Publications

Here you can find selected publications grouped by topic and pre-prints of things I’m currently working on.

Progression modelling: Methods

Unscrambling disease progression at scale: fast inference of event permutations with optimal transport

Subtype and stage inference with timescales

The temporal event-based model: Learning event timelines in progressive diseases

Progression modelling: Applications

Uncovering spatiotemporal patterns of atrophy in progressive supranuclear palsy using unsupervised machine learning

Identifying multiple sclerosis subtypes using unsupervised machine learning and MRI data

An image-based model of brain volume biomarker changes in Huntington’s disease

Software development

pySuStaIn: a Python implementation of the Subtype and Stage Inference algorithm

Clinical study analysis

Characterizing developing executive functions in the first 1000 days in South Africa and Malawi: The Khula Study

Robust markers and sample sizes for multicenter trials of Huntington disease

Drug delivery modelling

A quantitative in silico platform for simulating cytotoxic and nanoparticle drug delivery to solid tumours

Cancer growth modelling

Multiscale biphasic modelling of peritumoural collagen microstructure: The effect of tumour growth on permeability and fluid flow

Inverse problems in particle physics

Measurements of the pseudorapidity dependence of the total transverse energy in proton-proton collisions at √s=7 TeV with ATLAS