Amogelang R. Raphenya

CARD:Epi - Contextualizing Antimicrobial Resistance Determinants Using Deep Learning Language Models

The paper uses BioBERT to extract and analyze antimicrobial resistance gene transmission patterns from 204,094 publications, visualizing ARG spread across environments, hosts, and agriculture.

Structural diversification of phage tail fibres enables recognition of diverse type IV pili

The paper shows how phage tail fibre structure determines their ability to recognize diverse type IV pils despite receptor variation.

Analysing antimicrobial resistance mobility patterns using a diverse dataset of over 8000 bacterial species

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

Increasing the predictive accuracy of the Resistance Gene Identifier by evaluating antimicrobial resistance gene over- and underprediction

This study evaluates the accuracy of antimicrobial resistance gene prediction by analyzing bit-score cutoff values in CARD models and identifies sources of over- and underprediction in the RGI tool.

CARD k-mers: Unmasking the pathogen hosts and genomic contexts of antimicrobial resistance genes in metagenomic sequences

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

CARPDM: cost-effective antibiotic resistome profiling of metagenomic samples using targeted enrichment

CARPDM enables cost-effective antibiotic resistome profiling in metagenomic samples through targeted enrichment and in-house probe synthesis.

Simultaneous detection of pathogens and antimicrobial resistance genes with the open source, cloud-based, CZ ID pipeline

The paper develops an open-source, cloud-based tool for detecting pathogens and antimicrobial resistance genes in metagenomic and whole-genome sequencing data, demonstrating its application across clinical and environmental studies.

hAMRonization: Enhancing antimicrobial resistance prediction using the PHA4GE AMR detection specification and tooling

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

Exploring the mobilome and resistome of Enterococcus faecium in a One Health context across two continents

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.

Performance characteristics of next-generation sequencing for antimicrobial resistance gene detection in genomes and metagenomes

This study evaluates the performance of short-read sequencing for detecting antimicrobial resistance genes in genomes and metagenomes, finding that assembly-based methods require 15X coverage for reliable detection.