faramarz Fekri |
| 2007 | SECON | Efficient Broadcast Authentication for Wireless Sensor Networks. | Erman Ayday, Farshid Delgosha, Faramarz Fekri |
| 2006 | SECON | Security Services in Wireless Sensor Networks Using Sparse Random Coding. | Farshid Delgosha, Erman Ayday, Kevin Sean Chan, Faramarz Fekri |