S. P. Holmes

Longitudinal dynamics of the human vaginal ecosystem across the reproductive cycle

This study tracks changes in the vaginal microbiome and inflammation across the reproductive cycle, finding that childbirth disrupts microbial communities and reduces Lactobacillus dominance, with limited recovery over one year.

Disrupted memory T cell expansion in HIV-exposed uninfected infants is preceded by premature skewing of T cell receptor clonality.

This study shows that HIV/ARV-exposed uninfected infants have reduced T cell receptor diversity and altered immune development, increasing infection risk.

Comparative analysis of cell-cell communication at single-cell resolution

This paper introduces Scriabin, a framework for analyzing cell-cell communication at single-cell resolution, validating its findings through multiple experimental approaches and demonstrating its application in uncovering communication pathways in health and disease.

Profiling of the human intestinal microbiome and bile acids under physiologic conditions using an ingestible sampling device

The paper develops an ingestible device to collect intestinal samples and identifies regional differences in microbiota and bile acids compared to stool.

Sub-communities of the vaginal ecosystem in pregnant and non-pregnant women.

The paper identifies non-Lactobacillus-dominated sub-communities in vaginal ecosystems of pregnant and non-pregnant women using mixed membership models, revealing associations with preterm birth and menstrual cycle changes.

Stereotypic expansion of Tregulatory and Th17 cells during infancy is disrupted by HIV exposure and gut epithelial damage.

The paper examines Treg and Th17 cell dynamics in infants, finding HIV exposure disrupts their stereotypic expansion and correlates with gut damage.

Combined use of metagenomic sequencing and host response profiling for the diagnosis of suspected sepsis.

This study combines metagenomic sequencing and host response profiling to improve sepsis diagnosis by detecting pathogens and guiding clinical decisions.

Characterization of the impact of daclizumab beta on circulating natural killer cells by mass cytometry

This study uses mass cytometry to analyze how daclizumab beta affects NK cell phenotypes in RMS patients, showing distinct changes in CD56bright and CD56dim subsets.

Microbiota Assembly, Structure, and Dynamics Among Tsimane Horticulturalists of the Bolivian Amazon

This study examines microbiota assembly in Tsimane infants and adults, finding that neutral processes dominate infant colonization, but are reduced in villages with more market access.

Gut microbiota plasticity is correlated with sustained weight loss on a low-carb or low-fat dietary intervention

The paper examines how gut microbiota plasticity relates to sustained weight loss on low-carb or low-fat diets, finding diet-dependent associations in a discovery cohort but not in a validation cohort.

Metagenomic analysis with strain-level resolution reveals fine-scale variation in the human pregnancy microbiome

This study uses metagenomic analysis with strain-level resolution to examine the human pregnancy microbiome, revealing gestational age and health complications influence microbial community composition and function.

Exact sequence variants should replace operational taxonomic units in marker gene data analysis

The paper argues that exact sequence variants (SVs) should replace operational taxonomic units (OTUs) in marker gene analysis due to their higher resolution and better reproducibility.