John P. Vogel

This study analyzes the origins and evolutionary dynamics of the allopolyploid grass Brachypodium hybridum using whole-genome sequencing and phylogenomic approaches, revealing three independent allopolyploidization events and subgenome-specific evolutionary patterns.

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

This study presents chromosome-level assemblies of two perennial Brachypodium species, revealing genomic features like polyploidy and transposable element dynamics that shaped genome evolution.

This study identifies hundreds of drought-responsive genes in sorghum using multi-season transcriptomic data from field experiments.

This study shows that diverse soil microbiomes consistently enhance plant biomass by decomposing organic matter, suggesting a universal microbial function in nutrient cycling.

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 breeds microbiomes that confer salt tolerance to plants by selecting for beneficial microbial communities, showing increased seed weight and reduced sodium concentration in treated plants.

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

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

This paper constructs a sorghum pangenome and identifies trait-associated variants to inform climate-aware genome-enabled breeding strategies.

AlloSHP detects single homeologous polymorphisms in allopolyploids without genome assembly, enabling phylogenetic analysis of diploid-polyploid complexes.

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

The paper investigates the factors influencing LTR-RT mobility in Brachypodium distachyon, finding that environmental stress has limited effects while RNA polymerase IV loss significantly increases transposon activity.

PolyCRACKER separates closely related polyploid subgenomes using repetitive DNA signatures without prior knowledge or related genomes.

The paper introduces an algorithm to correct habitat filtering in microbial correlation networks, improving accuracy on simulated and real data.