Publications
Publications
All publications from the lab, newest first. You can also follow new work on Google Scholar.
2026
- Technical replicates and multiple sequencing approaches reveal weak and inconsistent microbiome signals in lung tumour and blood samples from patients with lung cancer
- The biotechnological applications of marine bacteria
- Population-based characterisation of child and adolescent oral bacterial microbiomes
- From classification to confirmation: Verification of metagenomic taxonomic classifications through mapping of classified reads to reference genomes
- Association between the oral microbiome and clinical indicators of resectable non-small cell lung cancer (NSCLC)
- Effect of bedrest on the human gut and oral microbiome: implications for frailty
- Personalized AZithromycin/metronidAZole (PAZAZ) + dietary therapy in paediatric Crohn disease: results of a pilot study
2025
- JarrVis: Visualising Taxa-function relationships from meta-omic data
- Lime amendment to chronically acidified forest soils results in shifts in prokaryotic communities
- The trans-kingdom spectrum of Mpox-like lesion pustules of suspect patients in the Mpox Clade Ib outbreak in Eastern Democratic Republic of the Congo
- Characterization of the salivary microbiome of adults with inflammatory bowel disease
- PICRUSt2-SC: an update to the reference database used for functional prediction within PICRUSt2
- Profiling lateral gene transfer events in the human microbiome using WAAFLE
2024
- Nitrogen-fixation in the widely distributed model marine γ-proteobacterial diazotroph Candidatus Thalassolituus haligoni
- Oral microbial signatures associated with age and frailty in Canadian adults
2023
- Microbial hitchhikers harbouring antimicrobial-resistance genes in the riverine plastisphere
- Cross-study analyses of microbial abundance using generalized common factor methods
- Betaproteobacteria are a key component of surface water biofilters that maintain sustained manganese removal in response to fluctuations in influent water temperature
- Supplementation of cyanidin-3-O-B-glucoside-rich haskap (Lonicera caerulea L.) berry extract attenuates hepatic lipid dysregulation in diet-induced obese mice
- Investigating the oral microbiome in retrospective and prospective cases of prostate, colon, and breast cancer
- Exploring the microbiome of oral epithelial dysplasia as a predictor of malignant progression
- Hepatotoxicity of polymeric proanthocyanidins is caused by translocation of bacterial lipopolysaccharides through impaired gut epithelium
- From defaults to databases: parameter and database choice dramatically impact the performance of metagenomic taxonomic classification tools
- The gastrointestinal antibiotic resistome in pediatric leukemia and lymphoma patients
- Changes to Soil Microbiome Resulting from Synergetic Effects of Fungistatic Compounds Pyrimethanil and Fluopyram in Lowbush Blueberry Agriculture, with Nine Fungicide Products Tested
- Personalised Azithromycin + Metronidazole (PAZAZ), in combination with standard induction therapy, to achieve a faecal microbiome community structure and metagenome changes associated with sustained remission in paediatric Crohn’s Disease (CD): protocol of a pilot study
- Understanding the impact of different source water types on the biofilm characteristics and microbial communities of manganese removing biofilters
- Efficient computation of contributional diversity metrics from microbiome data with FuncDiv
2022
- Integrating phylogenetic and functional data in microbiome studies
- Antibiotic and antifungal use in pediatric leukemia and lymphoma patients are associated with increasing opportunistic pathogens and decreasing bacteria responsible for activities that enhance colonic defense
- Microbiome differential abundance methods produce different results across 38 datasets
2021
- Investigation of the impact of commonly used medications on the oral microbiome of individuals living without major chronic conditions
- Reporting guidelines for human microbiome research: the STORMS checklist
- Biological and physico-chemical mechanisms accelerating the acclimation of Mn-removing biofilters
- Gut bacterial gene changes following pegaspargase treatment in pediatric patients with acute lymphoblastic leukemia
- A multi-OMIC characterisation of biodegradation and microbial community succession within the PET plastisphere
- Identifying biases and their potential solutions in human microbiome studies
- A primer and discussion on DNA-based microbiome data and related bioinformatics analyses
- An in vivo genome-wide shRNA screen identifies BCL6 as a targetable biomarker of paclitaxel resistance in breast cancer
- Harnessing the plant microbiome to promote the growth of agricultural crops
2020
- Transcriptomic profiling of Brassica napus responses to Pseudomonas aeruginosa
- Investigating the gut microbial community and genes in children with differing levels of change in serum asparaginase activity during pegaspargase treatment for acute lymphoblastic leukemia
- Food or just a free ride? A meta-analysis reveals the global diversity of the plastisphere
- Assessing the variation within the oral microbiome of healthy adults
- Microbial co-occurrence network analysis of soils receiving short- and long-term applications of alkaline treated biosolids
- Re-evaluating the relationship between missing heritability and the microbiome
- PICRUSt2 for prediction of metagenome functions
- The human tumor microbiome is composed of tumor type-specific intra-cellular bacteria
- Age-related variation of bacterial and fungal communities in different body habitats across the young, elderly and centenarians in Sardinia
- Detection of Helicobacter pylori microevolution and multiple infection from gastric biopsies by housekeeping gene amplicon sequencing
- Bacterial taxa and functions are predictive of sustained remission following exclusive enteral nutrition in pediatric Crohn’s disease
2019
- Current and promising approaches to identify horizontal gene transfer events in metagenomes
- Reproducible, interactive, scalable, and extensible microbiome data science using QIIME 2
- Metagenomic functional shifts to plant induced environmental changes
- Drivers of regional bacterial community structure and diversity over depth and time in the Northwest Atlantic Ocean
- Infectious complications are associated with alterations in the gut microbiome in pediatric patients with Acute Lymphoblastic Leukemia
- Enhancement of Gut Barrier Integrity by a Microbial Metabolite through Nrf2 Pathway
2018
- The phosphate binder ferric citrate alters the gut microbiome in rats with chronic kidney disease
- Selective sensitivity of the gut microbiome to iron chelators in polybacterial abdominal sepsis
- The impact of chemerin or chemokine-like receptor 1 loss on the mouse gut microbiome
- Denoising the Denoisers: an independent evaluation of microbiome sequence error-correction approaches
- Differences in adiposity and diet quality among individuals with inflammatory bowel disease in Eastern Canada
- Dissecting community structure in wild blueberry root and soil microbiome
- Exploring linkages between taxonomic and functional profiles of the human microbiome
- Polyphenol-based prebiotics and synbiotics: potential for cancer chemoprevention
- Multi-omics differentially classify disease state and treatment outcome in pediatric Crohn’s disease
- Available Upon Request: not good enough for microbiome data!
2017
- Taxonomic differences of gut microbiomes drive cellulolytic enzymatic potential within hind-gut fermenting mammals
- The coupling of taxonomy and function in microbiomes
- Moderate exercise has limited but distinguishable effects on the mouse microbiome
- Variation in Bacterial and Eukaryotic Communities Associated with Natural and Managed Wild Blueberry Habitats
- The Impact of Exclusive Enteral Nutrition (EEN) on the Gut Microbiome in Crohn’s Disease: A Review
- Microbiome Helper: A custom and streamlined workflow for microbiome research
2016
- Discovery of an expanded set of avian leukosis subgroup E proviruses in chickens using Vermillion, a novel sequence capture and analysis pipeline
- Genomic analysis of a serotype 5 Streptococcus pneumoniae outbreak in Canada 2005-2009
2015
- GenomeD3Plot: A library for rich, interactive visualizations of genomic data in web applications
- IslandViewer 3: more flexible, interactive genomic island discovery, visualization and analysis
- Fecal microbes, short chain fatty acids, and colorectal cancer across racial/ethnic groups
2014
- Microbial shifts in the aging mouse gut
- Which is more important for classifying microbial communities: who's there, or what they can do?
- Interactions in the microbiome: communities of organisms and communities of genes
2005-2013
- Predictive functional profiling of microbial communities using 16S rRNA marker gene sequences
- GenGIS 2: Geospatial analysis of traditional and genetic biodiversity, with new gradient algorithms and an extensible plugin framework
- IslandViewer update: improved genomic island discovery and visualization
- Sifting through genomes with iterative-sequence clustering produces a large, phylogenetically diverse protein-family resource
- Functional biogeography of ocean microbes revealed through non-negative matrix factorization
- Sequencing of Seven Haloarchaeal Genomes Reveals Patterns of Genomic Flux
- MicrobeDB: a locally maintainable database of microbial genomic sequences
- Human Microbiome: A Genetic Bazaar for Microbes?
- Detection of genomic islands using bioinformatics approaches
- BioTorrents: A file sharing service for scientific data
- The association of virulence factors with genomic islands
- Bioinformatic detection of horizontally transferred DNA in bacterial genomes
- IslandViewer: an integrated interface for computational identification and visualization of genomic islands
- Newly introduced genomic prophage islands are critical determinants of in vivo competitiveness in the Liverpool Epidemic Strain of Pseudomonas aeruginosa
- Evaluation of genomic island predictors using a comparative genomics approach
- Parent genes of retrotransposition-generated gene duplicates in Drosophila melanogaster have distinct expression profiles
- Data standards for flow cytometry
- 3D live-wire-based semi-automatic segmentation of medical images
- Color Lesion Boundary Detection Using Live Wire