Katherine A. Hoadley

This study shows that BAP1 deletion in hepatocytes leads to an inflammatory transcriptional response and impaired immune cell recruitment in the liver.

The paper identifies an EGFR mutation signature (mSig) that captures transcriptional features of EGFR activation in LUAD, revealing subtype-dependent oncogene activity and potential therapeutic targets.

The paper expands detection of BAP1 alterations in cancer using multi-omic analyses and identifies a transcriptional signature linked to BAP1 disruption and cellular plasticity.

This paper develops a normalization and quality control approach for NanoString RNA data, showing improved handling of technical variation without loss of biological variation.

The paper identifies hundreds of genes deregulated by SVs in cancer, showing increased expression linked to SV breakpoints and enhancer elements.

The paper predicts cancer cell-of-origin from DNA sequences by matching mutational landscapes to chromatin modification patterns in normal tissues.

The paper analyzes RNA alterations across 27 cancer types using whole-genome sequencing data, identifying gene expression associations with DNA variants and structural fusions.

This study characterizes genomic, transcriptomic, and epigenomic artifacts in FFPE tissues and provides best practices to mitigate their impact on molecular analysis.