Stephen W. Eichhorn

A molecularly defined and spatially resolved cell atlas of the whole mouse brain

MERFISH profiling of >1,100 genes in ~8 million cells spanning the whole mouse brain, integrated with scRNA-seq, maps >5,000 clusters into the Allen Common Coordinate Framework.

Three-dimensional Interrogation of Cell Types and Instinctive Behavior in the Periaqueductal Gray

The paper uses spatially resolved single-cell transcriptomics to map transcriptional heterogeneity and spatial organization of cell types in the periaqueductal gray during instinctive behaviors.

Evaluating single-cell cluster stability using the Jaccard similarity index

The paper introduces tools to evaluate single-cell clustering stability using subsampling and the Jaccard similarity index, with an R package and Snakemake workflow for implementation.

Molecular, spatial and projection diversity of neurons in primary motor cortex revealed by in situ single-cell transcriptomics

MERFISH imaging of ~300,000 mouse primary motor cortex cells yields 95 clusters, layered inhibitory as well as excitatory, with intratelencephalic neurons forming a depth-linked expression gradient.

The Dynamics of Cytoplasmic mRNA Metabolism

The paper examines mRNA metabolism dynamics in mouse fibroblasts, finding that deadenylation rates determine cytoplasmic mRNA stability and degradation.

MicroRNAs Cause Accelerated Decay of Short-Tailed Target mRNAs

The paper shows miRNAs accelerate decay of short-tailed target mRNAs, preventing their accumulation despite promoting deadenylation.