Connor Brown

The paper expands plasmid diversity by analyzing long-read metagenomes, identifying novel plasmid lineages and providing tools for plasmid discovery.

This study characterizes the Danish environmental resistome across 7,000 samples, identifying core and habitat-specific ARGs and their connectivity across ecosystems.

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.

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

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

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

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

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.

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.