Julianus Pfeuffer

The paper introduces tools to generate proteogenomics databases using ENSEMBL resources, revealing non-canonical peptides in public datasets.

The paper introduces a standardized metadata format for proteomics datasets to improve reusability and integration across public repositories.

DIAproteomics is an automated pipeline for analyzing DIA proteomics and peptidomics data, offering tools for spectral library generation, alignment, and statistical analysis.

SPLICE-q quantifies splicing efficiency using RNA-seq data and is applied to yeast, human nascent RNA-seq, and prostate cancer samples.

EPIFANY improves protein inference accuracy and efficiency by combining loopy belief propagation with convolution trees, outperforming existing methods on benchmark data.