Karl R. Clauser

Peptide-HLA II interaction prediction for post-translationally modified peptides

The paper develops a deep learning model to predict peptide-HLA II interactions for post-translationally modified peptides, showing accurate predictions on unseen modifications.

Pan-viral ORFs discovery using Massively Parallel Ribosome Profiling

This study uses Massively Parallel Ribosome Profiling to identify thousands of viral ORFs, including non-canonical ones, and shows their impact on HLA-I peptides and protein synthesis regulation.

What can Ribo-seq and proteomics tell us about the non-canonical proteome?

This paper discusses the current state of research on non-canonical open reading frames (ORFs) and proposes standards for their investigation and reporting using Ribo-seq and proteomics.

TAILS identifies candidate substrates and biomarkers of ADAMTS7, a therapeutic protease target in coronary artery disease

The paper identifies ADAMTS7 substrates and cleavage sites using TAILS, revealing potential biomarkers for coronary artery disease.

PANOPLY: A cloud-based platform for automated and reproducible proteogenomic data analysis

PANOPLY is a cloud-based platform that automates and reproducibly analyzes proteogenomic data by integrating genomic, transcriptomic, proteomic, and post-translational modification data.

Proteomics Standards Initiative Extended FASTA Format (PEFF)

The paper introduces PEFF, a new format for proteomics data that enhances FASTA with metadata for sequence variants and PTMs, enabling better analysis in proteogenomics and top-down proteomics.