John Parkinson

The paper develops a multi-compartment metabolic model of the chicken gut to identify dietary interventions that enhance short-chain fatty acid production.

This study examines gut microbiome differences in infants with congenital heart disease, finding HLHS-specific pathobiont enrichment and functional shifts that respond to nutritional interventions.

PhylaChrome assigns deterministic colours to microbiome taxa to visually represent taxonomic relationships and improve cross-study comparisons.

The paper investigates genetic and phenotypic differences between Neisseria gonorrhoeae strains causing disseminated gonococcal infections (DGI) and non-invasive strains in Canada, identifying two porB alleles and other genetic determinants associated with DGI.

The paper uses metabolic modeling of chicken cecal microbiomes to show how Bacteroides fragilis influences community metabolism and how its absence leads to functional reconfiguration and disease-like profiles.

The paper analyzes 31,595 gonococcal genomes to identify genetic diversity, phase variability, and mobile elements linked to antimicrobial resistance and phenotypic traits.

Navargator selects representative variants based on phylogenetic trees to improve cross-reactivity in vaccines, validated using immunization studies.

This study examines the impact of gestational diabetes on infant gut microbiome function and composition, finding modest and transient effects.

Cell4D is a spatial stochastic simulator for cellular pathways that enables hypothesis generation and testing through interactive visualization and high-performance computing.

HiTaxon improves species-level taxonomic classification of short reads by combining reference-based and machine learning approaches in a hierarchical framework.

MetaPro processes and analyzes metatranscriptomic data, providing gene expression profiles and taxonomic breakdowns with improved performance over existing pipelines.

This paper describes a fluorescence-based platform for high-throughput Cystic Fibrosis therapy testing using iPSC-derived immature airway epithelium.

Architect improves metabolic model quality by combining enzyme annotations from multiple tools and gap-filling based on likelihood scores.

The paper models the metabolic interactions between a parasitic worm and its bacterial endosymbiont to identify potential drug targets.

This paper presents a systematic pipeline to classify bacterial operons and reveals the evolutionary landscape of biofilm machineries through phylogenetic clustering and genomic-proximity network analysis.

The paper identifies genetic variants associated with enhanced growth and reduced immune function in modern broilers through comparative genomic analysis of historical and commercial chicken lines.

This paper compares genomes of 81 nematode and platyhelminth species to identify gene families related to parasitism and prioritize new drug targets.

Gist improves taxonomic classification of metatranscriptomic data by combining machine learning and alignment methods, achieving high accuracy on synthetic data.