Jennifer A. Doherty

The paper shows that bulk transcriptomic subtypes in HGSC reflect tumor composition rather than intrinsic biology, with composition predicting subtype and prognosis.

The paper deconvolves adipocyte proportions from bulk RNA-seq data of HGSOC tumors and finds higher adipocyte content is associated with worse survival.

The paper examines how missing cell types in single-cell references affect deconvolution of bulk data and shows that missing cell-type profiles can be detected using non-negative matrix factorization.

This study identifies molecular subtypes of high-grade serous ovarian cancer across racial groups and gene expression platforms, finding similar subtype-specific survival rates despite differences in subtype prevalence.

The paper uses deconvolution on bulk transcriptomic data to show that HGSOC subtypes are driven by tumor microenvironment composition, particularly fibroblast and immune cell content.

This study evaluates how experimental factors affect the performance of tumor deconvolution algorithms using bulk RNA-seq data.

The paper evaluates genetic demultiplexing tools for pooled single-cell RNA-seq in cancer, showing they work effectively despite challenges from ambient RNA.

miQC is a probabilistic framework that jointly models mitochondrial DNA and gene detection metrics to improve single-cell RNA-seq quality control.

This study improves transcriptome-wide association studies by integrating pleiotropy-guided methods with GWAS data to identify new cancer susceptibility genes.

The paper examines telomere length variation across 6,391 tissue samples from 952 individuals, showing tissue-specific differences, positive correlations between tissues, and associations with age and ancestry.

The paper identifies genetic links between impaired pulmonary function and increased lung cancer risk, showing causal relationships through Mendelian randomization and highlighting immune-related pathways.

The paper estimates the contribution of direct telomere inheritance from parents to offspring to the heritability of leukocyte telomere length in humans.

The paper develops a method combining functional network community detection with pathway enrichment to reduce false positives in complex gene sets.