Julia M. Gauglitz

This study compares fermentation-induced molecular changes in cassava and cocoyam using metabolomics, revealing distinct catabolic and balanced metabolic responses.

The paper analyzes food metabolomics data to trace molecular signals from agricultural practices and environmental exposures, revealing contamination pathways and natural products.

TreeMS2 constructs molecular phylogenies from raw MS/MS data, revealing relationships based on molecular phenotype and identifying deviations from genetic-based trees.

The paper introduces an open-source platform for reference data-driven metabolomics analysis, demonstrating its ability to extract dietary patterns from stool metabolomics data.

SquiDBase provides a centralized repository for raw nanopore sequencing data from microbes, along with tools to process and expand reference datasets.

This study identifies temporal regulation of metabolic processes in Crocosphaera watsonii WH8501 using proteomics, revealing coordinated protein abundance patterns across diel cycles.

The paper creates a suspect spectral library for untargeted metabolomics by propagating annotations from public MS/MS spectra to improve interpretation of unannotated spectra.

The paper introduces Ion Identity Molecular Networking to connect ion species of the same molecule, improving network connectivity and annotation.

EMPress provides an interactive tool for visualizing phylogenetic trees alongside multi-omic data, enabling exploratory analyses of microbiome and metabolome datasets.

The paper introduces Qemistree, a method for analyzing metabolomics mass spectrometry data using hierarchical molecular fingerprints and chemical ontologies to explore chemical composition.

The paper introduces FBMN, a method for improving molecular networking by enhancing quantitative analysis and isomer distinction using feature detection and alignment tools in the GNPS platform.

The paper develops ReDU, a tool for discovering and re-analyzing metabolomics data in GNPS, following FAIR principles.

This paper expands the interpretability of human metabolomes by using food-based annotations, increasing the fraction of molecular features understood 7-fold.

The paper uses metabolomics to correct metadata classifications in cheetah microbiome studies, revealing antibiotic transfer via grooming and improving understanding of medication effects.

The paper identifies novel conjugated bile acids produced by the microbiome in mice and humans using mass spectrometry and a murine 3D model.

MASST enables querying of public small-molecule tandem MS data to discover molecular relationships in metabolomics and natural product datasets.

This paper uses untargeted mass spectrometry to analyze chemical changes in foods during preparation and storage, finding that some processes alter molecular composition while others primarily involve extraction.