Publications

List of publications for the DPPH and MedCo projects:

DPPH Consortium, DPPH Final Scientific Report, December 2021

Journal Papers 

• Sinem Sav, Jean-Philippe Bossuat, Juan R. Troncoso Pastoriza, Manfred Claassen, Jean-Pierre Hubaux, Privacy-Preserving Federated Neural Network Learning for Disease-associated Cell Classification. Cell Patterns, 2022
  
• Miran Kim, Arif Harmanci, Jean-Philippe Bossuat, Sergiu Carpov, Jung Hee Cheon, Ilaria Chillotti, Wonhee Cho, David Froelicher, Nicolas Gama, Mariya Georgieva, Seungwan Hong, Jean-Pierre Hubaux, Duhyeong Kim, Kristin Lauter, Yiping Ma, Lucila Ohno-Machado, Heidi Sofia, Yongha Son, Yongsoo Song, Juan Troncoso-Pastoriza, Xiaoqian Jiang, Ultra-Fast Homomorphic Encryption Models enable Secure Outsourcing of Genotype Imputation. Cell Systems, 2021
• D. Froelicher, J. R. Troncoso-Pastoriza, J.L. Raisaro, M. A. Cuendet, Joao Sa Sousa, H. Cho, B. Berger, J. Fellay, J.P. Hubaux, Truly Privacy-Preserving Federated Analytics for Precision Medicine with Multiparty Homomorphic Encryption. in Nature Communications 12,  October, 2021
• J. Scheibner, J. Sleigh, M. Ienca, and E. Vayena, Benefits, Challenges, and Contributors to Success for National eHealth Systems Implementation: A Scoping Review, Journal of the American Medical Informatics Association, September 2021
• James Scheibner, Jean Louis Raisaro, Juan Ramón Troncoso-Pastoriza, Marcello Ienca, Jacques Fellay, Effy Vayena, Jean-Pierre Hubaux, Revolutionizing Medical Data Sharing Using Advanced Privacy Enhancing Technologies: Technical, Legal and Ethical Synthesis. in Journal of Medical Internet Research (JMIR), vol.23, no. 2, 2021
• J. Scheibner, M. Ienca, and E. Vayena, Whose Health Record? A Comparison of Patient Rights under National Electronic Health Record (NEHR) Regulations in Europe and Asia-pacific Jurisdictions, Singapore Journal of Legal Studies, April 2021
• D. Grishin, JL. Raisaro, Juan Ramon Troncoso-Pastoriza, K. Obbad, K. Quinn, M. Misbach, J. Gollhardt, J. Sa Sousa, J. Fellay, GM. Church, and J-P. Hubaux, Citizen-Centered, Auditable and Privacy-Preserving Population Genomics, Nature Computational Science, March 2021
• Alexander Senf, Robert Davies, Frédéric Haziza, John Marshall, Juan Troncoso-Pastoriza, Oliver Hofmann, Thomas M. Keane, Crypt4GH: a file format standard enabling native access to encrypted data. in Bioinformatics, February, 2021
• JL Raisaro et al., SCOR: A secure international informatics infrastructure to investigate COVID-19. Journal of the American Medical Informatics Association (AMIA), August 2020

• Salem T. Argaw, Juan R. Troncoso-Pastoriza, Darren Lacey, Marie-Valentine Florin, Franck Calcavecchia, Denise Anderson, Wayne Burleson, Jan-Michael Vogel, Chana O’Leary, Bruce Eshaya-Chauvin & Antoine Flahault, Cybersecurity of Hospitals: discussing the challenges and working towards mitigating the risks. BMC Medical Genomics, July 2020
• Sergiu Carpov, Nicolas Gama, Mariya Georgieva & Juan Ramon Troncoso-Pastoriza, Privacy-preserving semi-parallel logistic regression training with fully homomorphic encryption. BMC Medical Genomics, July 2020
• Jean Louis Raisaro, Juan Ramón Troncoso-Pastoriza, Yamane El-Zein, Mathias Humbert, Carmela Troncoso, Jacques Fellay, Jean-Pierre Hubaux, GenoShare: Supporting Privacy-Informed Decisions for Sharing Individual-Level Genetic Data. Studies in Health Technology and Informatics, Volume 270: Digital Personalized Health and Medicine, Studies in Health Technology and Informatics, pp. 238 – 241, 2020
• David Froelicher, Mickaël Misbach, Juan R. Troncoso-Pastoriza, Jean Louis Raisaro, Jean-Pierre Hubaux, MedCo2: Privacy-Preserving Cohort Exploration and Analysis. Volume 270: Digital Personalized Health and Medicine, Studies in Health Technology and Informatics, pp. 317 – 321, 2020
• Jean Louis Raisaro, Juan Ramòn Troncoso-Pastoriza, Sylvain Pradervand, Michel Cuendet, Mickael Misbach, Joao Sa, Francesco Marino, Nicolas Freundler, Nicolas Rosat, David Cavin, Alexander Leichtle, Jacques Fellay, Olivier Michielin, Jean-Pierre Hubaux, SPHN/PHRT – MedCo in Action: Empowering the Swiss Molecular Tumor Board with Privacy-Preserving and Real-Time Patient Discovery. Volume 270: Digital Personalized Health and Medicine, Studies in Health Technology and Informatics, pp. 1161 – 1162, 2020
• U. Gasser, M. Ienca, J. Scheibner, J. Sleigh, and E. Vayena, Digital tools against COVID-19: taxonomy, ethical challenges, and navigation aid. The Lancet Digital Health, 2020
• J. Scheibner, M. Ienca, S. Kechagia, JR. Troncoso-Pastoriza, JL. Raisaro, J-P. Hubaux, and E. Vayena, Data Protection and Ethics Requirements for Multisite Research with Health Data: A Comparative Examination of Legislative Governance Frameworks and the Role of Data Protection Technologies. in Journal of Law and the Biosciences, 2020
• D. Froelicher, J. R. Troncoso-Pastoriza, J. S. Sousa and J. P. Hubaux, Drynx: Decentralized, Secure, Verifiable System for Statistical Queries and Machine Learning on Distributed Datasets. in IEEE Transactions on Information Forensics and Security, vol. 15, pp. 3035-3050, 2020, doi: 10.1109/TIFS.2020.2976612.
• I. Chillotti N. Gama, M. Georgieva, M. Izabachène, TFHE: Fast Fully Homomorphic Encryption over the Torus. in Journal of Cryptology, 2019.
• J. L. Raisaro, J. R. Troncoso-Pastoriza, M. Misbach, J. S. Sousa, S. Pradervand et al., MedCo: Enabling Secure and Privacy-Preserving Exploration of Distributed Clinical and Genomic Data. IEEE/ACM Transactions on computational biology and bioinformatics, 2018-07-13. DOI: 10.1109/TCBB.2018.2854776.

Conference Papers 

• S. Chatel, A. Pyrgelis, JR. Troncoso-Pastoriza, and J-P. Hubaux, Privacy and Integrity Preserving Computations with CRISP. in 30th Usenix Security Symposium, Vancouver, B.C., Canada, 2021

• J-P. Bossuat, C. Mouchet, JR. Troncoso-Pastoriza, and J-P. Hubaux, Efficient Bootstrapping for Approximate Homomorphic Encryption with Non-Sparse Keys. Cryptology ePrint Archive: Report 2020/1203, in 40th Annual International Conference on the Theory and Applications of Cryptographic Techniques (EuroCrypt), 2021
• C. Mouchet, J. R. Troncoso-Pastoriza, J-P. Bossuat and J.P. Hubaux, Multiparty Homomorphic Encryption from Ring-Learning-With-Errors. in Proceedings on Privacy Enhancing Technologies (PETS), 2021
• E. Kokoris-Kogias, E. Ceyhun Alp, S. D. Siby, N. Gailly, L. Gasser, P. Jovanovic, E. Syta and B. Ford, CALYPSO: Auditable Sharing of Private Data over Blockchains. in the 47th International Conference on Very Large Data Bases (VLDB), 2021
• S. Sav, A. Pyrgelis, JR. Troncoso-Pastoriza, D. Froelicher, J-P. Bossuat, J. Sa Sousa, and J-P. Hubaux, POSEIDON: Privacy Preserving Federated Neural Network Learning. in Proceedings of the 28th Networks and Distributed Systems Security Symposium (NDSS), 2021
• D. Froelicher, J. R. Troncoso-Pastoriza, A. Pyrgelis, S. Sav, J. S. Sousa, J.P. Bossuat and J.P. Hubaux, Scalable Privacy-Preserving Distributed Learning. CoRR abs/2005.09532, in Proceedings on Privacy Enhancing Technologies (PETS), 2021
• A. Pham, I. Dacosta, E. Losiouk, J. Stephan, K. Huguenin, J.P. Hubaux, HideMyApp : Hiding the Presence of Sensitive Apps on Android. Accepted to USENIX Security, August 14-16, Santa Clara, CA, USA, 2019.
• C. Boura, N. Gama, M. Georgieva, D. Jetchev, Simulating Homomorphic Evaluation of Deep Learning Predictions. Accepted to CSCML 2019, Israel June 27-28, 2019. 
• C. Boura, N. Gama, M. Georgieva, D. Jetchev, CHIMERA: Combining Ring-LWE-based Fully Homomorphic Encryption Schemes. Accepted to NuTMiC 2019, Paris June 24-27, 2019.
• E. Ceyhun Alp, E. Kokoris-Kogias, G. Fragkouli and B. Ford. Rethinking General-Purpose Decentralized Computing. The 17th Workshop on Hot Topics in Operating Systems, HotOS ‘19.
• E. Kokoris-Kogias, P. Jovanovic, L. Gasser, N. Gailly, E. Syta and B. Ford, OmniLedger: A Secure, Scale-Out, Decentralized Ledger via Sharding. IEEE Symposium on Security and Privacy ‘18.
• D. Froelicher, P. Egger, J. S. Sousa, J. L. Raisaro, Z. Huang, C. Mouchet, B. Ford, and J.P. Hubaux, UnLynx: A Decentralized System for Privacy-Conscious Data Sharing. Privacy Enhancing Technologies Symposium (PETS), volume 4, pages 152–170, Minneapolis, USA, 2017.

Workshop Papers 

• S. Sav, A. Pyrgelis, JR. Troncoso-Pastoriza, D. Froelicher, J-P. Bossuat, J. Sa Sousa, and J-P. Hubaux, POSEIDON: Privacy-Preserving Federated Neural Network Learning. in Privacy-Preserving Machine Learning Workshop (PPML), co-located with the 34th conference on Neural Information Processing Systems (NeurIPS), 2020
• C. Mouchet, J-P. Bossuat, JR. Troncoso-Pastoriza, and J-P. Hubaux, Lattigo: a Multiparty Homomorphic Encryption Library in Go. in the 8th Workshop on Encrypted Computing and Applied Homomorphic Cryptography (WAHC), 2020

Other publications (with minor contribution of the PHRT project) 

• S. Chatel, A. Pyrgelis, Juan Ramon Troncoso Pastoriza, and J-P. Hubaux, SoK:Privacy-Preserving Collaborative Tree-based Model Learning, in Proceedings on Privacy Enhancing Technologies (PETS), 2021
• M. Ienca and E. Vayena, On the responsible use of digital data to tackle the COVID-19 pandemic. in Nature medicine, 26(4), 463-464, 2020
• M. Ienca and J. Scheibner, What is neurohacking? Defining the conceptual, ethical and legal boundaries. in Ethical Dimensions of Commercial and DIY Neurotechnologies, 2020
• J. Scheibner, A. Jobin, and E. Vayena, Ethical Issues with Using Internet of Things Devices in Citizen Science Research: A Scoping Review. in Cambridge Handbook of Life Science, Information Technology and Human Rights, 2020
• RD. Gosselin, C. Redin, É. Ristorcelli, JL. Raisaro, and J. Fellay, Precision medicine: at the crossroad of molecular biology, information sciences and humanities. in Revue Medicale Suisse, 2020