A.-M. Baker

Epigenome and early selection determine the tumour-immune evolutionary trajectory of colorectal cancer

This study shows that immune evasion in colorectal cancer follows a 'Big Bang' pattern, where early genetic and epigenetic changes drive subsequent tumor-immune evolution.

Adaptive therapy achieves long-term control of chemotherapy resistance in high grade ovarian cancer

This study demonstrates that adaptive therapy reduces chemotherapy resistance in ovarian cancer by exploiting fitness costs of resistant cells, extending survival in mice and correlating with disease burden in patients.

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.

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.

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.

Negative selection may cause grossly altered but broadly stable karyotypes in metastatic colorectal cancer

This study analyzes longitudinal genomic data from colorectal cancer patients to show that negative selection stabilizes karyotypes during tumor progression and metastasis.

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.