CARD 2023: expanded curation, support for machine learning, and resistome prediction at the Comprehensive Antibiotic Resistance Database

Brian Alcock, William Huynh, Romeo Chalil, +42

Nucleic Acids Research

Interactive microbial genome visualization with GView

Aaron Petkau, Matthew Stuart-Edwards, Paul Stothard, +1

Bioinformatics

Surveillance of Enterococcus spp. reveals distinct species and antimicrobial resistance diversity across a One-Health continuum

Rahat Zaheer, Shaun R. Cook, Ruth Barbieri, +15

Scientific Reports

Correlation between Phenotypic and In Silico Detection of Antimicrobial Resistance in Salmonella enterica in Canada Using Staramr

Amrita Bharat, Aaron Petkau, Brent P. Avery, +20

Microorganisms

SNVPhyl: a single nucleotide variant phylogenomics pipeline for microbial genomic epidemiology

Aaron Petkau, Philip Mabon, Cameron Sieffert, +15

Microbial Genomics

GeneticsBioinformatics PipelineGenomicsHigh Throughput SequencingScalable Pipelines +15

Comparative Genomics of Vibrio cholerae from Haiti, Asia, and Africa

Aleisha Reimer, Gary Van Domselaar, Steven Stroika, +16

Emerging infectious diseases

Pfge Pattern-matched IsolatesPathogen DetectionMolecular EpidemiologyGenetic EpidemiologyGenomics +17

Evolutionary Dynamics of Vibrio cholerae O1 following a Single-Source Introduction to Haiti

Lee S. Katz, Aaron Petkau, John Beaulaurier, +22

mBio

A Comparative Analysis of the Lyve-SET Phylogenomics Pipeline for Genomic Epidemiology of Foodborne Pathogens

Lee S. Katz, Taylor Griswold, Amanda Williams, +6

Frontiers in Microbiology

The Integrated Rapid Infectious Disease Analysis (IRIDA) Platform

Thomas Matthews, Franklin Bristow, Emma Griffiths, +19

Pathogen DetectionDisease DetectionGenomicsBacterial PathogensHigh Throughput Sequencing +18

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

Aaron Petkau, Philip Mabon, Cameron Sieffert, +15

GeneticsGenomicsHigh Throughput SequencingScalable PipelinesPhylogenetic Analysis +15