Collaborative health projects
We work with clinicians and scientists to better understand human and microbial interactions in health and disease, bringing advanced bioinformatic methods to their studies.
See our recent papers ↓Research
Understanding the microbiome in health and disease
Our aim is to develop novel bioinformatic and computational methods to better understand the role of the microbiome in disease. The work rests on three connected pillars.
Application and resource development
We create and validate bioinformatic approaches that improve the biological insight we can draw from microbiome data, and release them as open software.
See our software →Integrated Microbiome Resource
A sequencing and bioinformatics service housed within the lab. The IMR offers current sequencing technologies and deep expertise in microbiome sequencing and analysis to scientists around the world.
Visit imr.bio →Recent work
Our newest papers across all three pillars. Choose a topic above to see the papers on it.
All publications →- 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
- JarrVis: Visualising Taxa-function relationships from meta-omic data
- 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
- Oral microbial signatures associated with age and frailty in Canadian adults
- 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
- From defaults to databases: parameter and database choice dramatically impact the performance of metagenomic taxonomic classification tools
- 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
- Efficient computation of contributional diversity metrics from microbiome data with FuncDiv
- Integrating phylogenetic and functional data in microbiome studies
- Microbiome differential abundance methods produce different results across 38 datasets
- 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
- Assessing the variation within the oral microbiome of healthy adults
- 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
- Bacterial taxa and functions are predictive of sustained remission following exclusive enteral nutrition in pediatric Crohn’s disease
- Reproducible, interactive, scalable, and extensible microbiome data science using QIIME 2
- 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
- Exploring linkages between taxonomic and functional profiles of the human microbiome
- Multi-omics differentially classify disease state and treatment outcome in pediatric Crohn’s disease
- The coupling of taxonomy and function in microbiomes
- The Impact of Exclusive Enteral Nutrition (EEN) on the Gut Microbiome in Crohn’s Disease: A Review
- Microbial shifts in the aging mouse gut
- Predictive functional profiling of microbial communities using 16S rRNA marker gene sequences