Toby M. Baker

Genome-wide classification of tumor-derived reads from bulk long-read sequencing

ROCIT classifies tumor or non-tumor origin of reads from bulk long-read sequencing with high accuracy, improving somatic variant calling in tumors.

Evolutionary trajectories of immune escape across cancers

This study investigates the evolutionary timing of immune escape mutations across 38 cancer types using functional genomics and tumor evolution reconstruction.

Reconstructing oral cavity tumor evolution through brush biopsy

This study shows brush biopsies can accurately reflect the genomic profile of oral premalignant lesions and their progression to OSCC, capturing most SNVs and CNAs comparable to tissue biopsies.

Synchronous L1 retrotransposition events promote chromosomal crossover early in human tumorigenesis

The paper analyzes L1 retrotransposition in tumors using long-read sequencing, revealing synchronous L1 insertions drive chromosomal crossovers early in tumorigenesis.

The history of chromosomal instability in genome doubled tumors

This paper introduces GRITIC, a method to time genomic gains in tumors, finding that copy number gains often accumulate after genome duplication.

Evolution of chromosome arm aberrations in breast cancer through genetic network rewiring

The paper investigates the evolution of chromosome 4p loss in basal breast cancer, identifying C4orf19 as a novel gene that suppresses proliferation and is part of a kinase module.

A Genetic Model for Central Chondrosarcoma Evolution Correlates with Patient Outcome

The paper presents a genetic model of central chondrosarcoma using genomic and epigenomic data to identify mutations and methylation patterns associated with patient outcomes.

Copy number-aware deconvolution of tumor-normal DNA methylation profiles

This paper introduces CAMDAC, a method to deconvolve tumor-normal DNA methylation profiles while accounting for copy number changes, revealing epigenetic instability and distinct patterns in lung cancer.