Lukas J. Vlahos

pyVIPER: A fast and scalable Python package for rank-based enrichment analysis of single-cell RNASeq data

pyVIPER is a Python package for fast, scalable rank-based enrichment analysis of scRNA-seq data, offering significant runtime improvements over VIPER for large datasets.

Elucidation and Pharmacologic Targeting of Master Regulator Dependencies in Coexisting Diffuse Midline Glioma Subpopulations

The paper identifies master regulator dependencies in coexisting diffuse midline glioma subpopulations and shows that combination therapy targeting these regulators improves survival in vivo.

An Information Theoretic Framework for Protein Activity Measurement

The paper introduces NaRnEA, a gene set analysis method that improves differential activity measurement of transcriptional regulatory proteins across cancer cohorts.

Systematic, Protein Activity-based Characterization of Single Cell State

The paper introduces PISCES, a platform that improves single-cell analysis by estimating protein activity's role in cell state, validated with experimental assays and applied to human tissue data.