Susan Holmes

This study identifies NKp30:B7-H6 and NKG2D:MICB/ULBP2 as receptor-ligand pairs that contribute to NK cell recognition of HIV-infected cells.

This study identifies sex-specific immune correlates of Long COVID development, persistence, and resolution using multi-omic analyses of blood samples from patients with and without Long COVID.

CytoGLMM provides statistical methods for differential analysis of flow and mass cytometry data, improving robustness to marker correlations and patient heterogeneity.

The paper assembles the pig-tailed macaque genome using linked-read sequencing and HiC scaffolding, achieving chromosome-level resolution and identifying large-scale chromosomal rearrangements with humans.

The paper shows that different analysis workflows by 70 teams on the same fMRI dataset led to varied results, but meta-analysis found consensus in activated regions.

The paper analyzes APOBEC-mutations in HIV-1 pol sequences across different NGS thresholds to assess their prevalence and association with PCR error and virus load.

This study quantifies variability in host proteins and bacterial taxa in stool samples from healthy individuals, showing greater inter-subject variation than temporal or technical variation.

decontam, an R package, classifies contaminant sequences in marker-gene and metagenomic data by their inverse frequency-DNA concentration relationship and higher prevalence in negative controls.

The paper applies two heteroscedasticity models to rfMRI data to analyze functional brain connectivity differences between short and conventional sleepers, finding stronger connectivity in short sleepers and recommending sleep duration as a covariate.

This paper introduces BUDS, a Bayesian method for visualizing uncertainty in high-dimensional datasets with latent ordering, and demonstrates its application to microbiome and gene expression data.