Amy J. Pruden

The broad ecological range of Salmonella enterica serotype Typhimurium is associated with genomic diversification

This study analyzes 595 Salmonella Typhimurium genomes to show that food animal isolates have more open pangenomes and antimicrobial resistance genes, with swine isolates showing the most diversity and plasmid prevalence.

Assessment of a Passive Sampler for Aquifer Microbial Community Profiling and Comparison of Porous Media Applied in a Managed Recharge Scenario

The paper evaluates a passive sampler for aquifer microbial community profiling and compares porous media in a managed recharge scenario, finding native aquifer sediment best reflects microbial dynamics.

ARGfore: A multivariate framework for forecasting antibiotic resistance gene abundances using time-series metagenomic datasets

ARGfore forecasts antibiotic resistance gene abundances from time-series metagenomic data, outperforming standard methods with lower error and better efficiency.

Resistance genes are distinct in protein-protein interaction networks according to drug class and gene mobility

The paper introduces a pipeline using PPINs and machine learning to identify ARGs, showing improved discrimination of ARGs from nonARGs and their association with mobile genetic elements.

Influence of Copper Dose on Mycobacterium avium and Legionella pneumophila Growth in Premise Plumbing

This study examines how different copper concentrations affect microbial growth in premise plumbing, finding non-linear effects on Legionella pneumophila and microbial communities.

ProtAlign-ARG: Antibiotic Resistance Gene Characterization Integrating Protein Language Models and Alignment-Based Scoring

ProtAlign-ARG improves antibiotic resistance gene detection by combining protein language models with alignment-based scoring, achieving higher recall than existing methods.

ARGContextProfiler: Extracting and Scoring the Genomic Contexts of Antibiotic Resistance Genes using Assembly Graphs

ARGContextProfiler improves accuracy in identifying antibiotic resistance gene contexts in metagenomic data using assembly graphs and read mapping.

Evidence of horizontal gene transfer and environmental selection impacting antibiotic resistance evolution in soil-dwelling Listeria

This study identifies horizontal gene transfer and environmental selection as key factors in the evolution of antibiotic resistance genes in soil-dwelling Listeria species.

MetaCompare 2.0: Differential ranking of ecological and human health resistome risks

MetaCompare 2.0 differentiates human health and ecological resistome risks using metagenomic data, showing higher risk scores for human-contaminated environments.

CIWARS: a web server for waterborne antibiotic resistance surveillance using longitudinal metagenomic data

CIWARS is a web server for analyzing longitudinal metagenomic data to detect antibiotic resistance genes and assess AR risks in environmental samples.

Phage-plasmid hybrids are found throughout diverse environments and encode niche-specific functional traits

The paper identifies and characterizes phage-plasmid hybrids across diverse environments, revealing their niche-specific functional traits and ecological roles.

Kairos infers in situ horizontal gene transfer in longitudinally sampled microbiomes through microdiversity-aware sequence analysis

Kairos detects in situ horizontal gene transfer in microbiomes using time-series metagenomic data and competitive read alignment, improving detection of antibiotic resistance genes compared to MAG-based methods.

mobileOG-db: a manually curated database of protein families mediating the life cycle of bacterial mobile genetic elements

The paper introduces mobileOG-db, a manually curated database of protein families involved in bacterial mobile genetic element life cycles, enabling improved MGE annotation and analysis.

MetaMLP: A fast word embedding based classifier to profile target gene databases in metagenomic samples

MetaMLP is a machine learning classifier for metagenomic functional profiling that uses word embeddings and a neural network to achieve high accuracy and speed.

ARG-miner: A web platform for crowdsourcing-based curation of antibiotic resistance genes

ARG-miner is a crowdsourcing-based platform for curating antibiotic resistance genes, achieving high accuracy and efficiency compared to manual curation.

NanoARG: A web service for identification of antimicrobial resistance elements from nanopore-derived environmental metagenomes

NanoARG identifies antimicrobial resistance elements from nanopore-derived environmental metagenomes, enabling analysis of ARGs, MRGs, MGEs, and pathogens.

DeepARG: A deep learning approach for predicting antibiotic resistance genes from metagenomic data

This paper introduces deepARG, a deep learning method for predicting antibiotic resistance genes from metagenomic data, achieving high precision and recall over traditional methods.