Scott Theodore Kelley

The paper shows that zero substitution before clr transformation creates multicollinearity artefacts in co-occurrence networks and demonstrates that rclr eliminates these artefacts.

ARGus co-assembles metagenomes to generate MAGs, detect ARGs, and analyze virulence factors in environmental samples.

The paper tests how moisture and building materials affect microbial diversity in the built environment, finding that disturbances reduce diversity in some cases and vary by material and microbe type.

This study evaluates imputation methods for untargeted metabolomics data, finding that kNN and RF imputation perform poorly with missing data, especially MNAR, and that missing data proportion significantly affects accuracy.

PyBootNet is a Python package for bootstrapping analysis and network construction, demonstrating its ability to compare microbial community networks and identify significant differences.

AncFlow automates ancestral sequence reconstruction and structural prediction for protein families, revealing structural basis of functional divergence.

This study uses a genetic hypogonadal mouse model to show that the HPG axis influences gut microbiome maturation during puberty, with some sex differences independent of the HPG axis and age also playing a role.

AutoPhy automatically clusters protein sequences into monophyletic subfamilies without pre-defined thresholds, resolving misannotations and identifying novel functional groups and viral strains.

The paper introduces CurvCut, a data-driven method to remove rare features from zero-inflated datasets by analyzing curvature in feature distribution histograms.