T. A. Graham

Mutational order and epistasis determine the consequences of FBXW7 mutations during colorectal cancer evolution

This study shows that the order of FBXW7 and APC mutations affects colorectal cancer initiation, with FBXW7 mutations before APC preventing cancer-like features.

FUME-TCRseq: Sensitive and accurate sequencing of the T-cell receptor from limited input of degraded RNA

FUME-TCRseq is a sensitive and accurate method for TCR sequencing from low-quality RNA, outperforming existing methods in detecting clonotypes and enabling analysis of archival tissue samples.

Cancer Prevalence Across Vertebrates

The paper analyzes cancer prevalence across 292 vertebrate species and finds that neoplasia prevalence increases with adult weight and mutation rate but decreases with gestation time.

Phenotypic plasticity and genetic control in colorectal cancer evolution

This study investigates phenotypic plasticity and genetic control in colorectal cancer by analyzing gene expression and genetic variation across multiple tumor regions.

The co-evolution of the genome and epigenome in colorectal cancer

This study examines the co-evolution of genome and epigenome in colorectal cancer using single-clone spatial multi-omic profiling, revealing epigenetic changes and their impact on mutation accumulation.

Mutation Rate Evolution Drives Immune Escape In Mismatch Repair-Deficient Cancer

The paper shows that mutation rate adaptation in MMRd cancers drives immune escape by modulating neoantigen diversity and subclonal mutation rates.

AI-powered pan-species computational pathology: bridging clinic and wildlife care

This study develops a pan-species computational pathology atlas using AI to analyze cancer morphology across species, finding that accuracy varies with morphological similarity and introduces a new metric for veterinary applications.

First passage time analysis of spatial mutation patterns reveals evolutionary dynamics of pre-existing resistance in colorectal cancer

This paper introduces a first passage time analysis framework to quantify spatial mutation patterns in colorectal cancer, revealing sub-clonal dynamics and replicative advantages of mutant cells.

VALIS: Virtual Alignment of pathoLogy Image Series

VALIS automates registration of immunohistochemistry and immunofluorescence images, enabling spatial analysis of whole slide images with low error and minimal computational time.

Assessment of the evolutionary consequence of putative driver mutations in colorectal cancer with spatial multiomic data

This study uses spatial multiomic data to assess the evolutionary impact of putative driver mutations in colorectal cancer, identifying both genetic and non-genetic factors influencing subclonal expansion.

Evolutionary dynamics of neoantigens in growing tumours

This study develops a mathematical model of neoantigen evolution in tumors and validates it with colorectal cancer data, showing how negative selection shapes tumor immunogenotype and clonality.

Platinum resistance induces diverse evolutionary trajectories in high grade serous ovarian cancer

This study investigates platinum resistance in high grade serous ovarian cancer by analyzing transcriptomic features and evolutionary trajectories in resistant models.

Niche engineering drives early passage through an immune bottleneck in progression to colorectal cancer

The paper models tumor-immune dynamics in colorectal cancer progression, showing immune evasion enables transition from immune-hot adenomas to immune-cold carcinomas.

Macrophage-mediated immunoediting drives ductal carcinoma evolution: Space is the game changer

This study uses immunohistochemistry data to model how macrophages influence tumor evolution through spatial dynamics and immune escape strategies in ductal carcinomas.

Measuring single cell divisions in human cancers from multi-region sequencing data

This study measures single-cell division rates and survival in human cancers using multi-region sequencing data, revealing per-cell mutation and survival rates across different cancer types and healthy tissues.

Quantification of subclonal selection in cancer from bulk sequencing data

This study quantifies subclonal selection in cancer using bulk sequencing data to determine mutation rates, selective advantages, and subclone emergence times in gastric and lung cancers.