Connah Johnson

Spatiotemporal 4D Whole-cell Modeling of a Minimal Autotroph Reveals Central Carbon Metabolism Regulated Locally by Protein Megacomplexes via Post-translational Modifications under Light Disturbance

The paper develops a 4D whole-cell model of Prochlorococcus marinus MED4 to show how spatial organization and redox PTMs regulate carbon fixation under light disturbance.

EcoKMER: One-stop shop for spatio-temporal metagenomic exploration using DataFed

An R-Shiny app built on DataFed lets researchers filter metagenomic sample metadata by location, date and environmental variables, then download only matching sequence files via Globus.

Synergy and antagonism in a genome-scale model of metabolic hijacking by bacteriophage

The paper integrates AMGs and phage assembly into a genome-scale metabolic model to predict their impact on host metabolism and phage production, revealing synergistic and antagonistic effects.

Sampling Microbial Dynamics in the Salish Sea Estuary: Evaluating Methods to Capture Cyanobacteria and Cyanophage

The paper develops and refines methods to sample and sequence cyanobacteria, cyanophages, and their environment in the Salish Sea to study host-pathogen dynamics.

Hydroplane I: one-shot probabilistic evolutionary analysis for scalable organizational identification.

Hydroplane introduces a fast Bayesian method for metagenomic evolutionary analysis, demonstrating effectiveness in detecting homologs and estimating lineage diversity using kmer data.

Genotype-phenotype modeling of light ecotypes in Prochlorococcus reveals genomic signatures of ecotypic divergence

This study identifies genomic signatures of light ecotypes in Prochlorococcus using machine learning and comparative genomics, showing accurate ecotype prediction from partial genomes.

ChemChaste: Simulating spatially inhomogenous biochemical reaction-diffusion systems for modelling cell-environment feedbacks

ChemChaste extends the Chaste library to simulate spatially inhomogeneous biochemical reaction-diffusion systems, enabling coupling of bulk and intracellular reactions.