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Author Details

John Parkinson
The Hospital for Sick Children
1994
131
48
Andrej Sali (CM4AI)
PMIDPaper TitleJournal TitlePublished Year
37370188MetaPro: a scalable and reproducible data processing and analysis pipeline for metatranscriptomic investigation of microbial communities.Microbiome2023
37090671The commensal protist <i>Tritrichomonas musculus</i> exhibits a dynamic life cycle that induces extensive remodeling of the gut microbiota.bioRxiv2023
34980288Performance of distinct microbial based solutions in a Campylobacter infection challenge model in poultry.Anim Microbiome2022
35477134Effects of therapeutic levels of dietary antibiotics on the cecal microbiome composition of broiler chickens.Poult Sci2022
35857765Toxoplasma infection in male mice alters dopamine-sensitive behaviors and host gene expression patterns associated with neuropsychiatric disease.PLoS Negl Trop Dis2022
36074804Architect: A tool for aiding the reconstruction of high-quality metabolic models through improved enzyme annotation.PLoS Comput Biol2022
35965349Systematic profiling of the chicken gut microbiome reveals dietary supplementation with antibiotics alters expression of multiple microbial pathways with minimal impact on community structure.Microbiome2022
34795270Micronutrient supplements can promote disruptive protozoan and fungal communities in the developing infant gut.Nat Commun2021
34751631E.coli Nissle increases transcription of flagella assembly and formate hydrogenlyase genes in response to colitis.Gut Microbes2021
34678210A new platform for high-throughput therapy testing on iPSC-derived lung progenitor cells from cystic fibrosis patients.Stem Cell Reports2021
32541926Author Correction: A transcriptomic analysis of the phylum Nematoda.Nat Genet2020
31952471Accumulation of genetic variants associated with immunity in the selective breeding of broilers.BMC Genet2020
32853540BraInMap Elucidates the Macromolecular Connectivity Landscape of Mammalian Brain.Cell Syst2020
32779567Modeling the metabolic interplay between a parasitic worm and its bacterial endosymbiont allows the identification of novel drug targets.Elife2020
32236137Discovery and characterization of a Gram-positive Pel polysaccharide biosynthetic gene cluster.PLoS Pathog2020
32236097A systematic pipeline for classifying bacterial operons reveals the evolutionary landscape of biofilm machineries.PLoS Comput Biol2020
31095319PopNetD3-A Network-Based Web Resource for Exploring Population Structure.Genome Biol Evol2019
31380556Future challenges and new approaches: general discussion.Faraday Discuss2019
31373341Data mining and visualisation: general discussion.Faraday Discuss2019
31542262Commensal gut microbiota can modulate adaptive immune responses in chickens vaccinated with whole inactivated avian influenza virus subtype H9N2.Vaccine2019
29176613Global landscape of cell envelope protein complexes in Escherichia coli.Nat Biotechnol2018
30181578Gut microbiota-mediated protection against influenza virus subtype H9N2 in chickens is associated with modulation of the innate responses.Sci Rep2018
30143032Comparative transcriptomic analyses and single-cell RNA sequencing of the freshwater planarian Schmidtea mediterranea identify major cell types and pathway conservation.Genome Biol2018
30572961Design and application of a novel two-amplicon approach for defining eukaryotic microbiota.Microbiome2018
30455975Lactobacillus elicits a 'Marmite effect' on the chicken cecal microbiome.NPJ Biofilms Microbiomes2018
30382111Author Correction: Gut microbiota-mediated protection against influenza virus subtype H9N2 in chickens is associated with modulation of the innate responses.Sci Rep2018
30298261Analyzing Metabolic Pathways in Microbiomes.Methods Mol Biol2018
30298246Characterization of Eukaryotic Microbiome Using 18S Amplicon Sequencing.Methods Mol Biol2018
29722785Improved enzyme annotation with EC-specific cutoffs using DETECT v2.Bioinformatics2018
29380643Gut microbiota modulates type I interferon and antibody-mediated immune responses in chickens infected with influenza virus subtype H9N2.Benef Microbes2018
29228270Influenza A virus subtype H9N2 infection disrupts the composition of intestinal microbiota of chickens.FEMS Microbiol Ecol2018
28877764Perilipin-2 modulates dietary fat-induced microbial global gene expression profiles in the mouse intestine.Microbiome2017
28383661PopNet: A Markov Clustering Approach to Study Population Genetic Structure.Mol Biol Evol2017
28276701Genomics of apicomplexan parasites.Crit Rev Biochem Mol Biol2017
28426969Chemogenetic Interrogation of a Brain-wide Fear Memory Network in Mice.Neuron2017
28288093Malaria parasites possess a telomere repeat-binding protein that shares ancestry with transcription factor IIIA.Nat Microbiol2017
29128334A Map of Human Mitochondrial Protein Interactions Linked to Neurodegeneration Reveals New Mechanisms of Redox Homeostasis and NF-κB Signaling.Cell Syst2017
26757703Metatranscriptomic analysis of diverse microbial communities reveals core metabolic pathways and microbiome-specific functionality.Microbiome2016
27869790The genome of Onchocerca volvulus, agent of river blindness.Nat Microbiol2016
27807038Metabolomic Changes in Serum of Children with Different Clinical Diagnoses of Malnutrition.J Nutr2016
26774489Conditional Epistatic Interaction Maps Reveal Global Functional Rewiring of Genome Integrity Pathways in Escherichia coli.Cell Rep2016
26738725Local admixture of amplified and diversified secreted pathogenesis determinants shapes mosaic Toxoplasma gondii genomes.Nat Commun2016
26980519PhyloPro2.0: a database for the dynamic exploration of phylogenetically conserved proteins and their domain architectures across the Eukarya.Database (Oxford)2016
25425642The role of palmitoylation for protein recruitment to the inner membrane complex of the malaria parasite.J Biol Chem2015
26621462Comparative Genomics and Evolutionary Modularity of Prokaryotes.Adv Exp Med Biol2015
26344197Panorama of ancient metazoan macromolecular complexes.Nature2015
26870755Proteome-wide dataset supporting the study of ancient metazoan macromolecular complexes.Data Brief2015
26125937Identification of Candidate Adherent-Invasive E. coli Signature Transcripts by Genomic/Transcriptomic Analysis.PLoS One2015
26218289Correction: Identification of Candidate Adherent-Invasive E. coli Signature Transcripts by Genomic/Transcriptomic Analysis.PLoS One2015
26108529Hyperscape: visualization for complex biological networks.Bioinformatics2015
  • 1 - 50 of 131

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Peer Bork
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Richard Bonneau
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Collaborators

Andrew Emili
Boston University School of Medicine, Boston University
Co-authored papers 13
James D Wasmuth
University of Calgary
Co-authored papers 12
Jos?? M Peregr??n-Alvarez
Hospital for Sick Children
Co-authored papers 10
Jack F Greenblatt
College Street, University of Toronto
Co-authored papers 10
Sadhna Phanse
University of Regina
Co-authored papers 9
Mohan Babu
University of Regina
Co-authored papers 8
James Vlasblom
University of Regina
Co-authored papers 7
Cedoljub Bundalovic-Torma
University of Toronto
Co-authored papers 6
Shoshana J Wodak
VIB-VUB Center for Structural Biology
Co-authored papers 5
Matthew Berriman
Wellcome Sanger Institute
Co-authored papers 5
Ramy H Malty
University of Toronto, University of Regina
Co-authored papers 4
Shuye Pu
College Street, University of Toronto
Co-authored papers 4
Ashwani Kumar
Bhabha Atomic Research Centre
Co-authored papers 4
Alla Gagarinova
University of Regina
Co-authored papers 4
Zhaolei Zhang
University of Toronto
Co-authored papers 4
Ashkan Golshani
Ottawa Institute of Systems Biology, Carleton University
Co-authored papers 4
Paul N Barlow
University of Edinburgh
Co-authored papers 4
Jill Cook
Co-authored papers 4
Yunchen Gong
University of Toronto
Co-authored papers 3
Hiroyuki Aoki
University of Regina
Co-authored papers 3
Elodie Ghedin
National Institute of Allergy and Infectious Diseases, National Institutes of Health
Co-authored papers 3
Gareth Butland
Lawrence Berkeley National Laboratory
Co-authored papers 3
Neil Hall
Earlham Institute
Co-authored papers 3
Xinghua Guo
University of Toronto, College Street
Co-authored papers 3
Viktor Deineko
University of Northern British Columbia
Co-authored papers 3
Andy Brass
Co-authored papers 3
Olga Kagan
Molloy University, NY The City University of New York School of Professional Studies
Co-authored papers 3
Haiyuan Yu
Weill Institute for Cell and Molecular Biology, Cornell University
Co-authored papers 3
Nevan J Krogan (CM4AI)
University of California San Francisco
Co-authored papers 3
Zoran Minic
University of Ottawa
Co-authored papers 3
Release 1.2