Elmer A. Fernández

The paper identifies microRNAs regulated by E2F transcription factors in human pluripotent stem cells through RNA-seq and RT-qPCR, revealing their potential roles in cell cycle and differentiation.

The paper benchmarks neoantigen immunogenicity predictors and finds that MHC-I binding affinity and its derived metrics are insufficient to predict immunogenicity or tumor neoantigen burden as biomarkers.

MIXTURE improves immune tumor microenvironment estimation by reducing overestimation of cell-type counts and improving accuracy in bulk RNA data.

This study benchmarks nine workflows for detecting differential splicing and isoform expression in RNA-seq, finding that workflow performance depends on replicates and heterogeneity, with Limma, DESeq2, and DEXSeq performing well.