Single-cell genomic technologies are revealing the cellular composition, identities and
states in tissues at unprecedented resolution. They have now scaled to the point that it is …

Non-coding genetic variants may cause disease by modulating gene expression. However,
identifying these expression quantitative trait loci (eQTLs) is complicated by differences in …

Expanding the efficacy of immune checkpoint blockade (ICB) in colorectal cancer (CRC)
presses for a comprehensive understanding of treatment responsiveness. Here, we analyze …

Joint analysis of single-cell genomics data from diseased tissues and a healthy reference
can reveal altered cell states. We investigate whether integrated collections of data from …

Systemic lupus erythematosus (SLE) is prototypical autoimmune disease driven by
pathological T cell–B cell interactions,. Expansion of T follicular helper (TFH) and T …

In this spotlight, we review technical issues that compromise single-cell analysis of tissue
macrophages, including limited and unrepresentative yields, fragmentation and generation …

Human brains vary across people and over time; such variation is not yet understood in
cellular terms. Here we describe a relationship between people's cortical neurons and …

In case-control single-cell RNA-seq studies, sample-level labels are transferred onto
individual cells, labeling all case cells as affected, when in reality only a small fraction of …

Fibroblasts are important regulators of inflammation, but whether fibroblasts change
phenotype during resolution of inflammation is not clear. Here we use positron emission …

Synovial tissue inflammation is a hallmark of rheumatoid arthritis (RA). Recent work has
identified prominent pathogenic cell states in inflamed RA synovial tissue, such as T …