Reproducible, scalable, and shareable analysis pipelines with bioinformatics workflow managers

L Wratten, A Wilm, J Göke - Nature methods, 2021 - nature.com
The rapid growth of high-throughput technologies has transformed biomedical research.
With the increasing amount and complexity of data, scalability and reproducibility have …

Using genomics to track global antimicrobial resistance

RS Hendriksen, V Bortolaia, H Tate, GH Tyson… - Frontiers in public …, 2019 - frontiersin.org
The recent advancements in rapid and affordable DNA sequencing technologies have
revolutionized diagnostic microbiology and microbial surveillance. The availability of …

An ISO-certified genomics workflow for identification and surveillance of antimicrobial resistance

NL Sherry, KA Horan, SA Ballard… - Nature …, 2023 - nature.com
Realising the promise of genomics to revolutionise identification and surveillance of
antimicrobial resistance (AMR) has been a long-standing challenge in clinical and public …

[HTML][HTML] Current and future technologies for the detection of antibiotic-resistant bacteria

D Yamin, V Uskoković, AM Wakil, MD Goni… - Diagnostics, 2023 - mdpi.com
Antibiotic resistance is a global public health concern, posing a significant threat to the
effectiveness of antibiotics in treating bacterial infections. The accurate and timely detection …

Whole genome sequencing of Mycobacterium tuberculosis: current standards and open issues

CJ Meehan, GA Goig, TA Kohl, L Verboven… - NATURE reviews …, 2019 - nature.com
Whole genome sequencing (WGS) of Mycobacterium tuberculosis has rapidly progressed
from a research tool to a clinical application for the diagnosis and management of …

Essential guidelines for computational method benchmarking

LM Weber, W Saelens, R Cannoodt, C Soneson… - Genome biology, 2019 - Springer
In computational biology and other sciences, researchers are frequently faced with a choice
between several computational methods for performing data analyses. Benchmarking …

Pulsed light as an emerging technology to cause disruption for food and adjacent industries–Quo vadis?

NJ Rowan - Trends in food science & technology, 2019 - Elsevier
Background–Despite verbose amount of publications and having gained approval by Food
and Drug Administration (FDA) since 1996 for food-surface disinfection applications, pulsed …

Genetic diversity, biochemical properties, and detection methods of minor carbapenemases in Enterobacterales

RA Bonnin, AB Jousset, C Emeraud, S Oueslati… - Frontiers in …, 2021 - frontiersin.org
Gram-negative bacteria, especially Enterobacterales, have emerged as major players in
antimicrobial resistance worldwide. Resistance may affect all major classes of anti-gram …

Enhancing clinical utility: utilization of international standards and guidelines for metagenomic sequencing in infectious disease diagnosis

CM Kan, HF Tsang, XM Pei, SSM Ng, AKY Yim… - International journal of …, 2024 - mdpi.com
Metagenomic sequencing has emerged as a transformative tool in infectious disease
diagnosis, offering a comprehensive and unbiased approach to pathogen detection …

Genomics for Molecular Epidemiology and Detecting Transmission of Carbapenemase-Producing Enterobacterales in Victoria, Australia, 2012 to 2016

NL Sherry, CR Lane, JC Kwong, M Schultz… - Journal of clinical …, 2019 - journals.asm.org
Carbapenemase-producing Enterobacterales (CPE) are being increasingly reported in
Australia, and integrated clinical and genomic surveillance is critical to effectively manage …