Sarah J. Aitken

Explainable machine learning relates histological to genomic pathology

This paper uses machine learning to predict genomic alterations from H&E images of liver tumors, revealing genotype-phenotype links and highlighting genetic background limitations.

Genetic background sets the trajectory of cancer evolution

This study shows that genetic background and environmental factors determine the trajectory of cancer evolution in mice, with distinct mutational paths despite similar final tumor states.

Paired CRISPR screens identify mitochondrial metabolism and UBE2H as aneuploid-specific dependencies in human cancer cell lines

A scalable approach for tissue microarray profiling using spatial single cell transcriptomics

The paper introduces a scalable method for profiling FFPE tissue microarrays using spatial single-cell transcriptomics, achieving subcellular resolution in human liver samples.

Germline and somatic variation influence nuclear-mitochondrial crosstalk in tumourigenesis

This study investigates how germline and somatic genetic variations affect mitochondrial DNA content, mutation patterns, and gene expression in liver tumors across four mouse strains.

Strand-resolved mutagenicity of DNA damage and repair

The paper investigates how strand-asymmetric processes like replication and transcription influence DNA damage, repair, and mutagenesis, revealing mechanisms that shape cancer genome evolution.

Clustered CTCF binding is an evolutionary mechanism to maintain topologically associating domains

The paper investigates how CTCF binding patterns across species contribute to the stability and evolution of TAD boundaries through clustered binding sites.