Anders Gonçalves da Silva

The paper presents four haplotype-resolved Cannabis genomes using Oxford Nanopore reads and Hi-C scaffolding, showing comparable contiguity to HiFi assemblies and enabling phylogenetic and pan-NLRome analysis.

This study identifies simple sequence repeats (SSRs) as key drivers of genetic heterogeneity and rapid adaptation in Staphylococcus aureus through loss-of-function mutations and phase-variable evolution.

The paper systematically evaluates key parameters affecting SNP-based transmission inference of MDROs, finding that using a closely-related reference genome and sliding-window analysis improves accuracy.

This study evaluates a pilot proficiency testing program for bacterial whole genome sequencing in clinical and public health labs, showing labs can generate and analyze high-quality data using diverse bioinformatics tools.

The paper presents complete microbial genomes for public health in Australia and the Southwest Pacific to enhance global genomic resources and support regional surveillance.

The paper analyzes genomic evolution in persistent Staphylococcus aureus bacteraemia, identifying a molecular signature with low mutation frequency and high non-silent mutations.

RM-seq detects and quantifies antibiotic resistance mutations in bacterial populations with high sensitivity and accuracy.

The paper analyzes the genomic epidemiology of VREfm in Victoria, Australia, finding that vanA-VREfm is associated with multiple STs and clonal transmission within hospitals, while vanB-VREfm is widespread and disseminated across institutions.

This study combines real-time genomic and epidemiological analysis to identify and manage KPC-producing Enterobacteriaceae outbreaks, revealing transmission networks and informing infection control.

This study reconstructs genomes of drug-resistant bacteria from human faeces using metagenomic sequencing and self-organising maps, demonstrating the potential for culture-independent pathogen analysis.

The paper develops a TaqMan qPCR assay for specific and rapid detection of M. chimaera DNA in clinical and environmental samples, showing higher sensitivity than culture methods.

NGMASTER enables in silico NG-MAST analysis of Neisseria gonorrhoeae genomes, comparing results with prior epidemiological studies.