StxTyper uses a standardized algorithm to accurately type both known and unknown Shiga toxin operons from assembled genomic sequence.

Kinetic modeling of glucose and acetate metabolisms in E. coli

Data and tools necessary to construct iJL1678b-ME, a genome-scale model of E. coli K-12 MG1655 metabolism and expression

Escherichia coli Transcriptome Assembly from a Compendium of RNA-seq Data Sets

EcoliTyper: A species-optimized computational pipeline for comprehensive genotyping and surveillance of Escherichia coli. Perfect for clinical microbiology, outbreak investigations, and genomic research.

The AMRnet dashboard aims to make high-quality, robust and reliable genome-derived AMR surveillance data accessible to a wide audience

Predicting the regulatory role of CRP transcription factor in Escherichia coli

Exploring correlations in an isobaric labeling mass spectrometry-based proteomic data set

IRIDA plugin for ECTyper (E.coli in silico typing tool)

Code for ML-based detection of unstable antibiotic heteroresistance in E. coli

13C metabolic flux analysis of the extracellular GL-GNT by-pass of E. coli

A WDL-based workflow for profiling Klebsiella & E. coli genomes using Kleborate. Supports local execution with Cromwell both local & cloud deployment in Terra, enabling automated analysis of assemblies with docker & integration with Terra data tables for scalable genomic surveillance.

The KlebGen project is a genomics surveillance initiative focused on Klebsiella Pneumoniae and E. Coli strains isolated from neonates across Africa. This repository contains all the scripts used to analyze the strains from the Cameroonian subset of the project.

Molecular docking is one of the molecular modeling methods that predicts the preferred orientation of one molecule (ligand) to another (receptor) when bound to each other to form a stable complex (lowest energy state).

In silico PCR command line tool for typing Escherichia coli ST131

Decipher polymorphism in E. coli strains with coevolutionary models

Supplementary information of Millard et al. 2023

Integrated development environment for the design of synthetic biological systems, from DNA sequence to systems level

Collection of planning documents, visualizations, and presentations for my dissertation research. "Investigating Multidrug Resistance in Escherichia coli with Phylogenetics and Machine Learning"

An optimal experimental design framework for accelerating knowledge discovery using gene expression data