Kathleen Noller

The paper identifies 17 consensus transcriptomic programs in ccRCC using NMF and links them to cellular sources and clinical outcomes, revealing converging trajectories toward aggressive disease.

PICTographPlus infers clone-resolved transcriptional programs from bulk RNA-seq by integrating clonal phylogenies and proportions, achieving high accuracy in recovering clone-level expression and localizing pathway changes.

The paper identifies multi-omic phenotypes in pancreatic precursor lesions to distinguish progressive from indolent precancers using integrative transcriptomic, genomic, and spatial data.

The paper introduces stemFinder, a method to predict single-cell differentiation time using cell cycle gene expression heterogeneity, showing it is computationally efficient and performs as well as or better than existing methods.