Erik N. Bergstrom

This study examines ecDNA in lung cancer, finding it in 18.9% of patients and associating it with worse survival and genomic instability.

This study shows that carcinogen-induced DNA adducts enhance APOBEC3B-mediated mutagenesis, leading to increased mutation rates in cancer genomes.

The paper identifies two lung cancer subtypes defined by APOBEC mutagenesis levels and shows their association with different genetic mutations, aging, and immune responses.

The paper introduces an updated tool for visualizing and exploring large mutational events in cancer genomes using two classification schemas.

SigProfilerExtractor is a tool for de novo mutational signature extraction that outperforms existing methods and identifies four novel signatures, including one linked to tobacco smoking.

SigProfilerClusters identifies all types of clustered mutations by calculating sample-dependent thresholds and subclassifies them into established categories.

SigProfilerSimulator generates realistic null mutational landscapes for cancer genomics to evaluate bioinformatics tools and statistical analyses.

This study identifies germline genetic variants influencing somatic mutation patterns in 2,642 cancer genomes across 39 cancer types.

This study characterizes mitochondrial genomes in 2,700 cancer patients across 37 types using whole-genome sequencing and RNA-seq, revealing mutational patterns, truncating mutations, and nuclear transfer of mitochondrial DNA.

SigProfilerMatrixGenerator classifies and visualizes small mutational events in cancer genomes, offering faster and more comprehensive analysis than existing tools.