Publications associées à Personal genomics

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

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

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

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

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

A comprehensive stroke risk assessment by combining atrial computational fluid dynamics simulations and functional patient data

Alfio Quarteroni

Stroke, a major global health concern often rooted in cardiac dynamics, demands precise risk evaluation for targeted intervention. Current risk models, like the CHA 2 DS 2 -VASc \documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepa ...

Nature Portfolio2024

A field-capable rapid plant DNA extraction protocol using microneedle patches for botanical surveying and monitoring

Sebastian Maerkl, Jonathan Selz, Nicolas Rémi Adam

PremiseA novel protocol for rapid plant DNA extraction using microneedles is proposed, which supports botanic surveys, taxonomy, and systematics. This protocol can be conducted in the field with limited laboratory skills and equipment. The protocol is vali ...

WILEY2023

Clinical efficacy of ONC201 in H3K27M-mutant diffuse midline gliomas is driven by disruption of integrated metabolic and epigenetic pathways

Sebastian Martin Waszak, Li Jiang

H3K27M-mutant diffuse midline glioma (DMG) patients have no proven effective therapies. ONC201 has recently demonstrated efficacy in these patients, but the mechanism behind this remains unknown. We assessed clinical outcomes, tumor sequencing, and tissue/ ...

2023

Chromatin modules and their implication in genomic organization and gene regulation

Bart Deplancke, Guido Van Mierlo, Judith Franziska Kribelbauer

Regulation of gene expression is a complex but highly guided process. While genomic technologies and computational approaches have allowed high-throughput mapping of cis-regulatory elements (CREs) and their interactions in 3D, their precise role in regulat ...

ELSEVIER SCIENCE LONDON2023

Regulation of sedimentation rate shapes the evolution of multicellularity in a close unicellular relative of animals

Omaya Pierre Dudin

Significant increases in sedimentation rate accompany the evolution of multicellularity. These increases should lead to rapid changes in ecological distribution, thereby affecting the costs and benefits of multicellularity and its likelihood to evolve. How ...

PUBLIC LIBRARY SCIENCE2022

Inferring Transmission Fitness Advantage of SARS-CoV-2 Variants of Concern in Wastewater Using Digital PCR

Tamar Kohn, Xavier Fernandez Cassi, Timothy R. Julian

Throughout the global COVID-19 pandemic, SARS-CoV-2 genetic variants of concern (VOCs) have repeatedly and independently arisen. VOCs are characterized by increased transmissibility, increased virulence, or reduced neutralization by antibodies obtained fro ...

2022

Ultrafast homomorphic encryption models enable secure outsourcing of genotype imputation

Jean-Pierre Hubaux, Juan Ramón Troncoso-Pastoriza, David Jules Froelicher, Jean-Philippe Léonard Bossuat, Yiping Ma

Genotype imputation is a fundamental step in genomic data analysis, where missing variant genotypes are predicted using the existing genotypes of nearby "tag"variants. Although researchers can outsource genotype imputation, privacy concerns may prohibit ge ...

CELL PRESS2021

Induction of a chromatin boundary in vivo upon insertion of a tad border

Denis Duboule, Christopher Chase Bolt, Lucille Delisle, Edgardo Rodriguez Carballo, Marie-Laure Gadolini

Author summary During development, enhancer sequences tightly regulate the spatio-temporal expression of target genes often located hundreds of kilobases away. This complex process is made possible by the folding of chromatin into domains, which are separa ...

2021

Wearable multi-electrode platform for ion sensing

Francesca Criscuolo

With the growth of personalized medicine and e-Health, there has been an increasing interest in the development of accurate sensing systems able to support this healthcare revolution for both in- and off-hospital monitoring. Remote biosensing devices can d ...

EPFL2020

Structural mechanism of cGAS inhibition by the nucleosome

Rudolf Hovius, Beat Fierz, Andrea Ablasser, Baptiste Claude André Guey, Alexiane Clara Decout, Pauline Ambre Melenec, Simone Cavadini, Kristina Makasheva, Sélène-Véronique Glück

The DNA sensor cGAS initiates innate immune responses following microbial infection, cellular stress, and cancer1. Upon activation by double-stranded DNA, cytosolic cGAS produces 2’3’ cyclic GMP-AMP and triggers inflammatory cytokine and type I interferon ...

2020

The evolution of the type VI secretion system as a disintegration weapon

Julius Hans Bernd Winter

The type VI secretion system (T6SS) is a nanomachine used by many bacteria to drive a toxin-laden needle into other bacterial cells. Although the potential to influence bacterial competition is clear, the fitness impacts of wielding a T6SS are not well und ...

PUBLIC LIBRARY SCIENCE2020

Population Genomics of Mycobacterium leprae Reveals a New Genotype in Madagascar and the Comoros

Stewart Cole, Stefanie Boy-Röttger, Andrej Benjak, Charlotte Avanzi, Philippe Busso, Pushpendra Singh, Thyago Leal Calvo

Human settlement of Madagascar traces back to the beginning of the first millennium with the arrival of Austronesians from Southeast Asia, followed by migrations from Africa and the Middle East. Remains of these different cultural, genetic, and linguistic ...

Frontiers Media SA2020

A Crowdsourced Gameplay for Whole-Genome Assembly via Short Reads

Kalpani Anuradha Welivita

Next-generation sequencing has revolutionized the field of genomics by producing accurate, rapid and cost-effective genome analysis with the use of high throughput sequencing technologies. This has intensified the need for accurate and performance efficien ...

2020

Genomic Analysis of European Drosophila melanogaster Populations Reveals Longitudinal Structure, Continent-Wide Selection, and Previously Unknown DNA Viruses

Bart Deplancke

Genetic variation is the fuel of evolution, with standing genetic variation especially important for short-term evolution and local adaptation. To date, studies of spatiotemporal patterns of genetic variation in natural populations have been challenging, a ...

2020

Parallel and Scalable Bioinformatics

Stuart Anthony Byma

The field of genomics is likely to become the largest producer of data as a consequence of the large-scale application of next-generation sequencing technology for biological research and personalized medical treatments. The raw sequence data produced by t ...

EPFL2020

Exploring the interactions between the human and viral genomes

Jacques Fellay

Over the last decade, genome-wide association studies led to major advances in identifying human genetic variants associated with infectious disease susceptibility. On the pathogen side, comparable methods are now applied to identify disease-modulating pat ...

SPRINGER2020

Predicting the Occurrence of Variants in RAG1 and RAG2

Jacques Fellay, Flavia Aurelia Shoko Hodel, Dylan Lawless

While widespread genome sequencing ushers in a new era of preventive medicine, the tools for predictive genomics are still lacking. Time and resource limitations mean that human diseases remain uncharacterized because of an inability to predict clinically ...

2019

Blacklisting variants common in private cohorts but not in public databases optimizes human exome analysis

Jacques Fellay, Alessandro Borghesi

Computational analyses of human patient exomes aim to filter out as many nonpathogenic genetic variants (NPVs) as possible, without removing the true disease-causing mutations. This involves comparing the patient's exome with public databases to remove rep ...

National Academy of Sciences2019