Linking regulatory DNA elements to their target genes, which may be located hundreds of
kilobases away, remains challenging. Here, we introduce Cicero, an algorithm that identifies co…

Over one million candidate regulatory elements have been identified across the human
genome, but nearly all are unvalidated and their target genes uncertain. Approaches based on …

High-throughput chemical screens typically use coarse assays such as cell survival, limiting
what can be learned about mechanisms of action, off-target effects, and heterogeneous …

To study the development of the human retina, we use single-cell RNA sequencing (RNA-seq)
at key fetal stages and follow the development of the major cell types as well as …

Several groups recently coupled CRISPR perturbations and single-cell RNA-seq for pooled
genetic screens. We demonstrate that vector designs of these studies are susceptible to ∼50…

Integrating single-cell trajectory analysis with pooled genetic screening could reveal the
genetic architecture that guides cellular decisions in development and disease. We applied this …

During embryogenesis, waves of hematopoietic progenitors develop from hemogenic
endothelium (HE) prior to the emergence of self-renewing hematopoietic stem cells (HSCs). …

In recent years, macrophages have been shown to be tremendously plastic in both in vitro
and in vivo settings; however, it remains unclear whether macrophages retain any persistent …

Microscopy is a powerful tool for characterizing complex cellular phenotypes, but linking
these phenotypes to genotype or RNA expression at scale remains challenging. Here, we …

Background Hyperphosphatemia is associated with increased fibroblast growth factor 23 (FGF23),
arterial calcification, and cardiovascular mortality. Effects of phosphate-lowering …