Robert G. Beiko
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View article: Automated eDNA and eRNA Profiling for Biodiversity Monitoring in Marine and Freshwater Ecosystems
Automated eDNA and eRNA Profiling for Biodiversity Monitoring in Marine and Freshwater Ecosystems Open
Automated sampling enables the collection and analysis of eDNA from regions that are limited by site access, sampling times, and operator safety. eDNA sampling devices must be rigorously tested against existing technologies to demonstrate …
View article: CARD k-mers: Unmasking the pathogen hosts and genomic contexts of antimicrobial resistance genes in metagenomic sequences
CARD k-mers: Unmasking the pathogen hosts and genomic contexts of antimicrobial resistance genes in metagenomic sequences Open
Antimicrobial resistance (AMR) is a global health crisis requiring rapid surveillance across human, agricultural, and environmental systems. A major challenge during outbreaks is not only detecting antimicrobial resistance genes (ARGs), bu…
View article: ParallelEvolCCM: Quantifying Coevolutionary Patterns Among Genomic Features
ParallelEvolCCM: Quantifying Coevolutionary Patterns Among Genomic Features Open
Concerted gains and losses of genomic features such as genes and mobile genetic elements can provide key clues into related functional roles and shared evolutionary trajectories. By capturing phylogenetic signals, a coevolutionary model ca…
View article: The case for microbiome stewardship: what it is and how to get there
The case for microbiome stewardship: what it is and how to get there Open
Microbiomes are essential for human, animal, plant, and ecosystem health. Despite widespread recognition of the importance of microbiomes, there is little attention paid to monitoring and safeguarding microbial ecologies on policy levels. …
View article: Comparison of spatio-temporal dynamics and composition in size-fractionated and unfractionated Northwestern Atlantic microbial communities
Comparison of spatio-temporal dynamics and composition in size-fractionated and unfractionated Northwestern Atlantic microbial communities Open
Size fractionation is a widely applied approach to target specific microbial size ranges, differentiating between larger particle-associated, and smaller free-living microorganisms. To characterize its impact on microbial diversity and its…
View article: Plaseval: a framework for comparing and evaluating plasmid detection tools
Plaseval: a framework for comparing and evaluating plasmid detection tools Open
Background Plasmids play a major role in the transfer of antimicrobial resistance (AMR) genes among bacteria via horizontal gene transfer. The identification of plasmids in short-read assemblies is a challenging problem and a very active r…
View article: Identification of key drivers of antimicrobial resistance in <i>Enterococcus</i> using machine learning
Identification of key drivers of antimicrobial resistance in <i>Enterococcus</i> using machine learning Open
With antimicrobial resistance (AMR) rapidly evolving in pathogens, quick and accurate identification of genetic determinants of phenotypic resistance is essential for improving surveillance, stewardship, and clinical mitigation. Machine le…
View article: ParallelEvolCCM: Quantifying co-evolutionary patterns among genomic features
ParallelEvolCCM: Quantifying co-evolutionary patterns among genomic features Open
Concerted gains and losses of genomic features such as genes and mobile genetic elements can provide key clues into related functional roles and shared evolutionary trajectories. By capturing phylogenetic signals, a co-evolutionary model c…
View article: PlasEval: a framework for comparing and evaluating plasmid detection tools
PlasEval: a framework for comparing and evaluating plasmid detection tools Open
Plasmids play a major role in the transfer of antimicrobial resistance (AMR) genes among bacteria via horizontal gene transfer. The identification of plasmids in short-read assemblies is a challenging problem and a very active research are…
View article: Mock microbial community meta‐analysis using different trimming of amplicon read lengths
Mock microbial community meta‐analysis using different trimming of amplicon read lengths Open
Trimming of sequencing reads is a pre‐processing step that aims to discard sequence segments such as primers, adapters and low quality nucleotides that will interfere with clustering and classification steps. We evaluated the impact of tri…
View article: Sarand: Exploring Antimicrobial Resistance Gene Neighborhoods in Complex Metagenomic Assembly Graphs
Sarand: Exploring Antimicrobial Resistance Gene Neighborhoods in Complex Metagenomic Assembly Graphs Open
Antimicrobial resistance (AMR) is a major global challenge to human and animal health. The genomic element (e.g., chromosome, plasmid, and genomic islands) and neighbouring genes associated with an AMR gene play a major role in its functio…
View article: Profiling novel lateral gene transfer events in the human microbiome
Profiling novel lateral gene transfer events in the human microbiome Open
Lateral gene transfer (LGT) is an important mechanism for genome diversification in microbial populations, including the human microbiome. While prior work has surveyed LGT events in human-associated microbial isolate genomes, the scope an…
View article: Integrating seascape resistances and gene flow to produce area-based metrics of functional connectivity for marine conservation planning
Integrating seascape resistances and gene flow to produce area-based metrics of functional connectivity for marine conservation planning Open
Context Prioritizing regions that facilitate connectivity among populations is an essential principle for conservation planning. However, the lack of conspicuous geographical and environmental features that constrain dispersal and gene flo…
View article: Correction: Suspension of oral hygiene practices highlights key bacterial shifts in saliva, tongue, and tooth plaque during gingival inflammation and resolution
Correction: Suspension of oral hygiene practices highlights key bacterial shifts in saliva, tongue, and tooth plaque during gingival inflammation and resolution Open
View article: Compact and automated eDNA sampler for in situ monitoring of marine environments
Compact and automated eDNA sampler for in situ monitoring of marine environments Open
View article: Suspension of oral hygiene practices highlights key bacterial shifts in saliva, tongue, and tooth plaque during gingival inflammation and resolution
Suspension of oral hygiene practices highlights key bacterial shifts in saliva, tongue, and tooth plaque during gingival inflammation and resolution Open
Experimentally induced gingivitis is associated with inflammatory and microbiological changes in an otherwise healthy subject, demonstrating the impacts of discontinuing oral hygiene routines. Understanding the bacterial dynamics during th…
View article: Integrating seascape resistances and gene flow to produce area-based metrics of functional connectivity for marine conservation planning
Integrating seascape resistances and gene flow to produce area-based metrics of functional connectivity for marine conservation planning Open
Context Prioritizing regions that facilitate connectivity among populations is an essential principle for conservation planning. However, the lack of conspicuous geographical and environmental features that constrain dispersal and geneflow…
View article: Vaginal microbiota in women with spontaneous preterm labor versus those with term labor in Kenya: a case control study
Vaginal microbiota in women with spontaneous preterm labor versus those with term labor in Kenya: a case control study Open
View article: CARD 2023: expanded curation, support for machine learning, and resistome prediction at the Comprehensive Antibiotic Resistance Database
CARD 2023: expanded curation, support for machine learning, and resistome prediction at the Comprehensive Antibiotic Resistance Database Open
The Comprehensive Antibiotic Resistance Database (CARD; card.mcmaster.ca) combines the Antibiotic Resistance Ontology (ARO) with curated AMR gene (ARG) sequences and resistance-conferring mutations to provide an informatics framework for a…
View article: Exploring the mobilome and resistome of Enterococcus faecium in a One Health context across two continents
Exploring the mobilome and resistome of Enterococcus faecium in a One Health context across two continents Open
Enterococcus faecium is a ubiquitous opportunistic pathogen that is exhibiting increasing levels of antimicrobial resistance (AMR). Many of the genes that confer resistance and pathogenic functions are localized on mobile genetic elements …
View article: A search for “perio-probiotics” by longitudinal dissection of oral bacterial community shifts during the onset and resolution of gingivitis
A search for “perio-probiotics” by longitudinal dissection of oral bacterial community shifts during the onset and resolution of gingivitis Open
Aim To understand the spatiotemporal dynamics of bacterial succession during gingivitis, and to identify taxa with a critical role in gum health with prognostic value. Materials and methods Longitudinal microbiome data were collected from …
View article: The Community Coevolution Model with Application to the Study of Evolutionary Relationships between Genes Based on Phylogenetic Profiles
The Community Coevolution Model with Application to the Study of Evolutionary Relationships between Genes Based on Phylogenetic Profiles Open
Organismal traits can evolve in a coordinated way, with correlated patterns of gains and losses reflecting important evolutionary associations. Discovering these associations can reveal important information about the functional and ecolog…
View article: Machine Learning for Antimicrobial Resistance Prediction: Current Practice, Limitations, and Clinical Perspective
Machine Learning for Antimicrobial Resistance Prediction: Current Practice, Limitations, and Clinical Perspective Open
Antimicrobial resistance (AMR) is a global health crisis that poses a great threat to modern medicine. Effective prevention strategies are urgently required to slow the emergence and further dissemination of AMR.
View article: deepSimDEF: deep neural embeddings of gene products and gene ontology terms for functional analysis of genes
deepSimDEF: deep neural embeddings of gene products and gene ontology terms for functional analysis of genes Open
Motivation There is a plethora of measures to evaluate functional similarity (FS) of genes based on their co-expression, protein–protein interactions and sequence similarity. These measures are typically derived from hand-engineered and ap…
View article: Exploring the mobilome and resistome of <i>Enterococcus faecium</i> in a One Health context across two continents
Exploring the mobilome and resistome of <i>Enterococcus faecium</i> in a One Health context across two continents Open
Enterococcus faecium is a ubiquitous opportunistic pathogen that is exhibiting increasing levels of antimicrobial resistance (AMR). Many of the genes that confer resistance and pathogenic functions are localized on mobile genetic elements …
View article: 11th international meeting on visualizing biological data (VIZBI 2021)
11th international meeting on visualizing biological data (VIZBI 2021) Open
International audience
View article: Changes in Bacterial Communities During Treatment of Municipal Wastewater in Arctic Wastewater Stabilization Ponds
Changes in Bacterial Communities During Treatment of Municipal Wastewater in Arctic Wastewater Stabilization Ponds Open
Wastewater stabilization ponds (WSPs) are commonly used to treat municipal wastewater in the Canadian Arctic. Bacterial community structure and functionality remain mostly uncharacterized for arctic WSPs, yet are presumed important for tre…
View article: Identifying novel β-lactamase substrate activity through in silico prediction of antimicrobial resistance
Identifying novel β-lactamase substrate activity through in silico prediction of antimicrobial resistance Open
Diagnosing antimicrobial resistance (AMR) in the clinic is based on empirical evidence and current gold standard laboratory phenotypic methods. Genotypic methods have the potential advantages of being faster and cheaper, and having improve…
View article: Metagenome-assembled genome binning methods with short reads disproportionately fail for plasmids and genomic Islands
Metagenome-assembled genome binning methods with short reads disproportionately fail for plasmids and genomic Islands Open
Metagenomic methods enable the simultaneous characterization of microbial communities without time-consuming and bias-inducing culturing. Metagenome-assembled genome (MAG) binning methods aim to reassemble individual genomes from this data…
View article: HAB Hunter
HAB Hunter Open
Harmful algal blooms, or HABs, are destructive ecological phenomena caused by unchecked growth of specific species of microbes present in fresh, marine and brackish water environments.HABs deprive areas of oxygen and can produce toxins tha…