Sarah K. Nyquist

PPARγ downregulation in colonic CD8+ T cells results in epithelial barrier disruption in people with HIV on antiretroviral therapy

This study shows that PPARγ downregulation in colonic CD8+ T cells of people with HIV on ART leads to epithelial barrier disruption by promoting lipid uptake and apoptosis.

Integrated omics analysis reveals human milk oligosaccharide biosynthesis programs in human lactocytes

The paper identifies gene expression patterns and regulatory elements associated with HMO biosynthesis in lactocytes using scRNA-seq and HMO concentration data.

Systematic deconstruction of myeloid cell signaling in tuberculosis granulomas reveals IFN-γ, TGF-β, and time are associated with conserved myeloid diversity

This study uses multi-omics approaches to analyze myeloid cell diversity in TB granulomas and identifies IFN-γ, TGF-β, and time as factors driving macrophage diversity.

Expanding the HDAC druggable landscape beyond enzymatic activity

This paper identifies a non-enzymatic HDAC inhibitor with anti-tumor and anti-psychedelic effects, showing reduced gene modulation compared to enzymatic inhibitors.

Cellular and transcriptional diversity over the course of human lactation

This study uses scRNA-seq to analyze human breast milk cells over lactation, identifying cell type shifts and functional changes linked to time and maternal factors.

Integrated analyses of single-cell atlases reveal age, gender, and smoking status associations with cell type-specific expression of mediators of SARS-CoV-2 viral entry and highlights inflammatory programs in putative target cells

Across 1,176,683 airway and lung cells from 22 datasets, ACE2 rises with age, in males and in smokers' multiciliated cells, and is lowest in young children.

Hi-C yields chromosome-length scaffolds for a legume genome, Trifolium subterraneum

The paper uses Hi-C data to improve the genome assembly of Trifolium subterraneum, resulting in chromosome-length scaffolds covering 95% of the genome.

The Juicebox Assembly Tools module facilitates de novo assembly of mammalian genomes with chromosome-length scaffolds for under $1000

Point-and-click correction of misassemblies on Hi-C heatmaps, paired with the automated 3D-DNA pipeline, gave chromosome-length wombat, opossum and raccoon scaffolds from just short-insert DNA-Seq and in situ Hi-C reads.