Joshua M. Akey

The paper measures recombination rates between inversion haplotypes at 17q21.31, finds gene flux occurs despite suppression, and shows its impact on fertility and genetic diversity.

This paper develops a framework to improve polygenic risk scores by using correlated traits, showing that helper traits can significantly enhance prediction accuracy for type 2 diabetes.

CYClones is a yeast mapping population with high genetic diversity and power to detect low-heritability variants, enabling genetic dissection of complex traits.

This paper introduces an interpretable machine learning framework to infer dog breeds from genomic data, achieving high accuracy and identifying key genetic variants.

The paper analyzes the canine gut microbiome across 900 dogs to identify factors influencing microbiome composition and develops a metagenomics-based aging clock.

LongHap improves genome-wide haplotype reconstruction by integrating methylation data, increasing phase block lengths and reducing switch errors across diverse datasets.

This study identifies blood biomarkers and genetic factors associated with aging in dogs using genomic and phenotypic data from 7,627 dogs.

The paper identifies and analyzes human intrinsically disordered regions (IDRs) in transcription factors, revealing their unique functional, phenotypic, and evolutionary characteristics compared to non-TF IDRs.

The paper identifies a Denisovan-derived Alu insertion in OCA2 associated with increased pigmentation in Melanesians and demonstrates its functional impact in melanocytes.

The paper identifies shared plasma metabolomic biomarkers of mortality in dogs and humans, showing strong correlations between metabolite effects on all-cause mortality in both species.

The paper uses a multiparent yeast population to identify QTL for growth rates across environments, revealing context-dependent genetic architectures and allelic heterogeneity.

MutagenesisForge simulates codon-level mutagenesis and calculates dN/dS ratios under user-defined conditions to test evolutionary hypotheses.

This study remaps Neanderthal and Denisovan genomes onto new and old references, finds improved mapping with T2T-CHM13, and identifies new introgressed sequences and population-specific archaic ancestry.

The paper analyzes somatic mutations across tissues and individuals using exome sequencing data from GTEx donors, identifying 8,470 variants and providing insights into mutation rates and mechanisms.

The paper assesses STR variation across 96 Arabidopsis thaliana strains, finding high polymorphism and functional consequences, including novel STR-phenotype associations.

The paper designs a genotyping array (ADPC) for African-specific genetic variation using whole genome sequences from the CAAPA consortium, improving GWAS for African ancestry populations.