Stephenie D. Prokopec

Integrated analysis of cell-free DNA for the early detection of cancer in people with Li-Fraumeni Syndrome

This study evaluates an integrated liquid biopsy approach for early cancer detection in Li-Fraumeni syndrome patients, showing improved detection rates compared to individual methods.

Identifying TCDD-resistance genes via murine and rat comparative genomics and transcriptomics

The paper identifies genes associated with TCDD-response phenotypes by comparing genomic and transcriptomic data from transgenic mice and rats.

BPG: Seamless, Automated and Interactive Visualization of Scientific Data

BPG is an R package that generates publication-quality, customizable plots and offers an interactive web tool for figure customization and integration with computational pipelines.

Accurate Reference-Free Somatic Variant-Calling by Integrating Genomic, Sequencing and Population Data

S22S is a reference-free method for somatic variant calling that uses genomic and population data to accurately identify SNVs without matched normal samples.

The Origins and Consequences of Localized and Global Somatic Hypermutation

This study identifies genes driving localized and global hypermutation in tumors and finds that kataegis (localized mutation rainstorms) are associated with specific genetic alterations and patient outcomes.