James E. Johnson

The paper introduces a modular pipeline for neoantigen discovery, verification, and prioritization in cancer research using immunopeptidogenomic data.

This study compares Scribe and database search engines in metaproteomic analysis of a ground-truth microbiome dataset, finding Scribe detects more proteins and quantifies microbial composition more accurately.

The paper introduces a clinical metaproteomics workflow that enables analysis of host-microbe dynamics in disease by integrating mass spectrometry and bioinformatics tools.

This paper evaluates classification errors in WGS datasets using Kraken2 and Metaphlan2, finding that Kraken2's errors create 'phantom' taxa that affect statistical inference.

This paper evaluates six metaproteomics tools for functional annotation using GO terms, finding differences in sensitivity and specificity, and integrates two into Galaxy for broader accessibility.

The paper evaluates and implements two label-free quantification tools in the Galaxy platform for proteomics and multi-omics analysis.

The paper introduces a sectioning method to improve peptide spectrum matching in large genome-guided protein sequence databases by increasing sensitivity while maintaining acceptable false discovery rates.

The paper introduces a Galaxy plugin for proteogenomic data visualization and exploration, enabling interactive analysis and sharing of results.

The paper introduces PMD-FDR, a Bayesian confidence measure to filter high-scoring but likely false peptide-spectrum matches in proteomics, improving accuracy in standard, proteogenomics, and metaproteomics datasets.

Bioconda provides a sustainable, comprehensive distribution of bioinformatics software using Conda for reproducible analysis across platforms.

The paper integrates NCBI BLAST+ into Galaxy to enable sequence comparison workflows, making both simple and advanced BLAST tasks accessible.