Privacy in the Genomic Era

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Colorectal cancer (CRC) is among the three most commonly diagnosed cancers and one of the major causes of cancer-related morbidity and mortality. Despite the discovery of several predictive biomarkers, the 5-year survival rate for metastatic CRC is 15%. A ...

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 ...

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 ...

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 ...

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 ...

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 ...

Global change exposes ecosystems to changes in the frequency, magnitude, and concomitancy of disturbances, which impact the composition and functioning of these systems. Here, we experimentally evaluate the effects of salinity disturbances and eutrophicati ...

Growing evidence indicates that transposable elements (TEs) play important roles in evolution by providing genomes with coding and non-coding sequences. Identification of TE-derived functional elements, however, has relied on TE annotations in individual s ...

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 ...

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 ...

Understanding the ecological impacts of viruses on natural and engineered ecosystems relies on the accurate identification of viral sequences from community sequencing data. To maximize viral recovery from metagenomes, researchers frequently combine viral ...

Decentralized learning is appealing as it enables the scalable usage of large amounts of distributed data and resources (without resorting to any central entity), while promoting privacy since every user minimizes the direct exposure of their data. Yet, wi ...

Microorganisms are a key component in the chain of life. They are essential for agriculture, produce a large proportion of oxygen, and play a central role in the cycle of elements. Microorganisms are widely used in the production of food and alcoholic beve ...

Aerobic granular sludge (AGS) consists of a microbial consortium that has an important role in wastewater treatment. This study investigates AGS microorganisms cultivated in a laboratory-scale sequencing batch reactor. Metagenomic sequencing was conducted ...

The advancement of face recognition technology has delivered substantial societal advantages. However, it has also raised global privacy concerns due to the ubiquitous collection and potential misuse of individuals' facial data. This presents a notable par ...

Graph Neural Networks (GNNs) have emerged as a powerful tool for learning on graphs, demonstrating exceptional performance in various domains. However, as GNNs become increasingly popular, new challenges arise. One of the most pressing is the need to ensur ...

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 ...

DNA-binding proteins physically interact with the DNA and directly affect genomic functions. The eukaryotic genome is compacted into chromatin, limiting the DNA access to nuclear factors. In this Ph.D. thesis, I explored the dynamic mechanisms, that allow ...

Two anaerobic, tetrachloroethene- (PCE-) respiring bacterial isolates, designated strain ACSDCE T and strain ACSTCE, were characterized using a polyphasic approach. Cells were Gram-stain-negative, motile, non-spore-forming and shared a vibrioid- to spirill ...

The local physical properties - such as shape and flexibility - of the DNA double-helix is today widely believed to be influenced by nucleic acid sequence in a non-trivial way. Furthermore, there is strong evidence that these properties play a role in many ...

Privacy in the Genomic Era

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Abstract 4588: Cell states and resistance in colorectal cancer: What can we learn from patient-derived organoids?

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

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

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

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

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

The cost of adaptability: resource availability constrains functional stability under pulsed disturbances

Ancestral genome reconstruction enhances transposable element annotation by identifying degenerate integrants

Differentially private multi-agent constraint optimization

Optimization Algorithms for Decentralized, Distributed and Collaborative Machine Learning

Benchmarking informatics approaches for virus discovery: caution is needed when combining in silico identification methods

The Privacy Power of Correlated Noise in Decentralized Learning

Reconstruction and analysis of genome-scale metabolic networks in single organisms and microbial communities

Microbial genome collection of aerobic granular sludge cultivated in sequencing batch reactors using different carbon source mixtures

PRO-Face C: Privacy-Preserving Recognition of Obfuscated Face via Feature Compensation

Privacy-Preserving Machine Learning on Graphs

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

Development of multiplexed single-molecule imaging techniques to study chromatin invasion dynamics of chromatin effector proteins

Sulfurospirillum diekertiae sp. nov., a tetrachloroethene-respiring bacterium isolated from contaminated soil

Landscapes of DNA Mechanics and Genomes