Ted Liefeld

The paper evaluates ssGSEA's performance on scRNA-seq data, finds it unreliable due to sparsity, and identifies UCell as more robust for pseudobulk analysis.

AmpliconSuite identifies focal amplifications in cancer genomes, showing ecDNA has higher copy numbers and stronger oncogene enrichment compared to other amplification types.

The paper introduces computational tools for NMF analysis of single-cell RNA-seq data, demonstrating their use in quantifying cell state transitions in pancreatic cancer.

NMFClustering provides GPU-accelerated non-negative matrix factorization for efficient clustering of large RNA-Seq and scRNA-seq datasets.

The paper describes a standardized RNA-Seq pipeline for spaceflight data, enabling reproducible analysis of gene expression changes in astronauts and organisms exposed to spaceflight.

GeNets provides a platform to compare genomic networks using machine learning and allows analysis of genetic and RNA sequencing data.