Publications related to Unveiling Viruses Associated with Gastroenteritis Using a Metagenomics Approach

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, 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

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

Jaspreet Singh Saini

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 ...

Amer Soc Microbiology2024

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

Christof Holliger, Aline Sondra Adler, Laetitia Janine Andrée Cardona, Jaspreet Singh Saini, Pilar Natalia Rodilla Ramírez, Ruizhe Pei

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 ...

Amer Soc Microbiology2024

Peptide-based virucidal drugs

Francesca Olgiati

Before the COVID-19 pandemic, viruses were not a major priority for the scientific community. Today, many events have changed the world and the importance of studying viruses, vaccines, and antiviral drugs is fully appreciated. The development of effective ...

EPFL2024

Stability of influenza A virus in droplets and aerosols is heightened by the presence of commensal respiratory bacteria

Tamar Kohn, Athanasios Nenes, Ghislain Gilles Jean-Michel Motos, Htet Kyi Wynn, Kalliopi Violaki, Céline Terrettaz, Aline Laetitia Schaub, Walter Hugentobler, Shannon Christa David, Laura José Costa Henriques

Aerosol transmission remains a major challenge for control of respiratory viruses, particularly those causing recurrent epidemics, like influenza A virus (IAV). These viruses are rarely expelled alone, but instead are embedded in a consortium of microorgan ...

American Society for Microbiology2024

Optimised set of oligonucleotides for bulk rna barcoding and sequencing

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

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

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

Electronic readout of DNA amplification in nanoliter chambers. Strategies towards highly parallel semiconductor-based nucleic acid amplification testing

Saurabh Tomar

Polymerase chain reaction (PCR) has been the most significant driver in the field of nucleic acid testing (NAT) since its invention. Popularized as an abbreviation by the Covid-19 pandemic, PCR-based methods are the gold standard in the field of diagnostic ...

EPFL2023

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