Joseph L. Gage

HyARQ is a Snakemake workflow for allele-specific read counting and quality control across multiple assays in F1 hybrids, showing accurate recovery of parental proportions.

The paper identifies ribosome stalling positions, spacing, and A-site occupancy in plants, showing their impact on translation and co-translational mRNA decay.

This paper uses aerial imagery and deep learning to estimate maize foliar disease severity, achieving results comparable to expert visual assessments.

This study investigates how genotype, environment, and rhizosphere microbiome interactions influence heat response in maize and sorghum using a systems-level metatranscriptomics approach.

The paper examines allelic variation in diel transcription patterns across maize inbreds and identifies cis-regulatory sequence variation influencing gene expression.

The paper reports on a competition to predict maize yield using genetic and environmental data, showing that diverse modeling approaches can achieve good results.

The paper shows that variations in upstream open reading frames (uORFs) affect protein abundance by repressing or derepressing translation of the main open reading frame (mORF), contributing to allelic diversity in protein levels.

The paper constructs a maize pangenome haplotype graph (PHG) to improve genotype imputation accuracy across diverse germplasm using WGS and GBS data.

This study evaluates how different phenotyping methods affect GWAS results by simulating traits with varying heritability and causative loci, finding that lower heritability and more loci reduce AUCs.

This study identifies selection signatures in maize genes associated with reduced tassel size during hybrid breeding.