Heather M. Geiger

DECONVersation: Single Cell Foundation Model-Derived Embeddings for Robust Cell Type Deconvolution of Bulk RNA-seq

DECONVersation uses single-cell foundation model embeddings to improve bulk RNA-seq deconvolution by reducing batch effects and eliminating marker gene selection.

Comprehensive Molecular Characterization of High-Grade Endometrial Cancer in an Ancestrally-Diverse Cohort

This study characterizes the molecular differences in high-grade endometrial cancer across an ancestrally diverse cohort, identifying ancestry-associated mutations and immune microenvironment differences.

Single-nucleus multiome sequencing identifies candidate regulators of mouse gastric epithelial homeostasis

An explainable boosting machine model for identifying artifacts caused by formalin-fixed paraffin embedding

This paper introduces an explainable boosting machine model to identify and filter variant artifacts caused by formalin-fixed paraffin embedding in cancer genomics.

The Interplay between Mutagenesis and Extrachromosomal DNA Shapes Urothelial Cancer Evolution

This study examines how mutagenesis and extrachromosomal DNA contribute to urothelial cancer evolution, revealing clonal APOBEC3 mutations and chemotherapy-induced mutational bursts within ecDNA.

Diverse tumorigenic consequences of human papillomavirus integration in primary oropharyngeal cancers

This study identifies HPV integration hotspots in oropharyngeal cancers and shows their role in disrupting host gene expression and genomic stability.

SCANVIS: a tool for SCoring, ANnotating and VISualing splice junctions

SCANVIS scores, annotates, and visualizes splice junctions across samples, showing separation of tissue/cancer types using a few thousand SJs.