Daniel Petras

The paper investigates how gut commensal strains modulate the growth and virulence of Clostridium perfringens through substrate competition and protein level changes.

The Everything Bagel feature finder automates metabolomics data processing, achieving comparable or better performance than existing methods with significantly reduced computational time.

This paper discovers NHAP, a fungal metabolite that selectively inhibits Gi-signaling, demonstrating functional blockade in cardiomyocytes without cytotoxicity.

The paper develops an agentic AI system using LLMs and domain tools to hypothesize and validate structures of unknown drug metabolites from mass spectrometry data.

This paper introduces MT-GEM and STEP to predict discrete structural transformations in metabolites from MS/MS spectra, achieving significant improvements over existing methods.

This paper develops a continuous bioreactor to maintain stable nasal microbiomes from swab specimens and synthetic communities, showing long-term stability and S. aureus decolonization.

The paper shows that cooperative siderophore exchange between Rhodotorula kratochvilovae and Pseudomonas species stabilizes the leaf microbiome and protects plants from pathogens.

The paper constructs synthetic nasal communities to study how community composition influences metabolic competition and S. aureus colonization resistance.

This study shows that melon seeds primed with two closely related Bacillus strains trigger different physiological and defense responses based on microbial identity and inoculum dose.

The paper introduces microbiomeMASST, a metadata network graph linking metabolites across datasets, enabling cross-study analysis of microbial metabolites and their biological context.

The paper develops a functional metabolomics framework using synthetic microbial communities and computational analysis to track drug metabolism by gut microbes, identifying metabolites and their correlations with microbial taxa.

The paper introduces a collaborative platform for curating microbial metabolite knowledge to enhance metabolomics data interpretation.

The paper identifies pteridines, including lumazine dehydroxyxanthopterin B2, as natural ligands of CutA that modulate copper binding and redox homeostasis in E. coli and Synechococcus elongatus.

This study shows that Bacillus subtilis uses its extracellular matrix protein TasA to suppress Botrytis cinerea by disrupting fungal structures and delivering antimicrobial compounds, while the fungus responds with adaptive strategies.

This paper introduces a method to simultaneously detect CRISPRi strain barcodes and metabolites using FI-MS, revealing pathway-specific metabolic changes in engineered bacteria.

The paper investigates microbe-microbe interactions in a synthetic microbial community on Arabidopsis leaves, finding that in vitro pairwise interactions differ from in planta correlation networks, suggesting community-level synergism over competition.

ModiFinder localizes structural modification sites in small molecules by aligning MS/MS spectra of known and unknown compounds.

This study analyzes venom composition across seven Turkish viper taxa using proteomics and peptidomics, identifying new toxin sequences and comparing them to other Palearctic vipers to improve snakebite risk assessment.

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

This study uses native metabolomics to identify a family of protease inhibitors from cyanobacteria, revealing their structure and potent biological activity.

MassQL, an open-source query language, lets users search raw mass spectrometry data from any vendor for isotope, fragmentation and neutral-loss patterns, from one file to entire public repositories.

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

The paper introduces a web-based tool for collaborative analysis of mass spectrometry data, enabling remote inspection, visualization, and analysis of private and public datasets.

CANOPUS is a tool that predicts compound classes from fragmentation spectra, enabling annotation of unknown compounds without reference data.

The paper maps chemical modifications in an ant fungus garden as plant material passes through, revealing its role in nutrient uptake.

The paper develops a machine learning workflow for auto-deconvolution of GC-MS data within GNPS, enabling molecular networking and applications in breathomics and volatilome mapping.

ZODIAC improves molecular formula annotation in metabolomics by combining SIRIUS results with Gibbs sampling, reducing errors and discovering novel compounds.

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 study shows that Escherichia coli can adapt to use fluorinated indoles as essential precursors for protein synthesis through few genetic mutations and significant regulatory and cellular changes.