David E. Cook

The paper analyzes genomic changes in mini-chromosomes of wheat blast fungal pathogens over time, showing their dynamic presence, sequence alterations, and role in pathogen adaptation.

The paper identifies two distinct Starship families in Pyricularia oryzae, showing differences in sequence evolution, epigenetic modifications, and impacts on genome variation and plant-fungal interactions.

The paper investigates genomic plasticity in Magnaporthe oryzae by analyzing supernumerary mini-chromosomes and their structural variations.

This study uses Bi-LSTM models to detect mini-chromosomes in M. oryzae strains, finding their prevalence increased in recent wheat strains.

The paper investigates genetic relationships among Magnaporthe oryzae isolates causing wheat blast outbreaks in Bangladesh and Zambia, finding that outbreaks were caused by genetically distinct isolates with divergent mini-chromosomes.

The paper identifies adaptive genomic regions in the fungus Verticillium dahliae by analyzing chromatin features, showing these regions have unique epigenetic marks and are associated with adaptive traits.

This study identifies and characterizes centromeres in ten Verticillium species, revealing conserved and variable features linked to repetitive elements and genome evolution.

The paper reports the genome of a wheat blast fungus, revealing dispensable mini-chromosomes containing effector genes that evolve rapidly and contribute to pathogen adaptation.

The paper analyzes co-transcriptome networks between Arabidopsis and B. cinerea to uncover virulence mechanisms and cross-kingdom interactions during infection.

LoReAn improves genome annotation by integrating long-read cDNA sequencing with other data types, outperforming existing pipelines in gene structure prediction and discovery.