Benjamin P. Bowen

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

This study shows dopamine affects rhizosphere microbial community composition by influencing bacterial growth and abundance in Brachypodium distachyon root exudates.

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 study shows that the peptide hormone PSY1 promotes root growth by inducing flavonol biosynthesis, which regulates cell elongation and differentiation in Arabidopsis.

The paper introduces a Bayesian Personalized Ranking model to predict microbial substrate preferences and develops an agent that integrates this model with a growth model and LLM for autonomous microbial analysis.

This study shows that desiccation-induced dormancy in Arthrobacter sp. AZCC_0090 preserves mRNA and metabolite profiles, with changes only occurring during drying and rehydration transitions.

This study shows that transgenic rice genotypes overexpressing PSY genes reduce methane emissions by altering rhizosphere microbial hydrogen cycling through changes in gene activity and metabolic pathways.

The paper establishes reproducible methods for plant-microbiome research using fabricated ecosystems across multiple laboratories.

This study shows that co-culturing xylarialean fungi increases metabolite diversity and bioactivity, suggesting competitive interactions drive secondary metabolism.

The paper shows that PM-induced changes in host pyruvate metabolism bypass the PDHc to support lipid production for fungal reproduction.

The paper curates LC-MS/MS data from plant extracts to create a taxonomically focused database for exploring plant-derived molecules.

The paper studies how a geothermal spring community responds to diurnal stressors, revealing structured biotic interactions across domains of life.

This study shows that disrupting the indole glucosinolate pathway in Arabidopsis thaliana alters root exudate profiles and rhizobacterial communities.

BLINK rapidly computes cosine similarity scores for tandem mass spectra, achieving high accuracy and speed through sparse matrix operations.

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.

This study uses long-read metagenomics and metatranscriptomics to analyze soil communities, revealing phylum-specific secondary metabolite dynamics during wetting events.

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.

SIMILE aligns fragmentation mass spectra with statistical significance, identifying more structurally similar compound pairs than cosine-based methods.

MAGI integrates metabolomics and genomics data to improve metabolite identifications and gene annotations by scoring consensus through biochemical reactions.

This study uses BONCAT-FACS-Seq to show that a large fraction of soil microbes are actively translating, challenging previous assumptions about soil microbial inactivity.

The paper develops a model-guided framework to predict microbial interactions in synthetic human gut microbiome communities and identifies key ecological drivers and network design principles.