Reid F. Thompson

The paper evaluates the impact of methodological differences on splicing neoepitope prediction, finding high variability and limited reproducibility across pipelines.

This study benchmarks 12 HLA callers on RNA-seq data across 682 samples to evaluate accuracy, computational cost, and performance differences by ancestry.

recountmethylation provides processed blood DNA methylation data and analysis tools, showing genetic ancestry and cell fractions explain most DNAm variation and validating DMPs between sexes.

The paper evaluates four MHC binding affinity prediction tools across different peptide sources and alleles, revealing inconsistencies in their predictions and training data quality.

The paper compares retained intron detection in short and long RNA-seq reads, finding significant disagreement among tools and poor precision/recall.

This study examines the association between HLA genotype and SARS-CoV-2 disease severity in 3,235 individuals, finding limited impact compared to demographic and clinical factors.

Pepsickle predicts proteasomal cleavage sites more accurately and quickly than existing tools, improving neoantigen identification for vaccine development.

The paper analyzes 35,360 DNAm array samples from GEO, identifies tissue sources, evaluates quality assessments, and provides a database with annotated data through an R/Bioconductor package.

neoepiscope improves neoepitope prediction by incorporating germline context and somatic variant phasing, addressing limitations in existing tools.