NeoPredPipe: high-throughput neoantigen prediction and recognition potential pipeline. - Ryan O. Schenck; Eszter Lakatos; Chandler Gatenbee; Trevor A. Graham; Alexander R. A. Anderson (BMC Bioinform., 2019)

Spatially constrained tumour growth affects the patterns of clonal selection and neutral drift in cancer genomic data. - Ketevan Chkhaidze; Timon Heide; Benjamin Werner; Marc J. Williams; Weini Huang; Giulio Caravagna; Trevor A. Graham; Andrea Sottoriva (PLoS Comput. Biol., 2019)

The MOBSTER R package for tumour subclonal deconvolution from bulk DNA whole-genome sequencing data. - Giulio Caravagna; Guido Sanguinetti; Trevor A. Graham; Andrea Sottoriva (BMC Bioinform., 2020)

First passage time analysis of spatial mutation patterns reveals sub-clonal evolutionary dynamics in colorectal cancer. - Magnus J. Haughey; Aleix Bassolas; Sandro Sousa; Ann-Marie Baker; Trevor A. Graham; Vincenzo Nicosia; Weini Huang (PLoS Comput. Biol., 2023)

The tumour histopathology "glossary" for AI developers. - Soham Mandal; Ann-Marie Baker; Trevor A. Graham; Konstantin Bräutigam (PLoS Comput. Biol., 2025)