Théo van der Lee

Genus-wide homologous recombination of tail fibers maintains tailocin diversity in Pectobacterium

The paper investigates the evolutionary dynamics of carotovoricin in Pectobacterium, finding that tail fiber gene exchange maintains diversity and influences community interactions.

Temporal Shifts in Gene Expression Drive Quantitative Resistance to a Necrotrophic Fungus in a Tomato Crop Wild Relative

This study identifies genotype-specific gene expression patterns in Solanum pennellii that correlate with resistance to Sclerotinia sclerotiorum, highlighting early defense gene activation and a WRKY6-centered regulatory network.

Pangenomics to understand prophage dynamics in the Pectobacterium genus and the radiating lineages of P. brasiliense

The paper studies prophage dynamics in Pectobacterium species using a pangenome approach, finding that prophages contribute significantly to genome evolution and lineage diversification.

Exploring intra- and intergenomic variation in haplotype-resolved pangenomes

The paper introduces PanTools, a ploidy-aware pangenome analysis tool, and demonstrates its application to potato and apple genomes, revealing high allelic diversity and structural variants.

Comparative genome-scale constraint-based metabolic modeling reveals key lifestyle features of plant-associated Pseudomonas spp.

The paper uses metabolic modeling to compare plant-associated Pseudomonas strains and identifies metabolic differences between beneficial and pathogenic species.

Classification of the plant-associated phenotype of Pseudomonas strains using genome properties and machine learning

The paper uses genome properties and machine learning to classify Pseudomonas strains as plant-beneficial or pathogenic, identifying 28 key features that distinguish these phenotypes.