Olivia C. Haley

The paper introduces a new pangenome viewer for maize that integrates graph and linear genome visualization to enhance structural variation analysis and locus characterization.

The paper introduces a web tool and R package for analyzing the evolutionary origins of maize proteins, providing interactive visualizations and gene data for 26 maize inbreds.

The paper benchmarks AlphaFold, ESMFold, and Boltz in maize to assess their performance on plant proteins, finding lower confidence scores and geometry issues in less conserved proteins.

This paper applies RFdiffusion to predict interspecies protein-protein interactions between fungal pathogens and cereal crops, achieving high recall in identifying validated interactions.

The paper introduces the Fusarium Protein Toolkit, a web-based resource that provides structural models and variant effect predictions for Fusarium proteins to aid in understanding and mitigating crop diseases and mycotoxin contamination.

PanEffect visualizes variant effects across 51 maize genomes using ESM scores, enabling exploration of 550 million amino acid substitutions and 2.3 million natural variations.