Publications related to Privacy-enhancing technologies for medical tests using genomic data

Comparison of Three Viral Nucleic Acid Preamplification Pipelines for Sewage Viral Metagenomics

Viral metagenomics is a useful tool for detecting multiple human viruses in urban sewage. However, more refined protocols are required for its effective use in disease surveillance. In this study, we investigated the performance of three different preampli ...

2024

Multi-well plate lid for single-step pooling of 96 samples for high-throughput barcode-based sequencing

Bart Deplancke, Daniel Migliozzi, Hüseyin Baris Atakan, Mustafa Demir, Riccardo Dainese, Daniel Alpern, Dariia Gudkova, Gilles Weder

High-throughput transcriptomics is of increasing fundamental biological and clinical interest. The generation of molecular data from large collections of samples, such as biobanks and drug libraries, is boosting the development of new biomarkers and treatm ...

Springer2024

Secure and Efficient Cryptographic Algorithms in a Quantum World

Loïs Evan Huguenin-Dumittan

Since the advent of internet and mass communication, two public-key cryptographic algorithms have shared the monopoly of data encryption and authentication: Diffie-Hellman and RSA. However, in the last few years, progress made in quantum physics -- and mo ...

EPFL2024

Genome sequences of Vibrio cholerae strains isolated in the DRC between 2009 and 2012

Melanie Blokesch, Sandrine Stutzmann, Natalia Carolina Drebes Dorr, Alexandre Lemopoulos

Vibrio cholerae has caused seven cholera pandemics in the past two centuries. The seventh and ongoing pandemic has been particularly severe on the African continent. Here, we report long read-based genome sequences of six V. cholerae strains isolated in th ...

2024

Single-mitosis dissection of acute and chronic DNA mutagenesis and repair

Christina Ernst

How chronic mutational processes and punctuated bursts of DNA damage drive evolution of the cancer genome is poorly understood. Here, we demonstrate a strategy to disentangle and quantify distinct mechanisms underlying genome evolution in single cells, dur ...

Nature Portfolio2024

The microbial genomics of glacier-fed streams: adaptations to an extreme ecosystem

Massimo Bourquin

Glacier-fed streams are the cold, ultra-oligotrophic, and unstable streams that are fed by glacial meltwater. Despite these extreme conditions, they harbour a diverse and abundant microbial diversity that develops into biofilms, covering the boulders and s ...

EPFL2024

An Ultra-High Throughput AES-Based Authenticated Encryption Scheme for 6G: Design and Implementation

Andrea Felice Caforio, Subhadeep Banik

In this paper, we propose Rocca-S, an authenticated encryption scheme with a 256-bit key and a 256-bit tag targeting 6G applications bootstrapped from AES. Rocca-S achieves an encryption/decryption speed of more than 200 Gbps in the latest software environ ...

Springer International Publishing Ag2024

Differentially private multi-agent constraint optimization

Boi Faltings, Aleksei Triastcyn, Sujit Prakash Gujar, Sankarshan Damle

Distributed constraint optimization (DCOP) is a framework in which multiple agents with private constraints (or preferences) cooperate to achieve a common goal optimally. DCOPs are applicable in several multi-agent coordination/allocation problems, such as ...

Springer2024

On the Theory and Practice of Modern Secure Messaging

Daniel Patrick Collins

Billions of people now have conversations daily over the Internet. A large portion of this communication takes place via secure messaging protocols that offer "end-to-end encryption'" guarantees and resilience to compromise like the widely-used Double Ratc ...

EPFL2024

Optimization Algorithms for Decentralized, Distributed and Collaborative Machine Learning

Anastasiia Koloskova

Distributed learning is the key for enabling training of modern large-scale machine learning models, through parallelising the learning process. Collaborative learning is essential for learning from privacy-sensitive data that is distributed across various ...

EPFL2024

Inborn errors of type I interferon immunity in patients with symptomatic acute hepatitis E

Jacques Fellay

Background and Aims:The clinical spectrum of human infection by HEV ranges from asymptomatic to severe acute hepatitis. Furthermore, HEV can cause diverse neurological manifestations, especially Parsonage-Turner syndrome. Here, we used a large-scale human ...

Lippincott Williams & Wilkins2023

Optimised set of oligonucleotides for bulk rna barcoding and sequencing

Bart Deplancke, Riccardo Dainese, Daniel Alpern, Vincent Roland Julien Gardeux

The present invention relates generally to the field of nucleic acid sequencing and provides oligonucleotide molecules and barcodes contained therein. These oligonucleotide molecules and barcodes molecules are useful in sequencing to identify and resolve e ...

2023

Making Classical (Threshold) Signatures Post-quantum for Single Use on a Public Ledger

Serge Vaudenay, Laurane Chloé Angélina Marco, Abdullah Talayhan

The Bitcoin architecture heavily relies on the ECDSA signature scheme which is broken by quantum adversaries as the secret key can be computed from the public key in quantum polynomial time. To mitigate this attack, bitcoins can be paid to the hash of a pu ...

2023

Systematic benchmarking of single-cell ATAC-sequencing protocols

Bart Deplancke, Jörn Pezoldt, Camille Lucie Germaine Lambert

Benchmarking of scATAC-seq protocols demonstrates the effects of data quality on downstream analyses. ...

NATURE PORTFOLIO2023

Security in the Presence of Quantum Adversaries

Khashayar Barooti

With the looming threat of large-scale quantum computers, a fair portion of recent cryptographic research has focused on examining cryptographic primitives from the perspective of a quantum adversary. Shor's 1994 result revealed that quantum computers can ...

EPFL2023

Multiomic analysis of HER2-enriched and AR-positive breast carcinoma with apocrine differentiation and an oligometastatic course: a case report

Andrea Cavalli

Breast carcinoma is the most prevalent cancer among women globally. It has variable clinical courses depending on the stage and clinical-biological features. This case report describes a 56-year-old female with invasive breast cancer without estrogen or pr ...

FRONTIERS MEDIA SA2023

Modeling, analysis, and design of complex biological networks

Mohammadomid Oftadeh

Automating experimental procedures has resulted in an unprecedented increase in the volume of generated data, which, in turn, has caused an accumulation of unprocessed data. As a result, the need to develop tools to analyze data systematically has been ris ...

EPFL2023

Multienzyme deep learning models improve peptide de novo sequencing by mass spectrometry proteomics

Hamed Khakzad

Author summaryIn recent years, the application of deep learning represented a breakthrough in the mass spectrometry (MS) field by improving the assignment of the correct sequence of amino acids from observable MS spectra without prior knowledge, also known ...

PUBLIC LIBRARY SCIENCE2023

Automatic and high-precision microseismic monitoring of progressive failure prior, during, and after tunnel excavation

Brice Tanguy Alphonse Lecampion, Christophe Nussbaum, Seyyedmaalek Momeni

Acoustic emission (AE) monitoring is commonly used to inspect the health of a structure continuously. During fracture processes elastic waves of AE are created and emitted, and sensors can capture these waves. The acquired signals can be processed to track ...

2023

Public-Key Encryption with Quantum Keys

Khashayar Barooti

In the framework of Impagliazzo's five worlds, a distinction is often made between two worlds, one where public-key encryption exists (Cryptomania), and one in which only one-way functions exist (MiniCrypt). However, the boundaries between these worlds can ...

Springer International Publishing Ag2023