Ian P.M. Tomlinson

This paper introduces DUCK-Net, a deep learning model for automated segmentation of Ductular Reactions in murine liver injury, showing high accuracy and correlation with spatial transcriptomic data.

This paper introduces ARMS DNAseq, a scalable spatial genomic assay that maps copy number subclones in archival tissue, revealing tumor evolution and subclone associations with morphology and transcriptomic features.

This study uses whole genome sequencing of endometrial cancers to identify novel subgroups, drivers, and actionable alterations, improving precision medicine approaches.

This study identifies DNA methylation differences between microsatellite stable and microsatellite instable colorectal cancers, revealing MLH1-independent markers of mismatch repair deficiency and the impact of anatomical location.

This paper develops a co-differentiation platform using human iPSCs to generate transplantable colonic tissue that mimics native mucosa and responds to biological signals.

This study shows that germline MUTYH haploinsufficiency increases mutational signature SBS18 and CRC risk, but not other cancers, due to oxidative DNA damage in the colorectum.

This study shows that probiotic treatment alleviates colitis in naked mole rats caused by Citrobacter braakii, offering a new model for studying inflammatory bowel disease.

Pathological epithelial GREM1 expression induces therapeutically reversible ectopic stem cell niches through stromal remodelling.

The paper shows that hypermutational processes can explain the prevalence of weak driver mutations like atypical KRAS variants in cancers without requiring differential selection.

This study identifies rs3087967 as the causal variant at 11q23.1 that increases colorectal cancer risk by dysregulating POU2AF2, a key activator of tuft cell transcription.

The paper develops a framework for classifying variants of reduced penetrance in cancer susceptibility genes to improve variant interpretation consistency.

The paper quantifies the tumorigenic effect of partial APC inactivation in colorectal cancer, finding it confers a 50-fold higher cancer progression risk than complete inactivation.

The paper identifies 88 novel rare disease-gene associations using a burden analysis framework on whole genome sequencing data from the 100,000 Genomes Project, with potential clinical impact for undiagnosed cases.

The paper investigates the impact of genetic structure and ancestry on colorectal cancer risk in Colombian admixed populations using 20 known risk SNPs.

The paper analyzes gene expression in normal colorectal mucosa to assess associations with BMI and sex, finding no significant associations after replication.

The paper assesses breast cancer risks linked to rare missense variants in five susceptibility genes using logistic and mixture models, finding varying risk contributions across genes.

The paper shows that germline mutations in POLE or POLD1 lead to elevated mutation burdens in normal human cells and tissues, but do not cause premature aging or other phenotypic features beyond early-onset cancer.

This study assesses polygenicity and risk prediction using common variants across 14 cancers, finding varying numbers of susceptibility variants and risk score effectiveness.

This study combines genome-wide association data from four cancers to identify shared and novel genetic associations and pleiotropic effects.

The paper identifies genetic determinants of mosaic Y chromosome loss in blood and links it to genomic instability and non-haematological cancer risk.

This paper introduces a machine learning method to detect repeated cancer evolution patterns across patients using multi-region sequencing data, identifying prognostic patient subgroups.