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Universal whole-sequence-based plasmid typing and its utility to prediction of host range and epidemiological surveillance

The MOB-suite was developed to facilitate characterization of plasmids and a whole-sequence-based classification system based on clustering complete plasmid sequences using Mash distances was introduced, determining that clusters generated using Mash and complete-linkage clustering at a Mash distance of 0.06 resulted in highly homogeneous clusters while maintaining cluster size.
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ECTyper: in silico Escherichia coli serotype and species prediction from raw and assembled whole-genome sequence data

CTyper provides highly accurate and sensitive in silico serotype predictions, in addition to speciation, and is designed to be easily incorporated into bioinformatic workflows.
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The Effects of Threonine Phosphorylation on the Stability and Dynamics of the Central Molecular Switch Region of 18.5-kDa Myelin Basic Protein

The results support the hypothesis that the central conserved segment of MBP constitutes a molecular switch in which the conformation and/or intermolecular interactions are mediated by phosphorylation/dephosphorylation at T92 and T95.
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Exploring the mobilome and resistome of Enterococcus faecium in a One Health context across two continents

This study provides a workflow for MGE-centric surveillance of AMR in Enterococcus that can be adapted to other pathogens.
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Genome-wide association interaction analysis for Alzheimer's disease.

This work identifies a replicable epistasis associated with AD using a hypothesis free screening approach and identifies AD-associated interacting SNPs-pair from chromosome 6q11.1 and 13q12.11.
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Metagenomic sequencing of municipal wastewater provides a near-complete SARS-CoV-2 genome sequence identified as the B.1.1.7 variant of concern from a Canadian municipality concurrent with an outbreak

The results demonstrate that a combined interrogation of genome consensus-level sequences and alternative alleles enables the identification of a SARS-CoV-2 variant of concern and the detection of a new allele within a viral accessory gene that may be representative of a recently evolved B. 1.1.7 sublineage.
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Using eDNA to biomonitor the fish community in a tropical oligotrophic lake

Protocols that enabled the recovery of eDNA from tropical oligotrophic aquatic ecosystems are developed and confirmed their effectiveness in detecting diverse species of vertebrates including an invasive species of Amazon catfish.
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A reference library for Canadian invertebrates with 1.5 million barcodes, voucher specimens, and DNA samples

DNA barcodes are provided for 1,500,003 animal specimens collected from 23 terrestrial and aquatic ecozones at sites across Canada, a nation that comprises 7% of the planet’s land surface.
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A cautionary note on the impact of protocol changes for genome-wide association SNP × SNP interaction studies: an example on ankylosing spondylitis

Gene ontology biological function enrichment analysis across the 8 considered GWAI protocols suggested that AS could be associated to the central nervous system malfunctions, specifically, in nerve impulse propagation and in neurotransmitters metabolic processes.
Springer Nature (opens in a new tab)

Rapid and accurate SNP genotyping of clonal bacterial pathogens with BioHansel

BioHansel serves as a readily accessible and powerful WGS method, implementable on a laptop, for genotyping pathogens to detect, monitor, and control the emergence and spread of infectious disease through surveillance, screening, diagnostics, and outbreak investigation and response activities.
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