Joint analysis of host and pathogen genomes. - István Bartha; Amalio Telenti; Viktor Müller; Jacques Fellay (BIBM Workshops, 2011)

Privacy-Preserving Computation of Disease Risk by Using Genomic, Clinical, and Environmental Data. - Erman Ayday; Jean Louis Raisaro; Paul J. McLaren; Jacques Fellay; Jean-Pierre Hubaux (HealthTech, 2013)

Privacy and Security in the Genomic Era. - Muhammad Naveed 001; Erman Ayday; Ellen Wright Clayton; Jacques Fellay; Carl A. Gunter; Jean-Pierre Hubaux; Bradley A. Malin; XiaoFeng Wang 001 (CoRR, 2014)

Analysis of Stop-Gain and Frameshift Variants in Human Innate Immunity Genes. - Antonio Rausell; Pejman Mohammadi 001; Paul J. McLaren; István Bartha; Ioannis Xenarios; Jacques Fellay; Amalio Telenti (PLoS Comput. Biol., 2014)

GenoGuard: Protecting Genomic Data against Brute-Force Attacks. - Zhicong Huang; Erman Ayday; Jacques Fellay; Jean-Pierre Hubaux; Ari Juels (IEEE Symposium on Security and Privacy, 2015)

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; Zoltán Kutalik (IEEE Symposium on Security and Privacy Workshops, 2015)

Privacy in the Genomic Era. - Muhammad Naveed 001; Erman Ayday; Ellen Wright Clayton; Jacques Fellay; Carl A. Gunter; Jean-Pierre Hubaux; Bradley A. Malin; XiaoFeng Wang 001 (ACM Comput. Surv., 2015)

The Characteristics of Heterozygous Protein Truncating Variants in the Human Genome. - István Bartha; Antonio Rausell; Paul J. McLaren; Pejman Mohammadi 001; Manuel Tardaguila; Nimisha Chaturvedi; Jacques Fellay; Amalio Telenti (PLoS Comput. Biol., 2015)

SQC: secure quality control for meta-analysis of genome-wide association studies. - Zhicong Huang; Huang Lin; Jacques Fellay; Zoltán Kutalik; Jean-Pierre Hubaux (Bioinform., 2017)

Estimating the Respective Contributions of Human and Viral Genetic Variation to HIV Control. - István Bartha; Paul J. McLaren; Chanson J. Brumme; P. Richard Harrigan; Amalio Telenti; Jacques Fellay (PLoS Comput. Biol., 2017)

Sequence Alignment Through the Looking Glass. - Raja Appuswamy; Jacques Fellay; Nimisha Chaturvedi (IPDPS Workshops, 2018)

Are privacy-enhancing technologies for genomic data ready for the clinic? A survey of medical experts of the Swiss HIV Cohort Study. - Jean Louis Raisaro; Paul J. McLaren; Jacques Fellay; Matthias Cavassini; Catherine Klersy; Jean-Pierre Hubaux (J. Biomed. Informatics, 2018)

GenoShare: Supporting Privacy-Informed Decisions for Sharing Individual-Level Genetic Data. - Jean Louis Raisaro; Juan Ramón Troncoso-Pastoriza; Yamane El-Zein; Mathias Humbert; Jacques Fellay; Carmela Troncoso; Jean-Pierre Hubaux (AMIA, 2020)

SPHN/PHRT - MedCo in Action: Empowering the Swiss Molecular Tumor Board with Privacy-Preserving and Real-Time Patient Discovery. - Jean Louis Raisaro; Juan Ramón Troncoso-Pastoriza; Sylvain Pradervand; Michel A. Cuendet; Mickaël Misbach; João Sá Sousa; Francesco Marino; Nicolas Freundler; Nicolas Rosat; David Cavin; Alexander B. Leichtle; Jacques Fellay; et al. (MIE, 2020)

Revolutionizing Medical Data Sharing Using Advanced Privacy Enhancing Technologies: Technical, Legal and Ethical Synthesis. - James Scheibner; Jean Louis Raisaro; Juan Ramón Troncoso-Pastoriza; Marcello Ienca; Jacques Fellay; Effy Vayena; Jean-Pierre Hubaux (CoRR, 2020)

Citizen-centered, auditable and privacy-preserving population genomics. - Dennis Grishin; Jean Louis Raisaro; Juan Ramón Troncoso-Pastoriza; Kamal Obbad; Kevin Quinn 007; Mickaël Misbach; Jared Gollhardt; João Sá Sousa; Jacques Fellay; George M. Church; Jean-Pierre Hubaux (Nat. Comput. Sci., 2021)

Using population-specific add-on polymorphisms to improve genotype imputation in underrepresented populations. - Zhi Ming Xu; Sina Rüeger; Michaela Zwyer; Daniela Brites; Hellen Hiza; Miriam Reinhard; Liliana K. Rutaihwa; Sonia Borrell; Faima Isihaka; Hosiana Temba; Thomas Maroa; Rastard Naftari; et al. (PLoS Comput. Biol., 2022)

HIVMedQA: Benchmarking large language models for HIV medical decision support. - Gonzalo Cardenal-Antolin; Jacques Fellay; Bashkim Jaha; Roger D. Kouyos; Niko Beerenwinkel; Diane Duroux (CoRR, 2025)