CD4 + T cells are central mediators of autoimmune pathology; however, defining their key
effector functions in specific autoimmune diseases remains challenging. Pathogenic CD4 + T …

To define the cell populations that drive joint inflammation in rheumatoid arthritis (RA), we
applied single-cell RNA sequencing (scRNA-seq), mass cytometry, bulk RNA sequencing (…

A host of observations demonstrating the relationship between nuclear architecture and
processes such as gene expression have led to a number of new technologies for interrogating …

Fluorescence in situ hybridization (FISH) is a powerful single-cell technique for studying
nuclear structure and organization. Here we report two advances in FISH-based imaging. We …

Systemic lupus erythematosus (SLE) is an autoimmune disease characterized by pathologic
T cell–B cell interactions and autoantibody production. Defining the T cell populations that …

High-dimensional single-cell analyses have improved the ability to resolve complex mixtures
of cells from human disease samples; however, identifying disease-associated cell types or …

… Author links open overlay panel Chamith Y Fonseka 1 2 3 4 5 , Deepak A Rao 1 , … Diogo,
Y. Okada, RM Plenge … Kanno, Y. Furumoto, K. Jiang, SCJ Parker, MR Erdos, SR Davis, R. …

… Author links open overlay panel Aparna Nathan 1 2 3 4 5 , Yuriy Baglaenko 1 2 3 5 ,
Chamith Y Fonseka 1 2 3 4 5 , Jessica I Beynor 1 2 3 5 , Soumya Raychaudhuri 1 2 3 4 5 6 …

Ultraconserved elements (UCEs) are strongly depleted from segmental duplications and
copy number variations (CNVs) in the human genome, suggesting that deletion or duplication …

To estimate a study design's power to detect differential abundance, we require a framework
that simulates many multi-sample single-cell datasets. However, current simulation …