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

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)

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

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.

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).

Supplementary information of Millard et al. 2023

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. 2022

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

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

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

Short RStudios code showcasing how Fourrier transformations are used in finding three base periodicity in Escherichia Coli.

.m, .MAT, .PDF, .XLS files for "Canonical host-pathogen tradeoffs subverted by mutations with dual benefits"