SNMF: Integrated Learning of Mutational Signatures and Prediction of DNA Repair Deficiencies by Goossens S, Tepeli YI, Seale C, and Gonçalves JP (bioRxiv 2024)

Biologically informed deep learning to query gene programs in single-cell atlases

RNA-seq analysis pipeline for Brent lab (WUSTL)

MUSICiAn: Genome-wide Identification of Genes Involved in DNA Repair via Control-Free Mutational Spectra Analysis by Seale CF, Barazas M, van Schendel R, Tijsterman M, and Gonçalves JP (NAR Genomics and Bioinformatics 2025)