D. E. Cook

The Genome In A Bottle HG002 assembly-based variant benchmark set enables comprehensive benchmarking of small and structural variants.

The paper introduces a comprehensive variant benchmark set derived from a high-quality diploid assembly, improving small and structural variant detection across complex genomic regions.

Machine learning general transcriptional predictors of plant disease

This study uses machine learning to predict plant disease development across diverse pathogens by analyzing early transcriptional responses, identifying novel genes involved in a general immune response.

Genomic evolution of non-small cell lung cancer patient-derived xenograft models

This study examines how well PDX models capture intratumour heterogeneity in NSCLC, finding that most models originate from a single subclone but regional models can capture diversity.

Local adaptation and spatiotemporal patterns of genetic diversity revealed by repeated sampling of Caenorhabditis elegans across the Hawaiian Islands

This study samples C. elegans across Hawaii over three years, sequenced their genomes, and found seven genetic groups and 18 regions linked to local adaptation.

easyFulcrum: An R package to process and analyze ecological sampling data generated using the Fulcrum mobile application

The paper introduces easyFulcrum, an R package that processes and analyzes ecological sampling data from the Fulcrum mobile app, improving data accuracy and integration for microscopic organisms.

The distribution of mutational effects on fitness in Caenorhabditis elegans inferred from standing genetic variation

This study estimates the distribution of fitness effects from standing genetic variation in C. elegans and shows how self-fertilization and population structure bias DFE inferences.

Balancing selection maintains hyper-divergent haplotypes in C. elegans

The paper shows that balancing selection maintains genetic diversity in hyper-divergent regions of C. elegans, enabling adaptation despite selfing.

Deep sampling of Hawaiian Caenorhabditis elegans reveals high genetic diversity and admixture with global populations

The paper samples Hawaiian C. elegans strains, revealing high genetic diversity and admixture with global populations, suggesting ancestral diversity preserved in Hawaii.

Selection and gene flow shape niche-associated copy-number variation of pheromone receptor genes

The paper shows that copy-number variation of pheromone receptor genes in C. elegans is shaped by selection and gene flow, contributing to differences in pheromone responses across habitats.