Milan Malfait

The paper develops a workflow for differential detection analysis in single-cell RNA-seq data and shows it provides complementary information to differential expression analysis.

This paper evaluates strategies to address pseudoreplication in multi-patient scRNA-seq data, finding that Poisson GEEs and pseudobulk approaches outperform single-cell methods.

The paper introduces TargetDecoy, a Bioconductor package to assess and control the quality of the target-decoy approach for peptide identification in proteomics.