Jacob Pfeil

tauX: A Gene Expression Ratio Strategy to Improve Machine Learning Applications in Precision Medicine

The paper introduces tauX, a gene expression ratio strategy that improves machine learning performance in precision medicine by refining gene expression features.

The case for using Mapped Exonic Non-Duplicate (MEND) read counts in RNA-Seq experiments: examples from pediatric cancer datasets

The paper evaluates the informativeness of reads in bulk RNA-Seq datasets and recommends using MEND reads for accurate gene expression quantification in pediatric cancer studies.

ProTECT: Prediction of T-cell Epitopes for Cancer Therapy

ProTECT identifies and ranks tumor neoepitopes from raw sequencing data for cancer immunotherapy, outperforming existing tools in efficiency and scalability.

Genomic profiling of childhood tumor patient-derived xenograft models to enable rational clinical trial design

This paper genomically characterizes 261 pediatric cancer patient-derived xenograft models to guide rational clinical trial design and drug development.

Rapid and efficient analysis of 20,000 RNA-seq samples with Toil

The paper demonstrates Toil's ability to efficiently process 20,000 RNA-seq samples to create a batch-effect-free meta-analysis across five datasets.