Trent R. Northen

The paper describes engineered algal lipids that mimic the fatty acid profile and regioisomeric structure of human milk fat for infant formula.

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 shows that signaling metabolites from Microcoleus vaginatus repel soil bacteria and promote mutualistic partners under nutrient limitation.

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.

The paper presents a multi-omic dataset examining microbial exometabolite responses to root exudates from six tallgrass prairie plant species and a model grass under controlled conditions.

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 identifies glutamate and branched-chain amino acid metabolism as key factors in acid tolerance of a denitrifying bacterium from acidic groundwater.

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 uses consumer-resource models parametrized from monoculture exometabolite data to predict and design synthetic microbial consortia, revealing the importance of cross-feeding interactions and nonlinear dynamics.

The paper identifies dopamine biosynthesis pathway in plants using metabolite-based genome-wide association studies and demonstrates its role in tissue browning and stress tolerance.

This study uses third-harmonic generation microscopy to image plant roots and microbes in their natural environment without labels.

The paper identifies substrate-dependent genes for bacterial plant colonization in Paraburkholderia graminis and shows substrate influences on colonization fitness across multiple bacterial strains.

This study shows that TOR inhibition in algae increases amino acid levels through transcriptional activation of biosynthesis pathways and identifies a conserved transcription factor involved in nitrogen metabolism.

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

This study shows that modifying lignin composition in Brachypodium distachyon changes root exudates and microbiome composition, affecting microbial colonization and community structure.

This study identifies strain-specific functional diversity in Streptomyces endophytes under drought stress, showing enrichment does not correlate with plant growth promotion.

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

This study investigates how plant-bacteria-phage interactions affect nitrogen acquisition and exometabolite composition by comparing phage-lysed and uninfected bacterial necromass.

This paper develops a hyperspectral segmentation workflow using sparse mixed-scale convolution neural networks to analyze plant characteristics in fabricated ecosystems with minimal user annotation.

This paper introduces a modular polyketide synthase platform for producing diols, amino alcohols, and hydroxyacids using engineered Streptomyces albus strains.

The paper investigates microbial interactions in algal systems, finding that cooperation, not just competition, significantly influences carbon flow from algae to bacteria.

This study demonstrates the use of EcoFABs to measure horizontal gene transfer frequency in the rhizosphere of Brachypodium distachyon, showing dependencies on plant stage, root exudates, donor cell numbers, and environmental stress.

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

This paper introduces an adaptive optical third-harmonic generation microscope that improves in vivo imaging by correcting optical aberrations in complex tissues.

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

The paper maps soil microbiome functions in wetlands to understand methane emissions by analyzing microbial communities and gene expression across spatial and temporal gradients.

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

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