Faculty profile

John Parkinson

ResearcherUniversity of Toronto

This profile is built from public research funding records (CIHR, NSERC and SSHRC) and PubMed. We have not imported them from a University of Toronto directory, so their courses may be missing. Find their university profile.

John Parkinson

Researcher

Health Sciences

University of Toronto

Toronto, Ontario, Canada

Supervision signals

Has led research grants, which requires an independent research appointment. Ask their department whether they supervise graduate students.
22 publications in the last five years, latest in 2026.
Senior (last) author on 11 recent papers, a sign of leading a research group.
Principal investigator on 21 research grants (14 CIHR, 7 NSERC), most recently in 2025.
Supervised 2 trainees who won CIHR awards, most recently in 2025.

These signals come from public records, including CIHR, NSERC and SSHRC funding decisions. Ask the professor or the graduate program whether they are taking new students.

Academic metrics

104

Publications

399

Citations

h-index

Collaborators

Grants

Publications by year

Counts cover the works listed on the university profile; citation counts come from Dimensions.

Profiles and links

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Signals and details

Research

Microbiome Bioinformatics Global Health Computational Biology Parasites Metabolic Modeling Metagenomics Pathobionts

Latest papers

Phenotypic diversity and shared genomic determinants among isolates causing a large incidence of disseminated gonococcal infections in Canada.
mSphere · 2026
Whole Genome Sequence of the gut commensal protist Tritrichomonas musculus isolated from laboratory mice.
Scientific data · 2025
Correction: Metabolic modeling of microbial communities in the chicken ceca reveals a landscape of competition and co-operation.
Microbiome · 2025 · senior author

All 104 publications

Latest funding

The response of the maternal and infant gut microbiome to extreme heat events
CIHR · 2025 · Nominated PI
$1,048,050
Accelerating Advancements in Infant Probiotic Development and Clinical Trials
CIHR · 2025 · Principal investigator
$20,000
Elucidating stage-specific protein complexes that enable Plasmodium falciparum gametocyte transmission to mosquitoes.
CIHR · 2025 · Supervisor
$120,000

All 33 grants and awards

104 publications.

Phenotypic diversity and shared genomic determinants among isolates causing a large incidence of disseminated gonococcal infections in Canada.

Binepal G, Jurga E, Carruthers-Lay D, Krüger S, Zittermann S, Minion J, Diggle M, Alexander DC, Martin I, Allen V, Parkinson J, Gray-Owen SD

mSphere2026

DOI: 10.1128/msphere.00051-26 PMID: 42474140

Whole Genome Sequence of the gut commensal protist Tritrichomonas musculus isolated from laboratory mice.

Alves-Ferreira EVC, Galac MR, Lorenzi HA, Ho MCW, Tjhin ET, Popovic A, Parkinson J, Grigg ME

Scientific data2025

DOI: 10.1038/s41597-025-04921-0 PMID: 40199934

Correction: Metabolic modeling of microbial communities in the chicken ceca reveals a landscape of competition and co-operation.

Utkina I, Fan Y, Willing BP, Parkinson J

Microbiome2025Senior author

DOI: 10.1186/s40168-025-02323-3 PMID: 41430632

Cross-kingdom-mediated detection of intestinal protozoa through NLRP6.

Winsor NJ, Bayer G, Singh O, Chan JK, Li LY, Lieng BY, Foerster E, Popovic A, Tsankov BK, Maughan H, Lemire P, Tam E, Streutker C, Chen L, Heaver SL, Ley RE, Parkinson J, Montenegro-Burke JR, Birchenough GMH, Philpott DJ, Girardin SE

Cell host & microbe2025

DOI: 10.1016/j.chom.2025.02.008 PMID: 40043701

Ligand interaction landscape of transcription factors and essential enzymes in E. coli.

Peng H, Kotelnikov S, Egbert ME, Ofaim S, Stevens GC, Phanse S, Saccon T, Ignatov M, Dutta S, Istace Z, Moutaoufik MT, Aoki H, Kewalramani N, Sun J, Gong Y, Padhorny D, Poda G, Alekseenko A, Porter KA, Jones G, Rodionova I, Guo H, Pogoutse O, Datta S, Saier M, Crovella M, Vajda S, Moreno-Hagelsieb G, Parkinson J, Segre D, Babu M, Kozakov D, Emili A

Cell2025

DOI: 10.1016/j.cell.2025.01.003 PMID: 39862855

The gut microbiome and child and adolescent depression and anxiety: a systematic review and meta-analysis with youth consultation.

Campisi SC, Zhang F, Seo M, Muha J, Schumacher A, De Luca I, Bradley-Ridout G, Merriman K, Parkinson J, Korczak DJ

Gut microbiome (Cambridge, England)2025

DOI: 10.1017/gmb.2025.10013 PMID: 41079946

Metabolic modeling of microbial communities in the chicken ceca reveals a landscape of competition and co-operation.

Utkina I, Fan Y, Willing BP, Parkinson J

Microbiome2025Senior author

DOI: 10.1186/s40168-025-02241-4 PMID: 41310806

The impact of gestational diabetes on functional capacity of the infant gut microbiome is modest and transient.

Chieu RV, Hamilton K, Ryan PM, Copeland J, Wang PW, Retnakaran R, Guttman DS, Parkinson J, Hamilton JK

Gut microbes2024

DOI: 10.1080/19490976.2024.2356277 PMID: 38798005

Cell4D: a general purpose spatial stochastic simulator for cellular pathways.

Chan D, Cromar GL, Taj B, Parkinson J

BMC bioinformatics2024Senior author

DOI: 10.1186/s12859-024-05739-0 PMID: 38515063

The protozoan commensal Tritrichomonas musculis is a natural adjuvant for mucosal IgA.

Cao EY, Burrows K, Chiaranunt P, Popovic A, Zhou X, Xie C, Thakur A, Britton G, Spindler M, Ngai L, Tai SL, Dasoveanu DC, Nguyen A, Faith JJ, Parkinson J, Gommerman JL, Mortha A

The Journal of experimental medicine2024

DOI: 10.1084/jem.20221727 PMID: 39535524

The response of the maternal and infant gut microbiome to extreme heat events

Nominated PICIHR2025Project Grant

Principal investigators: Parkinson, John; Bhutta, Zulfiqar A

Keywords: Birth Outcomes; Climate Change; Extreme Heat; Global Health; Maternal Health; Microbiome; Pregnancy

$1,048,050

Accelerating Advancements in Infant Probiotic Development and Clinical Trials

Principal investigatorCIHR2025Planning and Dissemination Grants - Institute/Initiative Community Support

Principal investigators: Roth, Daniel E; Bandsma, Robert; Bassani, Diego G; Bhutta, Zulfiqar A; Comelli, Elena M; Morris, Shaun K; Parkinson, John; Shah, Prakeshkumar

Keywords: Clinical Trial; Global Health; Infants; Interventions; Microbiome; Neonatal Diseases; Probiotics; Regulations

$20,000

Elucidating stage-specific protein complexes that enable Plasmodium falciparum gametocyte transmission to mosquitoes.

SupervisorCIHR2025Doctoral Research Award - PA - Bioinformatics and Computational Biology

Principal investigators: Yusuff, Khairatun Fatima Binte

Keywords: Bioinformatics; Host Invasion; Host-Parasite Interactions; Malaria; Network Biology; Parasite Virulence; Protein Complexes; Protein-Protein Interactions; Proteomics; Systems Biology

$120,000

Protist:microbiome dynamics in the mammalian gut

Nominated PICIHR2024Project Grant

Principal investigators: Parkinson, John

Keywords: Computational Biology; Global Health; Metabolic Modeling; Metagenomics; Microbiome; Pathobionts; Protist:Microbiome Interactions; Protozoa; Single Cell Genomics; Tritrichomonas

$952,426

Protist:microbiome dynamics in the mammalian gut

Nominated PICIHR2023Project Grant - Priority Announcement: Global Health Research

Principal investigators: Parkinson, John

Keywords: Computational Biology; Global Health; Metabolic Modeling; Metagenomics; Microbiome; Pathobionts; Protist:Microbiome Interactions; Protozoa; Single Cell Genomics; Tritrichomonas

$100,000

Smart Capsule for non-invasive targeted sampling and delivery in the gut

Co-investigatorNSERC2022Idea to Innovation

Principal investigators: Diller, Eric ED

$125,000

Systematic interrogation of host:parasite interactions that allow Toxoplasma gondii to infect and persist

Nominated PICIHR2021Project Grant

Principal investigators: Parkinson, John

Keywords: Bioinformatics; Host Response; Host:Pathogen Interactions; Parasite Invasion; Proteomics; Rhoptry Proteins; Strain Variation; Toxoplasma Gondii

$952,425

Defining stable microbial communities through functional interrogation of microbiomes

Principal investigatorNSERC2019Discovery Grants Program - Individual

Principal investigators: Parkinson, John

$300,000

A mechanistic understanding of the impact of pathogen-microbiome dynamics on maternal nutrition during pregnancy in young women

Nominated PICIHR2019Team Grant: Canadian Microbiome Initiative 2: Research Teams

Principal investigators: Parkinson, John; Bandsma, Robert; Bhutta, Zulfiqar A; Hulst, Jessie; Mortha, Arthur; Suleman, Shazeen

Keywords: Adolescent Pregnancies; Animal Models; Bioinformatics; Global Child Health; Malnutrition; Maternal Nutrition; Metabolomics; Metagenomics/Metatranscriptomics; Microbiome; Parasites

$2,000,000

Overcoming drug resistance in gonorrhea through metabolic network analysis

Nominated PICIHR2018Project Grant

Principal investigators: Parkinson, John; Gray-Owen, Scott D

Keywords: Antimicrobial Resistance; Bioinformatics; Computational Biology; Constraints Based Modelling; Gonorrhea; Humanized Mouse Model; Metabolism; Population Genomics; Sexually Transmitted Infection; Systems Biology

$799,426

From CIHR, NSERC and SSHRC funding decisions: CIHR since 2008, NSERC since 1991 and SSHRC since 1998, including their latest published competition results.

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John Parkinson

Research

Latest papers

Latest funding

Phenotypic diversity and shared genomic determinants among isolates causing a large incidence of disseminated gonococcal infections in Canada.

Whole Genome Sequence of the gut commensal protist Tritrichomonas musculus isolated from laboratory mice.

Correction: Metabolic modeling of microbial communities in the chicken ceca reveals a landscape of competition and co-operation.

Cross-kingdom-mediated detection of intestinal protozoa through NLRP6.

Ligand interaction landscape of transcription factors and essential enzymes in E.&#xa0;coli.

The gut microbiome and child and adolescent depression and anxiety: a systematic review and meta-analysis with youth consultation.

Metabolic modeling of microbial communities in the chicken ceca reveals a landscape of competition and co-operation.

The impact of gestational diabetes on functional capacity of the infant gut microbiome is modest and transient.

Cell4D: a general purpose spatial stochastic simulator for cellular pathways.

The protozoan commensal Tritrichomonas musculis is a natural adjuvant for mucosal IgA.

Smart Capsule for non-invasive targeted sampling and delivery in the gut

Defining stable microbial communities through functional interrogation of microbiomes

Frequent collaborators

Andrew Emili

Shayan Sharif

Mohan Babu

Jack Greenblatt

Zhaolei Zhang

David He

Arthur Mortha

Jayne Danska

Daniela Rotin

Robert Bandsma

Peter Wong

Jessie Hulst

Hui Peng

Alexei Savchenko

Sachdev Sidhu

Derek Tsang

Felix Ratjen

Ronish Gupta

Angelo Canty

Philippe Poussier

Philip Kim

Peter Szatmari

Ravi Retnakaran

Peter Szatmari

Eric Brown

Karen Mossman

Ligand interaction landscape of transcription factors and essential enzymes in E. coli.