John Parkinson

University of Toronto — Canada

Biochemistry, Genetics and Molecular Biology · Life Sciences

61h-index18.1kcitations303works3.02yr avg
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Research Topics

Gut microbiota and health(51), Genomics and Phylogenetic Studies(42), Probiotics and Fermented Foods(34), Microbial Metabolic Engineering and Bioproduction(22), Bioinformatics and Genomic Networks(20)

Publications303 total

Multi-compartment spatiotemporal metabolic modeling of the chicken gut guides the design of dietary interventions
2026Open Access
Correction: Metabolic modeling of microbial communities in the chicken ceca reveals a landscape of competition and co-operation
Microbiome·2025Open Access
Metabolic modeling of microbial communities in the chicken ceca reveals a landscape of competition and co-operation
Microbiome·2025· 2 citedOpen Access
Preventative behavioural interventions that reduce health inequities: a systematic review using the theoretical domains framework
BMC Public Health·2025· 2 citedOpen Access
Whole Genome Sequence of the gut commensal protist Tritrichomonas musculus isolated from laboratory mice
Scientific Data·2025· 1 citedOpen Access
Network-based population analysis of 31,595 gonococcal genomes reveals phase variability, genetic diversity and mobile element dynamics drive antimicrobial resistance and phenotypic diversity
2025Open Access
Cross-kingdom-mediated detection of intestinal protozoa through NLRP6
Cell Host & Microbe·2025· 4 cited
Ligand interaction landscape of transcription factors and essential enzymes in E. coli
Cell·2025· 10 cited
The gut microbiome and child and adolescent depression and anxiety: a systematic review and meta-analysis with youth consultation
Gut Microbiome·2025Open Access
The protozoan commensal <i>Tritrichomonas musculis</i> is a natural adjuvant for mucosal IgA
The Journal of Experimental Medicine·2024· 3 citedOpen Access
Metabolic modeling of microbial communities in the chicken ceca reveals a landscape of competition and co-operation
2024· 1 citedOpen Access
Phenotypic diversity and shared genomic determinants among isolates causing a large incidence of disseminated gonococcal infections in Canada
2024Open Access
Phylogeny-based selection of representative variants with Navargator: Proof of principle using humoral cross-reactivity data from two immunization studies
2024· 1 cited
Elucidating the dynamics and impact of the gut microbiome on maternal nutritional status during pregnancy, effect on pregnancy outcomes and infant health in rural Pakistan: study protocol for a prospective, longitudinal observational study
BMJ Open·2024· 1 citedOpen Access
ToxoNet: A high confidence map of protein-protein interactions in Toxoplasma gondii
PLoS Computational Biology·2024· 5 citedOpen Access
The impact of gestational diabetes on functional capacity of the infant gut microbiome is modest and transient
Gut Microbes·2024· 5 citedOpen Access
Correction: Intestinal microbiome profiles in broiler chickens raised without antibiotics exhibit altered microbiome dynamics relative to conventionally raised chickens
PLoS ONE·2024· 2 citedOpen Access
Intestinal microbiome profiles in broiler chickens raised without antibiotics exhibit altered microbiome dynamics relative to conventionally raised chickens
PLoS ONE·2024· 10 citedOpen Access
Cell4D: a general purpose spatial stochastic simulator for cellular pathways
BMC Bioinformatics·2024Open Access
Commensal protist<i>Tritrichomonas musculus</i>exhibits a dynamic life cycle that induces extensive remodeling of the gut microbiota
The ISME Journal·2024· 11 citedOpen Access
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Frequent Co-authors

James D. Wasmuth(8), Andrew Emili(7), Mark Blaxter(7), Xuejian Xiong(6), José M. Peregrín-Alvarez(5), Jack Greenblatt(5), Matthew Berriman(5), Sadhna Phanse(5), Mohan Babu(5), James Vlasblom(4), Lakshmipuram S. Swapna(4), Michael E. Grigg(4), Nevan J. Krogan(3), Stacy Hung(3), David B. Guiliano(3), Chris Sanford(3), Alla Gagarinova(3), Ashkan Golshani(3), Haiyuan Yu(2), Xinghua Guo(2)