Finlay Maguire

This paper evaluates H5Nx influenza virus genotyping tools and finds they often group viruses with distinct evolutionary histories due to reassortment and reference bias.

Sarand extracts AMR gene contexts from metagenomic assembly graphs, improving precision and sensitivity over existing methods.

The paper analyzes antimicrobial resistance gene mobility across 8000 bacterial species, finding that certain resistance mechanisms are more associated with mobile elements than others.

This study tests whether white-tailed deer are a reservoir for divergent SARS-CoV-2 lineage B.1.641 and finds no active infections but evidence of past exposure.

This study evaluates graph-based tools for detecting antimicrobial resistance genes in metagenomes, finding that graph alignment improves detection while preserving genomic context.

CARD k-mers classifies antimicrobial resistance genes in metagenomic data by predicting taxonomy and genomic context, outperforming existing tools in accuracy and speed.

The paper presents a de novo genome and transcriptome assembly of Paramecium bursaria 186b, revealing intron characteristics and evolutionary dynamics in ciliates.

hAMRonization standardizes AMR gene detection outputs from multiple tools into a unified format for easier analysis and integration.

This study profiles resistance determinants, virulence factors, and mobile genetic elements in 1273 Enterococcus faecium genomes from UK and Canada, showing habitat-associated gene and MGE patterns and a workflow for AMR surveillance.

The paper identifies and validates the RNAi pathway in Paramecium bursaria, showing its role in feeding-induced gene knock-down and endosymbiosis genetics.

This study shows that short-read MAG binning methods poorly recover plasmids and genomic islands, missing key AMR and VF genes, and recommends using unassembled reads or long-read approaches instead.