Zachary A. Szpiech

This paper introduces a new method, D*, to detect introgression in a three-population tree with improved precision and recall over existing methods.

This study investigates how population history and genetic architecture affect the association between runs of homozygosity (ROH) and complex traits using simulations.

This study uses runs of homozygosity to link genetic diversity with non-disease phenotypes in dogs, finding associations with traits like height, weight, and fur length.

The paper shows how Barn Swallows overcame inbreeding challenges by expanding rapidly through behavioral flexibility and genetic variation during cross-hemisphere colonization.

The paper uses historical DNA to show that a small population's genetic load was not purged after a bottleneck, despite demographic recovery.

This study shows haplotype-based models are more effective than SFS methods for detecting selective sweeps in ancient populations with complex demographics.

The paper introduces enhanced features in selscan v3.0 for analyzing selection signals using EHH statistics and demonstrates their application on simulated and real genomic data.

EGGS generates empirical genotype data with missing values by replicating genotype distributions across segments, offering tools for data manipulation and format conversion.

The paper introduces a dynamic programming algorithm that improves the speed and memory efficiency of EHH-based selection scans for large-scale genomic datasets.

This study reconstructs the complex admixture history of Sao Tome's population, revealing nested admixture events and shared ancestries between African and European groups.

The paper introduces LODESTAR, a method to analyze local genetic relatedness patterns using Procrustes Analysis, to identify selection regions and inverted segments.

This paper uses genomic simulations to show that multiple mate-choice models can produce similar ancestry correlations in spouses, highlighting challenges in interpreting such data.

The paper produces gapless assemblies of ape sex chromosomes for five great apes and a lesser ape, revealing divergence in Y chromosomes and evolutionary dynamics.

This study analyzes genetic and linguistic data from Cabo Verde to trace admixture histories, finding early European-African mixing predating the Trans-Atlantic Slave Trade and ongoing effects of socio-cultural dynamics.

Over 400 million variants, 97% below 1% frequency, emerge from deep whole-genome sequencing of 53,831 diverse TOPMed participants; TOPMed haplotypes enable imputation down to ~0.01% frequency.

The paper analyzes ROH in admixed populations and finds that deleterious homozygotes are more common in ROH overlapping African ancestry segments.

This study identifies pharmacogenetic variants associated with albuterol bronchodilator response in minority children with asthma using whole genome sequencing.

This paper introduces a weighted likelihood method to detect genomic autozygosity patterns in dense genotype data, showing improved power over existing methods and robustness across different data types.

The paper analyzes amino acid mutation patterns across 29 cancers, identifying six mutation signatures, five of which are validated using COSMIC data.

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.

This study identifies novel asthma susceptibility loci in individuals of African ancestry through genome-wide association analysis and admixture mapping.