Emily Davenport

SCiMS: Sex Calling in Metagenomic Sequences

SCiMS predicts host chromosomal sex from metagenomic data, outperforming existing tools at low host coverage and across species.

Distinct trajectories of urbanization shape the human gut microbiome across South Asia

The paper analyzes the gut microbiome of South Asian communities to show that urbanization impacts microbiomes differently across communities, with geography and culture playing a stronger role than lifestyle.

Integrative host transcriptomic and mucosal microbiome profiling reveals region-specific host-microbiome associations across the human intestine

The paper identifies region-specific host-microbiome associations in the human intestine using transcriptomic and microbiome data from non-inflamed tissue.

Clade-specific long-read sequencing increases the accuracy and specificity of the gyrB phylogenetic marker gene

The paper develops long-read sequencing primers for the gyrB gene to improve phylogenetic accuracy and specificity in bacterial classification.

Nepali oral microbiomes reflect a gradient of lifestyles from traditional to industrialized

This study examines oral microbiomes of Nepali individuals with different lifestyles, finding that lifestyle, not geography, shapes microbiome composition across a gradient from foraging to industrialized.

Leveraging phenotypic variability to identify genetic interactions in human phenotypes

This paper develops a statistical framework to detect gene-environment interactions by focusing on variance-associated genetic variants, finding higher discovery rates for BMI and disease-related traits.