Robert Gerald Beiko

Lateral gene transfer shapes the distribution of nitrogen fixation within a cosmopolitan clade of marine Thalassolituus

The paper investigates the evolutionary distribution of nitrogen fixation in Thalassolituus by analyzing genome data, finding evidence of lateral gene transfer and recombination shaping nif loci.

Sarand: Exploring Antimicrobial Resistance Gene Neighborhoods in Complex Metagenomic Assembly Graphs

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

Automated eDNA and eRNA Profiling for Biodiversity Monitoring in Marine and Freshwater Ecosystems

This study tests an automated eDNA sampler in various aquatic environments, showing it can effectively profile eukaryotes, prokaryotes, and fish using ribosomal RNA genes and detect taxonomic groups and antimicrobial resistance genes.

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.

Effect of bedrest on the human gut and oral microbiome: implications for frailty

This study examines how bedrest affects gut and oral microbiomes in older adults, finding that inactivity reduces gut diversity and increases Bacteroides, while exercise mitigates these changes, and oral microbiome diversity is more strongly linked to frailty.

Comparison of spatio-temporal dynamics and composition in size-fractionated and unfractionated Northwestern Atlantic microbial communities

The paper compares the spatio-temporal dynamics and composition of size-fractionated and unfractionated microbial communities in the Northwestern Atlantic, finding that de-fractionating samples before or after sequencing closely resembles unfractionated samples.

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.

ParallelEvolCCM: Quantifying co-evolutionary patterns among genomic features

ParallelEvolCCM quantifies co-evolutionary patterns among genomic features by integrating phylogenetic signals and offers parallelization and filtering options for improved efficiency.

PlasEval: a framework for comparing and evaluating plasmid detection tools

PlasEval evaluates plasmid binning tools by comparing their results to ground truth or other methods using a dissimilarity measure.

Profiling novel lateral gene transfer events in the human microbiome

The paper develops and validates a method to detect novel lateral gene transfer events in human microbiomes, identifying over 100K putative LGT events across >2K metagenomes.

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.

Metagenome-Assembled Genome Binning Methods with Short Reads Disproportionately Fail for Plasmids and Genomic Islands

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.

The Integrated Rapid Infectious Disease Analysis (IRIDA) Platform

A decentralized open-source web platform lets public health labs run outbreak sequencing pipelines on local compute, keeping data under their own governance while still exchanging results between instances.

SNVPhyl: A Single Nucleotide Variant Phylogenomics pipeline for microbial genomic epidemiology

SNVPhyl is a phylogenomics pipeline that identifies SNVs and constructs whole-genome phylogenies from WGS data, showing high sensitivity and specificity in outbreak detection.